[English] 日本語
Yorodumi
- PDB-1bjv: BETA-TRYPSIN COMPLEXED WITH APPU -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1bjv
TitleBETA-TRYPSIN COMPLEXED WITH APPU
ComponentsBETA-TRYPSIN
KeywordsSERINE PROTEASE / HYDROLASE / DIGESTION / PANCREAS / ZYMOGEN
Function / homology
Function and homology information


trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / endopeptidase activity / proteolysis / serine-type endopeptidase activity / extracellular space / metal ion binding
Peptidase S1A, chymotrypsin family / Serine proteases, trypsin domain / Peptidase S1, PA clan, chymotrypsin-like fold / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site / Peptidase S1, PA clan / Trypsin-like serine proteases / Thrombin, subunit H / Beta Barrel / Mainly Beta
Cationic trypsin
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 1.8 Å
AuthorsPresnell, S. / Patil, G. / Mura, C. / Jude, K. / Conley, J. / Kam, C. / Bertrand, J. / Powers, J. / Williams, L.
Citation
#1: Journal: J.Mol.Biol. / Year: 1975
Title: The Refined Crystal Structure of Bovine Beta-Trypsin at 1.8 A Resolution. II. Crystallographic Refinement, Calcium Binding Site, Benzamidine Binding Site and Active Site at Ph 7.0
Authors: Bode, W. / Schwager, P.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJun 29, 1998-
Revision 1.0Dec 2, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BETA-TRYPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9816
Polymers23,3241
Non-polymers6575
Water2,972165
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)54.360, 58.200, 66.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein BETA-TRYPSIN


Mass: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: PANCREAS / References: UniProt: P00760, trypsin

-
Non-polymers , 5 types, 170 molecules

#2: Chemical ChemComp-CA / CALCIUM ION / Calcium


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-GP8 / 1-(2-AMIDINOPHENYL)-3-(PHENOXYPHENYL)UREA


Mass: 346.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H18N4O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsTHE TRYPSIN RESIDUE NUMBERING USED IN THIS ENTRY IS BASED ON THE CHYMOTRYPSINOGEN NUMBERING SYSTEM. ...THE TRYPSIN RESIDUE NUMBERING USED IN THIS ENTRY IS BASED ON THE CHYMOTRYPSINOGEN NUMBERING SYSTEM. ATOMS O2, C15 - C20 OF GP8 (APPU) HAVE OCCUPANCIES SET TO ZERO, AS DENSITY COULD NEVER BE LOCATED FOR THESE ATOMS DURING THE REFINEMENT.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 46 %
Crystal growpH: 6
Details: 0.9 M AMMONIUM SULFATE, 0.005 M MES, 0.001 M CACL2 0.0025 M BENZAMIDINE PH 6.0
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110-15 mg/mlbeta-trypsin1drop
21.0 mM1dropCaCl2
32.5 mMbenzamidine1drop
40.9 Mammonium sulfate1drop
55.0 mMMES1drop
65.0 mMMES1reservoir
71.0 mM1reservoirCaCl2
82.5 mMbenzamidine1reservoir
91.8 Mammonium sulfate1reservoir

-
Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Aug 1, 1993 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→7 Å / Num. obs: 19267 / % possible obs: 95 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 5.5
Reflection shellResolution: 1.8→1.94 Å / Redundancy: 3.35 % / Rmerge(I) obs: 0.4 / % possible all: 87
Reflection
*PLUS
Num. measured all: 105428
Reflection shell
*PLUS
% possible obs: 87 %

-
Processing

Software
NameVersionClassification
SDMSSOFTWAREdata collection
SDMSSOFTWAREdata reduction
X-PLORmodel building
X-PLORrefinement
SDMSdata scaling
X-PLORphasing
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: 3PTB
Resolution: 1.8→5 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.196 -
Obs0.196 19267
Refinement stepCycle: LAST / Resolution: 1.8→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 40 165 1834
Refine LS restraints
Refinement-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.82
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refinement-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19.PRO
X-RAY DIFFRACTION2

+
About Yorodumi

-
News

-
Aug 12, 2020. New: Covid-19 info

New: Covid-19 info

  • New page: Covid-19 featured information page in EM Navigator

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

-
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. New: Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB at PDBe / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more