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- PDB-3k1k: Green fluorescent protein bound to enhancer nanobody -

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Basic information

Entry
Database: PDB / ID: 3k1k
TitleGreen fluorescent protein bound to enhancer nanobody
Components
  • Enhancer
  • Green Fluorescent Protein
KeywordsLUMINESCENT PROTEIN/IMMUNE SYSTEM / nanobody / ANTIBODY-COMPLEX / CHROMOPHORE / LUMINESCENCE / PHOTOPROTEIN / LUMINESCENT PROTEIN-IMMUNE SYSTEM COMPLEX
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy / protein-chromophore linkage
Green fluorescent protein, GFP / Green fluorescent protein / Green fluorescent protein-related / Green fluorescent protein / Green Fluorescent Protein / Immunoglobulins / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Green fluorescent protein
Biological speciesAequorea Victoria (jellyfish)
Camelus dromedarius (Arabian camel)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å
AuthorsKirchhofer, A. / Helma, J. / Schmidthals, K. / Frauer, C. / Cui, S. / Karcher, A. / Pellis, M. / Muyldermans, S. / Delucci, C.C. / Cardoso, M.C. ...Kirchhofer, A. / Helma, J. / Schmidthals, K. / Frauer, C. / Cui, S. / Karcher, A. / Pellis, M. / Muyldermans, S. / Delucci, C.C. / Cardoso, M.C. / Leonhardt, H. / Hopfner, K.-P. / Rothbauer, U.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Modulation of protein properties in living cells using nanobodies
Authors: Kirchhofer, A. / Helma, J. / Schmidthals, K. / Frauer, C. / Cui, S. / Karcher, A. / Pellis, M. / Muyldermans, S. / Deulcci, C.C. / Cardoso, M.C. / Leonhardt, H. / Hopfner, K.-P. / Rothbauer, U.
Validation Report
SummaryFull reportAbout validation report
History
DepositionSep 28, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 18, 2013Group: Database references / Source and taxonomy
Revision 1.3Jan 25, 2017Group: Structure summary

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Green Fluorescent Protein
B: Green Fluorescent Protein
C: Enhancer
D: Enhancer


Theoretical massNumber of molelcules
Total (without water)81,5544
Polymers81,5544
Non-polymers00
Water7,332407
1
A: Green Fluorescent Protein
C: Enhancer


Theoretical massNumber of molelcules
Total (without water)40,7772
Polymers40,7772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Green Fluorescent Protein
D: Enhancer


Theoretical massNumber of molelcules
Total (without water)40,7772
Polymers40,7772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)160.470, 160.470, 78.828
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number93
Space group name H-MP4222
Components on special symmetry positions
IDModelComponents
11B-338-

HOH

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Components

#1: Protein Green Fluorescent Protein /


Mass: 27017.562 Da / Num. of mol.: 2 / Mutation: S2G, Q80R, F99S, M153T, V163A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea Victoria (jellyfish) / Gene: GFP / Plasmid: PRSET5D / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (Rosetta (DE3) / References: UniProt: P42212
#2: Antibody Enhancer


Mass: 13759.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Plasmid: Phen6 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 407 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsIN THE CHAINS A AND B, THE SKIPPED RESIDUE NUMBERS 65, 67 ARE DUE TO THE CHROMOPHORE. IN THE CHAINS ...IN THE CHAINS A AND B, THE SKIPPED RESIDUE NUMBERS 65, 67 ARE DUE TO THE CHROMOPHORE. IN THE CHAINS C AND D, THERE ARE RESIDUES WITH INSERTION CODES

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.12 Å3/Da / Density % sol: 60.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 60% MPD, 100MM NAAC PH 4.6, 10MM CACL2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 77.2 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9793 / Wavelength: 0.9793 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 21, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.15→46.048 Å / Num. obs: 56271 / % possible obs: 99.3 % / Observed criterion σ(I): 3 / Redundancy: 3.13 % / Rsym value: 0.046 / Net I/σ(I): 14.95
Reflection shellResolution: 2.15→2.29 Å / Mean I/σ(I) obs: 2.25 / Rsym value: 0.454 / % possible all: 98.9

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Processing

Software
NameVersionClassification
SHARPphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.15→46.048 Å / SU ML: 0.49 / σ(F): 1.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2547 2860 5.08 %
Rwork0.2125 --
Obs0.2146 56271 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.465 Å2 / ksol: 0.317 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.6978 Å20 Å20 Å2
2--3.6978 Å20 Å2
3----7.3957 Å2
Refinement stepCycle: LAST / Resolution: 2.15→46.048 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5378 0 0 407 5785
Refine LS restraints
Refinement-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085513
X-RAY DIFFRACTIONf_angle_d1.147448
X-RAY DIFFRACTIONf_dihedral_angle_d17.3932023
X-RAY DIFFRACTIONf_chiral_restr0.073785
X-RAY DIFFRACTIONf_plane_restr0.006978
LS refinement shell

Refinement-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1504-2.18750.3521420.3138260498
2.1875-2.22730.34851320.30672624100
2.2273-2.27010.36681440.29552630100
2.2701-2.31650.31491440.29192630100
2.3165-2.36680.33781520.28482614100
2.3668-2.42190.35691510.29222630100
2.4219-2.48240.34461340.27272654100
2.4824-2.54950.30981460.26742636100
2.5495-2.62460.31961580.26432641100
2.6246-2.70930.31581500.24542643100
2.7093-2.80610.28341480.23422645100
2.8061-2.91840.25141410.23692662100
2.9184-3.05120.27851490.21742635100
3.0512-3.2120.24021310.21132699100
3.212-3.41320.23311350.19542678100
3.4132-3.67670.22661390.18212682100
3.6767-4.04650.22931360.18552701100
4.0465-4.63150.21781390.1572735100
4.6315-5.83340.18721510.16962743100
5.8334-46.05860.22461380.20362925100

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