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- PDB-6h8n: Structure of peptidoglycan deacetylase PdaC from Bacillus subtili... -

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Basic information

Entry
Database: PDB / ID: 6h8n
TitleStructure of peptidoglycan deacetylase PdaC from Bacillus subtilis - mutant D285S
ComponentsPeptidoglycan-N-acetylmuramic acid deacetylase PdaC
KeywordsHYDROLASE / Deacetylase
Function / homology
Function and homology information


hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / Hydrolases, Acting on carbon-nitrogen bonds, other than peptide bonds, In linear amides / carbohydrate metabolic process / integral component of membrane / plasma membrane / metal ion binding
Domain of unknown function DUF3298 / Deacetylase PdaC / Polysaccharide deacetylase / PdaC/RsiV-like superfamily / NodB homology domain / Glycoside hydrolase/deacetylase, beta/alpha-barrel / Peptidoglycan GlcNAc deacetylase / Glycoside hydrolase/deacetylase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Peptidoglycan-N-acetylmuramic acid deacetylase PdaC
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 Å
AuthorsSainz-Polo, M.A. / Grifoll-Romero, L. / Albesa-Jove, D. / Planas, A. / Guerin, M.E.
CitationJournal: To Be Published
Title: Structure of peptidoglycan deacetylase PdaC from Bacillus subtilis with dual N-acetylmuramic and N-acetylglucosamine specificities
Authors: Grifoll-Romero, L. / Sainz-Polo, M.A. / Albesa-Jove, D. / Guerin, M.E. / Biarnes, X. / Planas, A.
Validation Report
SummaryFull reportAbout validation report
History
DepositionAug 2, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptidoglycan-N-acetylmuramic acid deacetylase PdaC
B: Peptidoglycan-N-acetylmuramic acid deacetylase PdaC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5739
Polymers48,9732
Non-polymers6007
Water8,413467
1
A: Peptidoglycan-N-acetylmuramic acid deacetylase PdaC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8345
Polymers24,4871
Non-polymers3474
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peptidoglycan-N-acetylmuramic acid deacetylase PdaC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7394
Polymers24,4871
Non-polymers2523
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)55.420, 61.800, 130.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide Peptidoglycan-N-acetylmuramic acid deacetylase PdaC / Peptidoglycan MurNAc deacetylase / Polysaccharide deacetylase PdaC


Mass: 24486.746 Da / Num. of mol.: 2 / Mutation: D285S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: pdaC, yjeA, BSU12100 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O34798, Hydrolases, Acting on carbon-nitrogen bonds, other than peptide bonds, In linear amides
#2: Chemical ChemComp-ZN / ZINC ION / Zinc


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 467 / Source method: isolated from a natural source / Formula: H2O

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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: 2.29 Å3/Da / Density % sol: 46.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.4 M Ammonium phosphate monobasic

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9796 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.26→22.11 Å / Num. obs: 120462 / % possible obs: 99 % / Redundancy: 5.7 % / Biso Wilson estimate: 12.29 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06804 / Rrim(I) all: 0.07441 / Net I/σ(I): 11.01
Reflection shellResolution: 1.26→1.3 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.4831 / Mean I/σ(I) obs: 1.74 / Num. unique obs: 10846 / CC1/2: 0.707 / Rrim(I) all: 0.595 / % possible all: 89

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Processing

Software
NameVersionClassification
PHENIX(dev_2219: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6H8L
Resolution: 1.26→22.116 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 0.04 / Phase error: 17.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1745 11264 4.92 %Random selection
Rwork0.16 ---
Obs0.1607 114541 97.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.26→22.116 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3254 0 29 467 3750
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealNumber
f_bond_d0.0073431
f_angle_d0.9774668
f_dihedral_angle_d22.6591329
f_chiral_restr0.074522
f_plane_restr0.006604
LS refinement shell

Refinement-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.26-1.27430.31962950.3244557476
1.2743-1.28930.31713430.3151623083
1.2893-1.3050.29773350.3082658989
1.305-1.32160.30113570.2893691393
1.3216-1.33890.30193750.2752715096
1.3389-1.35730.25653630.2574724698
1.3573-1.37670.25273940.247737099
1.3767-1.39720.25074090.23087402100
1.3972-1.4190.22773620.21947477100
1.419-1.44230.23224000.2047408100
1.4423-1.46720.21453960.1927408100
1.4672-1.49380.20433680.1887480100
1.4938-1.52260.19643890.18217392100
1.5226-1.55360.19274460.17047332100
1.5536-1.58740.18833980.16717464100
1.5874-1.62430.16793950.15467403100
1.6243-1.66490.16793440.15317478100
1.6649-1.70990.14573540.14847423100
1.7099-1.76020.15454020.14217468100
1.7602-1.8170.1734150.14367349100
1.817-1.88190.15173860.14347423100
1.8819-1.95720.17193960.13867405100
1.9572-2.04630.14363700.1377462100
2.0463-2.15410.15713850.13317402100
2.1541-2.28890.13053710.12897417100
2.2889-2.46540.16553340.13577473100
2.4654-2.71310.16183910.14367393100
2.7131-3.10480.16383970.14897454100
3.1048-3.90820.14973470.1497740399
3.9082-22.11980.17063470.1535743099

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