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- PDB-7ya2: Crystal structure of capsular polysaccharide synthesis enzyme Cap... -

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Basic information

Entry
Database: PDB / ID: 7ya2
TitleCrystal structure of capsular polysaccharide synthesis enzyme CapG from Staphylococcus aureus
ComponentsCapsular polysaccharide synthesis enzyme CapG
KeywordsISOMERASE / 2-epimerase
Function / homologyUDP-N-acetylglucosamine 2-epimerase activity / UDP-N-acetylglucosamine 2-epimerase WecB-like / UDP-N-acetylglucosamine 2-epimerase domain / UDP-N-acetylglucosamine 2-epimerase / Capsular polysaccharide synthesis enzyme CapG
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsChen, Y. / Wang, Y.C.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)109-2311-B-241-001 Taiwan
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2022
Title: Crystal structure of the capsular polysaccharide-synthesis enzyme CapG from Staphylococcus aureus.
Authors: Tien, N. / Ho, C.Y. / Lai, S.J. / Lin, Y.C. / Yang, C.S. / Wang, Y.C. / Huang, W.C. / Chen, Y. / Chang, J.J.
History
DepositionJun 27, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Capsular polysaccharide synthesis enzyme CapG
B: Capsular polysaccharide synthesis enzyme CapG
C: Capsular polysaccharide synthesis enzyme CapG
D: Capsular polysaccharide synthesis enzyme CapG
E: Capsular polysaccharide synthesis enzyme CapG
F: Capsular polysaccharide synthesis enzyme CapG


Theoretical massNumber of molelcules
Total (without water)257,4356
Polymers257,4356
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25170 Å2
ΔGint-80 kcal/mol
Surface area78580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)302.909, 84.340, 145.085
Angle α, β, γ (deg.)90.000, 110.650, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein
Capsular polysaccharide synthesis enzyme CapG / UDP-N-acetylglucosamine 2-epimerase (Non-hydrolyzing)


Mass: 42905.785 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: Newman / Gene: capG, NWMN_0101, CNH35_00585 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3K5M7

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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: 3.37 Å3/Da / Density % sol: 63.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium citrate tribasic pH 7.2, 18 % w/v polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→30 Å / Num. obs: 56178 / % possible obs: 99.4 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.126 / Net I/σ(I): 9.675
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 3.4 % / Num. unique obs: 5591 / CC1/2: 0.591 / CC star: 0.862 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HWG

4hwg


Resolution: 3.2→25.57 Å / Cross valid method: THROUGHOUT
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2411 --
Rwork0.1832 --
obs-47544 87.92 %
Displacement parametersBiso mean: 74.66 Å2
Refinement stepCycle: LAST / Resolution: 3.2→25.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18050 0 0 0 18050
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01418379
X-RAY DIFFRACTIONf_angle_d1.891424852
X-RAY DIFFRACTIONf_chiral_restr0.29122813
X-RAY DIFFRACTIONf_plane_restr0.00733224
X-RAY DIFFRACTIONf_dihedral_angle_d23.95427006

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