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- PDB-9cr1: Crystal structure of histidine racemase (HisR) of Fusobacterium n... -

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Basic information

Entry
Database: PDB / ID: 9cr1
TitleCrystal structure of histidine racemase (HisR) of Fusobacterium nucleatum (C67S)
ComponentsHistidine racemase
KeywordsISOMERASE / D-Histidine / racemase / stereochemistry / cofactor-independent / lanthionine / Fusobacterium nucleatum / staphylopine / CntK / Staphylococcus aureus
Function / homologyhistidine racemase / Histidine racemase
Function and homology information
Biological speciesFusobacterium nucleatum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsChen, P. / Lamer, T. / Vederas, J.C. / Lemieux, M.J.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Discovery, characterization, and structure of a cofactor-independent histidine racemase from the oral pathogen Fusobacterium nucleatum.
Authors: Lamer, T. / Chen, P. / Venter, M.J. / van Belkum, M.J. / Wijewardane, A. / Wu, C. / Lemieux, M.J. / Vederas, J.C.
History
DepositionJul 20, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histidine racemase
B: Histidine racemase
C: Histidine racemase
D: Histidine racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,11812
Polymers124,3504
Non-polymers7698
Water1,33374
1
A: Histidine racemase
C: Histidine racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5596
Polymers62,1752
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-72 kcal/mol
Surface area23650 Å2
MethodPISA
2
B: Histidine racemase
D: Histidine racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5596
Polymers62,1752
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-71 kcal/mol
Surface area23600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.144, 149.607, 138.232
Angle α, β, γ (deg.)90.00, 89.98, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Histidine racemase


Mass: 31087.467 Da / Num. of mol.: 4 / Mutation: C67S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusobacterium nucleatum (bacteria) / Gene: FN1732 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8RI81
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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 Å3/Da / Density % sol: 58.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 0.1 M HEPES sodium pH 7.5, 2% v/v Polyethylene glycol 400, 2.0 M Ammonium sulfate
PH range: 7.0-8.0

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Data collection

DiffractionMean temperature: 93.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 25, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→37.58 Å / Num. obs: 49178 / % possible obs: 97.35 % / Redundancy: 7.1 % / CC1/2: 0.994 / Rmerge(I) obs: 0.049 / Rrim(I) all: 0.069 / Net I/σ(I): 5.28
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.5-2.650.31650420.8920.4481
2.65-2.840.24947490.9080.3521
2.84-3.060.18240570.9470.2571
3.06-3.350.08439230.9850.1191
3.35-3.740.0636240.9890.0841
3.74-4.320.04730290.9920.0661
4.32-5.270.04423340.9890.0621
5.27-7.390.04116170.9930.0581
7.39-37.580.0349530.9920.0481

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→37.58 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 41.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2967 2339 4.76 %
Rwork0.2537 --
obs0.2557 49177 97.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→37.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8450 0 40 74 8564
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048638
X-RAY DIFFRACTIONf_angle_d0.61211611
X-RAY DIFFRACTIONf_dihedral_angle_d18.1673249
X-RAY DIFFRACTIONf_chiral_restr0.0471249
X-RAY DIFFRACTIONf_plane_restr0.0061488
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.550.54471320.55332573X-RAY DIFFRACTION92
2.55-2.610.49251710.4852753X-RAY DIFFRACTION98
2.61-2.670.49771310.46332775X-RAY DIFFRACTION98
2.67-2.740.4891010.45122814X-RAY DIFFRACTION99
2.74-2.810.44741120.41142779X-RAY DIFFRACTION98
2.81-2.890.44461360.40782780X-RAY DIFFRACTION98
2.89-2.990.4171530.3852772X-RAY DIFFRACTION97
2.99-3.090.36951590.38182489X-RAY DIFFRACTION90
3.09-3.220.39231490.35982708X-RAY DIFFRACTION97
3.22-3.360.3311270.30352836X-RAY DIFFRACTION99
3.36-3.540.32821350.28812797X-RAY DIFFRACTION99
3.54-3.760.29471340.26632846X-RAY DIFFRACTION99
3.76-4.050.32611210.23192803X-RAY DIFFRACTION99
4.05-4.460.25071420.19952814X-RAY DIFFRACTION99
4.46-5.10.23011030.17172840X-RAY DIFFRACTION99
5.1-6.420.29931530.21422639X-RAY DIFFRACTION93
6.43-37.580.20311800.17522820X-RAY DIFFRACTION99

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