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- PDB-9cr6: Crystal structure of histidine racemase (HisR) of Fusobacterium n... -

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Basic information

Entry
Database: PDB / ID: 9cr6
TitleCrystal structure of histidine racemase (HisR) of Fusobacterium nucleatum (C209S)
ComponentsHistidine racemase
KeywordsISOMERASE / D-Histidine / racemase / stereochemistry / cofactor-independent / lanthionine / Fusobacterium nucleatum / staphylopine / CntK / Staphylococcus aureus
Function / homologyhistidine racemase / PHOSPHATE ION / Histidine racemase
Function and homology information
Biological speciesFusobacterium nucleatum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 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)124,6357
Polymers124,3504
Non-polymers2853
Water39622
1
A: Histidine racemase
B: Histidine racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,3654
Polymers62,1752
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Histidine racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1822
Polymers31,0871
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: Histidine racemase


Theoretical massNumber of molelcules
Total (without water)31,0871
Polymers31,0871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.845, 89.119, 100.331
Angle α, β, γ (deg.)90.00, 100.91, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Histidine racemase


Mass: 31087.467 Da / Num. of mol.: 4 / Mutation: C209S
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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.57 Å3/Da / Density % sol: 52.17 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1M Phosphate/citrate pH 4.2, 40% v/v Ethanol, 5% w/v PEG 1000
PH range: 4.0-5.0

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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: 2.49→35.86 Å / Num. obs: 43369 / % possible obs: 97.86 % / Redundancy: 6.8 % / 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
7.39-35.760.0349530.9920.0481

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.49→35.86 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3132 2176 5.02 %
Rwork0.261 --
obs0.2636 43369 97.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.49→35.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8223 0 15 22 8260
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038381
X-RAY DIFFRACTIONf_angle_d0.52611258
X-RAY DIFFRACTIONf_dihedral_angle_d18.8153140
X-RAY DIFFRACTIONf_chiral_restr0.0461221
X-RAY DIFFRACTIONf_plane_restr0.0031442
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.49-2.540.47991240.4132389X-RAY DIFFRACTION91
2.54-2.60.43261370.39392600X-RAY DIFFRACTION99
2.6-2.670.39791410.37812568X-RAY DIFFRACTION99
2.67-2.740.37651620.37212579X-RAY DIFFRACTION99
2.74-2.820.38131470.35182580X-RAY DIFFRACTION99
2.82-2.910.42891300.34272574X-RAY DIFFRACTION99
2.91-3.010.38951410.32472506X-RAY DIFFRACTION96
3.01-3.130.36831210.2982513X-RAY DIFFRACTION95
3.13-3.280.31241430.28152619X-RAY DIFFRACTION99
3.28-3.450.34011330.26972600X-RAY DIFFRACTION99
3.45-3.660.32691300.24852624X-RAY DIFFRACTION99
3.66-3.950.26841280.25462601X-RAY DIFFRACTION99
3.95-4.340.24411350.22492643X-RAY DIFFRACTION99
4.34-4.970.28851530.19812585X-RAY DIFFRACTION99
4.97-6.260.24571180.2432543X-RAY DIFFRACTION95
6.26-35.860.29641330.22082669X-RAY DIFFRACTION98

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