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- PDB-7vdy: Crystal structure of O-ureidoserine racemase -

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Basic information

Entry
Database: PDB / ID: 7vdy
TitleCrystal structure of O-ureidoserine racemase
ComponentsO-ureido-serine racemase
KeywordsISOMERASE / racemase
Function / homologyO-ureido-serine racemase / diaminopimelate epimerase activity / Diaminopimelate epimerase, DapF / Diaminopimelate epimerase / racemase and epimerase activity, acting on amino acids and derivatives / lysine biosynthetic process via diaminopimelate / antibiotic biosynthetic process / cytoplasm / O-ureido-serine racemase
Function and homology information
Biological speciesStreptomyces lavendulae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsOda, K. / Matoba, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Proteins / Year: 2022
Title: Crystal structure of O-ureidoserine racemase found in the d-cycloserine biosynthetic pathway.
Authors: Oda, K. / Sakaguchi, T. / Matoba, Y.
History
DepositionSep 7, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 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: O-ureido-serine racemase
B: O-ureido-serine racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,94412
Polymers62,9832
Non-polymers96110
Water6,936385
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint-159 kcal/mol
Surface area22740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.121, 96.051, 57.286
Angle α, β, γ (deg.)90.000, 92.130, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein O-ureido-serine racemase


Mass: 31491.559 Da / Num. of mol.: 2 / Fragment: O-ureido-serine racemase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lavendulae (bacteria) / Gene: dcsC, dapF / Plasmid: pET21 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: D2Z026, O-ureido-serine racemase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 385 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.32 Å3/Da / Density % sol: 46.96 % / Mosaicity: 0.46 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 1.45 M ammonium sulfate, 10%(v/v) dioxane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.12→49.17 Å / Num. obs: 32385 / % possible obs: 99.4 % / Redundancy: 7 % / CC1/2: 0.994 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.052 / Rrim(I) all: 0.139 / Net I/σ(I): 9.6 / Num. measured all: 225765 / Scaling rejects: 305
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.12-2.187.20.6081887226050.8880.2420.6553.399
8.99-49.176.20.10628084520.9890.0460.11618.499.6

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GQZ

1gqz


Resolution: 2.12→39.67 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2099 1575 4.87 %
Rwork0.166 30771 -
obs0.1682 32346 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.91 Å2 / Biso mean: 29.2221 Å2 / Biso min: 10.81 Å2
Refinement stepCycle: final / Resolution: 2.12→39.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4183 0 50 385 4618
Biso mean--45.74 35.7 -
Num. residues----564
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.12-2.190.2641200.19082787290799
2.19-2.270.27111280.19062764289299
2.27-2.360.22051410.17812767290899
2.36-2.460.24331180.17022805292399
2.46-2.590.26261260.18082830295699
2.59-2.760.28141450.18462773291899
2.76-2.970.25241460.18442813295999
2.97-3.270.21921450.1672778292399
3.27-3.740.19541920.144827582950100
3.74-4.710.14911680.135928152983100
4.71-39.670.19461460.176428813027100

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