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- PDB-3dez: Crystal structure of Orotate phosphoribosyltransferase from Strep... -

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Basic information

Entry
Database: PDB / ID: 3dez
TitleCrystal structure of Orotate phosphoribosyltransferase from Streptococcus mutans
ComponentsOrotate phosphoribosyltransferase
KeywordsTRANSFERASE / OROTATE PHOSPHORIBOSYLTRANSFERASE / Glycosyltransferase / Magnesium / Pyrimidine biosynthesis
Function / homology
Function and homology information


orotate phosphoribosyltransferase / orotate phosphoribosyltransferase activity / pyrimidine nucleobase biosynthetic process / 'de novo' UMP biosynthetic process / magnesium ion binding
Similarity search - Function
Orotate phosphoribosyl transferase domain / Orotate phosphoribosyltransferase / Purine/pyrimidine phosphoribosyl transferases signature. / Rossmann fold - #2020 / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Orotate phosphoribosyltransferase
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLiu, C.P. / Gao, Z.Q. / Hou, H.F. / Li, L.F. / Su, X.D. / Dong, Y.H.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Structure of orotate phosphoribosyltransferase from the caries pathogen Streptococcus mutans
Authors: Liu, C.P. / Xu, R. / Gao, Z.Q. / Xu, J.H. / Hou, H.F. / Li, L.Q. / She, Z. / Li, L.F. / Su, X.D. / Liu, P. / Dong, Y.H.
History
DepositionJun 11, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 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

Downloads & links

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Assembly

Deposited unit
A: Orotate phosphoribosyltransferase
B: Orotate phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1066
Polymers52,7222
Non-polymers3844
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-66 kcal/mol
Surface area17400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.798, 73.798, 184.779
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Orotate phosphoribosyltransferase / OPRT / OPRTase


Mass: 26361.088 Da / Num. of mol.: 2 / Mutation: F92L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Strain: UA159 / Gene: pyrE / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q8DTV2, orotate phosphoribosyltransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.39 Å3/Da / Density % sol: 48.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: 0.1M Tris hydrochloride, 2.3M Ammonium sulfate, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 7, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 19803 / % possible obs: 85.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 12 %
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 10.9 % / Num. unique all: 2026 / % possible all: 100

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Processing

Software
NameClassification
HKL-2000data collection
PHASESphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2AEE

2aee


Resolution: 2.4→50 Å / σ(F): 1 / Stereochemistry target values: maximum likelihood
RfactorNum. reflectionSelection details
Rfree0.249 951 RANDOM
Rwork0.218 --
obs0.218 17826 -
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3089 0 20 89 3198
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4

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