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- PDB-2prz: S. cerevisiae orotate phosphoribosyltransferase complexed with OMP -

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Basic information

Entry
Database: PDB / ID: 2prz
TitleS. cerevisiae orotate phosphoribosyltransferase complexed with OMP
ComponentsOrotate phosphoribosyltransferase 1
KeywordsTRANSFERASE / ALPHA BETA / OPRTase-OMP complex
Function / homology
Function and homology information


pyrimidine ribonucleoside biosynthetic process / orotate phosphoribosyltransferase / orotate phosphoribosyltransferase activity / pyrimidine nucleotide biosynthetic process / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / nucleus / cytoplasm
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
OROTIDINE-5'-MONOPHOSPHATE / Orotate phosphoribosyltransferase 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.895 Å
AuthorsGonzalez-Segura, L. / Hurley, T.D. / McClard, R.W.
CitationJournal: Biochemistry / Year: 2007
Title: Ternary complex formation and induced asymmetry in orotate phosphoribosyltransferase.
Authors: Gonzalez-Segura, L. / Witte, J.F. / McClard, R.W. / Hurley, T.D.
History
DepositionMay 4, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Orotate phosphoribosyltransferase 1
B: Orotate phosphoribosyltransferase 1
C: Orotate phosphoribosyltransferase 1
D: Orotate phosphoribosyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,37212
Polymers98,7584
Non-polymers1,6158
Water8,017445
1
A: Orotate phosphoribosyltransferase 1
B: Orotate phosphoribosyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1866
Polymers49,3792
Non-polymers8074
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
MethodPISA
2
C: Orotate phosphoribosyltransferase 1
D: Orotate phosphoribosyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1866
Polymers49,3792
Non-polymers8074
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.063, 99.475, 111.995
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Orotate phosphoribosyltransferase 1 / OPRT 1 / OPRTase 1


Mass: 24689.439 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: URA5, PYR5 / Plasmid: pREJ2 / Production host: Escherichia coli (E. coli) / Strain (production host): CS101-4UI
References: UniProt: P13298, orotate phosphoribosyltransferase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-OMP / OROTIDINE-5'-MONOPHOSPHATE


Mass: 368.191 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H13N2O11P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 445 / 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: 2.43 Å3/Da / Density % sol: 49.31 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 28% PEG 6000, 0.08M magnesium acetate, 0.1M Tris HCl, 2.5mM magnesium chloride, 5.0mM OMP, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 31, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.89→50 Å / Num. all: 77826 / Num. obs: 74091 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0.2 / Redundancy: 5.1 % / Biso Wilson estimate: 27.025 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.048 / Χ2: 1.044 / Net I/σ(I): 11.7
Reflection shellResolution: 1.89→1.96 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 2.4 / Num. unique all: 5115 / Rsym value: 0.376 / Χ2: 0.86 / % possible all: 66.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PRY (S. cerevisiae OPRTase apo form)

2pry


Resolution: 1.895→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.182 / SU ML: 0.123 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.187 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.262 3715 5 %RANDOM
Rwork0.229 ---
obs0.23 73711 95.82 %-
all-76926 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.996 Å2
Baniso -1Baniso -2Baniso -3
1-0.92 Å20 Å20 Å2
2--1.16 Å20 Å2
3----2.08 Å2
Refinement stepCycle: LAST / Resolution: 1.895→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6656 0 100 445 7201
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0226852
X-RAY DIFFRACTIONr_angle_refined_deg1.0461.9939257
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0345855
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.59125.217276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.849151238
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.751524
X-RAY DIFFRACTIONr_chiral_restr0.0730.21090
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024968
X-RAY DIFFRACTIONr_nbd_refined0.1870.23407
X-RAY DIFFRACTIONr_nbtor_refined0.2990.24865
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1120.2519
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1250.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1350.228
X-RAY DIFFRACTIONr_mcbond_it0.4991.54420
X-RAY DIFFRACTIONr_mcangle_it0.8726845
X-RAY DIFFRACTIONr_scbond_it1.08132780
X-RAY DIFFRACTIONr_scangle_it1.7454.52412
LS refinement shellResolution: 1.895→1.944 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 233 -
Rwork0.337 3686 -
obs-3919 69.88 %

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