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- PDB-2pry: Apo form of S. cerevisiae orotate phosphoribosyltransferase -

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Basic information

Entry
Database: PDB / ID: 2pry
TitleApo form of S. cerevisiae orotate phosphoribosyltransferase
ComponentsOrotate phosphoribosyltransferase 1
KeywordsTRANSFERASE / ALPHA BETA / OPRTase apo form
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
Orotate phosphoribosyltransferase 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 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: Derived calculations / 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _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

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Assembly

Deposited unit
A: Orotate phosphoribosyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7142
Polymers24,6891
Non-polymers241
Water1,802100
1
A: Orotate phosphoribosyltransferase 1
hetero molecules

A: Orotate phosphoribosyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4274
Polymers49,3792
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area2690 Å2
ΔGint-25 kcal/mol
Surface area20660 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)59.791, 59.791, 135.595
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
DetailsThe biological assembly is a dimer generated by: -y, -x, 1/2-z

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Components

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


Mass: 24689.439 Da / Num. of mol.: 1
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.45 Å3/Da / Density % sol: 49.87 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 26% PEG 6000, 0.2M magnesium acetate, 0.1M Tris HCl, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 93.15 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 7, 2004 / Details: Osmic confocal
RadiationMonochromator: Osmic confocal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.35→25 Å / Num. all: 10881 / Num. obs: 10718 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0.2 / Biso Wilson estimate: 48.52 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Χ2: 1.036 / Net I/σ(I): 24.4
Reflection shellResolution: 2.35→2.43 Å / Rmerge(I) obs: 0.246 / Mean I/σ(I) obs: 3.7 / Num. unique all: 870 / Rsym value: 0.246 / Χ2: 1.034 / % possible all: 84.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1STO

1sto


Resolution: 2.35→24.92 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.92 / SU B: 8.323 / SU ML: 0.194 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.432 / ESU R Free: 0.26 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26 522 4.9 %RANDOM
Rwork0.238 ---
obs0.239 10666 98.47 %-
all-10831 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 49.601 Å2
Baniso -1Baniso -2Baniso -3
1-1.02 Å20 Å20 Å2
2--1.02 Å20 Å2
3----2.04 Å2
Refinement stepCycle: LAST / Resolution: 2.35→24.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1663 0 1 100 1764
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221685
X-RAY DIFFRACTIONr_angle_refined_deg1.0651.9732269
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1015212
X-RAY DIFFRACTIONr_chiral_restr0.0670.2268
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021221
X-RAY DIFFRACTIONr_nbd_refined0.1970.2752
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.280
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1730.28
X-RAY DIFFRACTIONr_mcbond_it0.8651.51061
X-RAY DIFFRACTIONr_mcangle_it1.59421703
X-RAY DIFFRACTIONr_scbond_it1.5153624
X-RAY DIFFRACTIONr_scangle_it2.7164.5566
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.404 36
Rwork0.289 577
obs-613

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