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- PDB-2ps1: S. cerevisiae orotate phosphoribosyltransferase complexed with or... -

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Basic information

Entry
Database: PDB / ID: 2ps1
TitleS. cerevisiae orotate phosphoribosyltransferase complexed with orotic acid and PRPP
ComponentsOrotate phosphoribosyltransferase 1
KeywordsTRANSFERASE / ALPHA BETA / OPRTase-OA-PRPP 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
OROTIC ACID / Chem-PRP / Orotate phosphoribosyltransferase 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)50,5208
Polymers49,3792
Non-polymers1,1416
Water5,801322
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5670 Å2
ΔGint-56 kcal/mol
Surface area18640 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)41.788, 50.051, 50.078
Angle α, β, γ (deg.)90.59, 105.88, 92.99
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 24689.439 Da / Num. of mol.: 2
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.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ORO / OROTIC ACID


Mass: 156.096 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H4N2O4
#4: Sugar ChemComp-PRP / 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose / ALPHA-PHOSPHORIBOSYLPYROPHOSPHORIC ACID / 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribose / 1-O-pyrophosphono-5-O-phosphono-D-ribose / 1-O-pyrophosphono-5-O-phosphono-ribose


Type: D-saccharide / Mass: 390.070 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H13O14P3
IdentifierTypeProgram
a-D-Ribf1PO35PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / 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: 2.04 Å3/Da / Density % sol: 39.6 %
Crystal growTemperature: 288.15 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 38% PEG 4000, 0.14M ammonium acetate, 0.1M sodium acetate, 2.0mM magnesium chloride, 5.0mM PRPP, 5.0mM orotic acid, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 288.15K

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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: Apr 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. all: 39461 / Num. obs: 36660 / % possible obs: 92.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0.2 / Redundancy: 3.6 % / Biso Wilson estimate: 21.245 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.043 / Χ2: 1.064 / Net I/σ(I): 17.8
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.251 / Mean I/σ(I) obs: 3.2 / Num. unique all: 2533 / Rsym value: 0.211 / Χ2: 0.944 / % possible all: 63.7

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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 2PRZ (S. cerevisiae OPRTase complexed with OMP)

2prz


Resolution: 1.75→49.94 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.715 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.157 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.217 1844 5 %RANDOM
Rwork0.194 ---
all0.195 39534 --
obs0.195 36660 92.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.628 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20.09 Å21.14 Å2
2--0.32 Å20.63 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.75→49.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3446 0 68 322 3836
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223562
X-RAY DIFFRACTIONr_angle_refined_deg1.111.9954814
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8315446
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.19625.278144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.73315640
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.8631512
X-RAY DIFFRACTIONr_chiral_restr0.0690.2558
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022584
X-RAY DIFFRACTIONr_nbd_refined0.180.21821
X-RAY DIFFRACTIONr_nbtor_refined0.2980.22552
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0910.2314
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1390.295
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1110.237
X-RAY DIFFRACTIONr_mcbond_it0.4841.52288
X-RAY DIFFRACTIONr_mcangle_it0.85323546
X-RAY DIFFRACTIONr_scbond_it0.98231442
X-RAY DIFFRACTIONr_scangle_it1.5364.51268
LS refinement shellResolution: 1.75→1.792 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 87 -
Rwork0.264 1604 -
obs-1691 57.99 %

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