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- PDB-1opr: THE CRYSTAL STRUCTURE OF THE OROTATE PHOSPHORIBOSYLTRANSFERASE CO... -

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Basic information

Entry
Database: PDB / ID: 1opr
TitleTHE CRYSTAL STRUCTURE OF THE OROTATE PHOSPHORIBOSYLTRANSFERASE COMPLEXED WITH OROTATE AND ALPHA-D-5-PHOSPHORIBOSYL-1-PYROPHOSPHATE
ComponentsOROTATE PHOSPHORIBOSYLTRANSFERASE
KeywordsTRANSFERASE
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 / magnesium ion binding / 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
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsScapin, G. / Sacchettini, J.C.
Citation
Journal: Biochemistry / Year: 1995
Title: The crystal structure of the orotate phosphoribosyltransferase complexed with orotate and alpha-D-5-phosphoribosyl-1-pyrophosphate.
Authors: Scapin, G. / Ozturk, D.H. / Grubmeyer, C. / Sacchettini, J.C.
#1: Journal: Biochemistry / Year: 1994
Title: Crystal Structure of Orotate Phosphoribosyltransferase
Authors: Scapin, G. / Grubmeyer, C. / Sacchettini, J.C.
History
DepositionJan 6, 1995Processing site: BNL
Revision 1.0Jan 6, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 17, 2019Group: Data collection / Other / Refinement description / Category: pdbx_database_status / software
Item: _pdbx_database_status.process_site / _software.classification
Revision 1.4Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.5Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_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 1.6Feb 14, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1624
Polymers23,5921
Non-polymers5703
Water1,09961
1
A: OROTATE PHOSPHORIBOSYLTRANSFERASE
hetero molecules

A: OROTATE PHOSPHORIBOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3258
Polymers47,1842
Non-polymers1,1416
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area5130 Å2
ΔGint-49 kcal/mol
Surface area18220 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)47.300, 47.300, 216.600
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 / OPRTASE


Mass: 23591.973 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: P08870, orotate phosphoribosyltransferase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ORO / OROTIC ACID


Mass: 156.096 Da / Num. of mol.: 1 / 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.: 1 / 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.: 61 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.08 %
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
130-40 mg/mlprotein 1drop
210 mMorotidine monophosphate1drop
365 %satammonium sulfate1drop
470 mMNaHepes1drop
50.05 mM1dropNaN3
610 mMbeta-mercaptoethanol1drop
730-40 %(w/v)PEG40001reservoir
870 mMNaHepes1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.04→19 Å / Num. obs: 12880 / % possible obs: 77.5 % / Observed criterion σ(I): 0
Reflection
*PLUS
Highest resolution: 2.03 Å / Num. measured all: 38356 / Rmerge(I) obs: 0.08
Reflection shell
*PLUS
Highest resolution: 2.03 Å / Lowest resolution: 2.17 Å / Num. unique obs: 1182

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Processing

Software
NameClassification
X-PLORmodel building
TNTrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.3→15 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.187 --
obs-8993 76 %
Refinement stepCycle: LAST / Resolution: 2.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1645 0 34 61 1740
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Rfactor obs: 0.187
Solvent computation
*PLUS
Displacement parameters
*PLUS

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