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- PDB-4wml: Crystal structure of Saccharomyces cerevisiae OMP synthase in com... -

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Basic information

Entry
Database: PDB / ID: 4wml
TitleCrystal structure of Saccharomyces cerevisiae OMP synthase in complex with PRP(CH2)P
ComponentsOrotate phosphoribosyltransferase 1
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 / 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
Chem-PPC / Orotate phosphoribosyltransferase 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsBang, M.B. / Molich, U. / Hansen, M.R. / Grubmeyer, C. / Harris, P.
CitationJournal: To Be Published
Title: Crystal structure of Saccharomyces cerevisia OMP synthase in complex with PRP(CH2)P
Authors: Bang, M.B. / Molich, U. / Hansen, M.R. / Grubmeyer, C. / Harris, P.
History
DepositionOct 9, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jul 29, 2020Group: Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / 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.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 1.3Jan 10, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Orotate phosphoribosyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7653
Polymers25,3531
Non-polymers4122
Water2,504139
1
A: Orotate phosphoribosyltransferase 1
hetero molecules

A: Orotate phosphoribosyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5316
Polymers50,7062
Non-polymers8254
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3980 Å2
ΔGint-49 kcal/mol
Surface area19930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.560, 61.560, 132.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-438-

HOH

21A-449-

HOH

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Components

#1: Protein Orotate phosphoribosyltransferase 1 / OPRTase 1


Mass: 25353.096 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: URA5, PYR5, YML106W, YM8339.13 / Production host: Escherichia coli (E. coli)
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: Sugar ChemComp-PPC / 1-O-[(R)-hydroxy(phosphonomethyl)phosphoryl]-5-O-phosphono-alpha-D-ribofuranose / 5-PHOSPHORIBOSYL-1-(BETA-METHYLENE) PYROPHOSPHATE / 1-O-[(R)-hydroxy(phosphonomethyl)phosphoryl]-5-O-phosphono-alpha-D-ribose / 1-O-[(R)-hydroxy(phosphonomethyl)phosphoryl]-5-O-phosphono-D-ribose / 1-O-[(R)-hydroxy(phosphonomethyl)phosphoryl]-5-O-phosphono-ribose


Type: D-saccharide / Mass: 388.097 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15O13P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.48 Å3/Da / Density % sol: 50.31 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M NaHEPES pH 7.5, 10 % Isopropanol, 20 % PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.73→33.14 Å / Num. all: 26807 / Num. obs: 26807 / % possible obs: 97.4 % / Redundancy: 13.5 % / Rsym value: 0.058 / Net I/σ(I): 28.63
Reflection shellResolution: 1.73→1.77 Å / Redundancy: 10.8 % / Mean I/σ(I) obs: 1.45 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XSCALEdata scaling
Cootmodel building
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PRY

2pry


Resolution: 1.73→31 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.707 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25017 1337 5 %RANDOM
Rwork0.21138 ---
obs0.21335 25402 97.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.806 Å2
Baniso -1Baniso -2Baniso -3
1-1.68 Å20 Å2-0 Å2
2--1.68 Å2-0 Å2
3----3.35 Å2
Refinement stepCycle: 1 / Resolution: 1.73→31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1668 0 23 139 1830
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191738
X-RAY DIFFRACTIONr_bond_other_d0.0010.021724
X-RAY DIFFRACTIONr_angle_refined_deg1.9841.9912351
X-RAY DIFFRACTIONr_angle_other_deg0.93633969
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1695220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.30324.78971
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.73415319
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.946158
X-RAY DIFFRACTIONr_chiral_restr0.1170.2276
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021931
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02379
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.5863.511871
X-RAY DIFFRACTIONr_mcbond_other3.5833.506870
X-RAY DIFFRACTIONr_mcangle_it5.1345.2461088
X-RAY DIFFRACTIONr_mcangle_other5.1325.2521089
X-RAY DIFFRACTIONr_scbond_it4.2753.938867
X-RAY DIFFRACTIONr_scbond_other4.253.94863
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.4015.6951256
X-RAY DIFFRACTIONr_long_range_B_refined8.0428.5212074
X-RAY DIFFRACTIONr_long_range_B_other8.01328.3082031
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.73→1.775 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 100 -
Rwork0.33 1886 -
obs--100 %

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