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- PDB-9hor: Variant K281R of Orotidine 5'-monophosphate decarboxylase-domain ... -

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Basic information

Entry
Database: PDB / ID: 9hor
TitleVariant K281R of Orotidine 5'-monophosphate decarboxylase-domain of human UMPS in complex with the substrate OMP at 1.3 Angstrom resolution
ComponentsUridine 5'-monophosphate synthase
KeywordsLYASE / Uridine 5'-monophosphate synthase Pyrimidine metabolism Homo sapiens
Function / homology
Function and homology information


UMP biosynthetic process / orotate phosphoribosyltransferase / orotate phosphoribosyltransferase activity / pyrimidine nucleobase biosynthetic process / Pyrimidine biosynthesis / orotidine-5'-phosphate decarboxylase / orotidine-5'-phosphate decarboxylase activity / UDP biosynthetic process / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process ...UMP biosynthetic process / orotate phosphoribosyltransferase / orotate phosphoribosyltransferase activity / pyrimidine nucleobase biosynthetic process / Pyrimidine biosynthesis / orotidine-5'-phosphate decarboxylase / orotidine-5'-phosphate decarboxylase activity / UDP biosynthetic process / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Orotate phosphoribosyl transferase domain / Orotate phosphoribosyltransferase / Purine/pyrimidine phosphoribosyl transferases signature. / Orotidine 5'-phosphate decarboxylase / Orotidine 5'-phosphate decarboxylase, active site / Orotidine 5'-phosphate decarboxylase active site. / Orotidine 5'-phosphate decarboxylase domain / Orotidine 5'-phosphate decarboxylase / HUMPS family / Orotidine 5'-phosphate decarboxylase / HUMPS family / Phosphoribosyl transferase domain ...Orotate phosphoribosyl transferase domain / Orotate phosphoribosyltransferase / Purine/pyrimidine phosphoribosyl transferases signature. / Orotidine 5'-phosphate decarboxylase / Orotidine 5'-phosphate decarboxylase, active site / Orotidine 5'-phosphate decarboxylase active site. / Orotidine 5'-phosphate decarboxylase domain / Orotidine 5'-phosphate decarboxylase / HUMPS family / Orotidine 5'-phosphate decarboxylase / HUMPS family / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Ribulose-phosphate binding barrel / Aldolase-type TIM barrel
Similarity search - Domain/homology
OROTIDINE-5'-MONOPHOSPHATE / Uridine 5'-monophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsKirck, L.L. / Tittmann, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Variant K281R of Orotidine 5'-monophosphate decarboxylase-domain of human UMPS in complex with the substrate OMP at 1.3 Angstrom resolution
Authors: Kirck, L.L. / Tittmann, K.
History
DepositionDec 12, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uridine 5'-monophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6002
Polymers28,2321
Non-polymers3681
Water4,648258
1
A: Uridine 5'-monophosphate synthase
hetero molecules

A: Uridine 5'-monophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2004
Polymers56,4632
Non-polymers7362
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area5200 Å2
ΔGint-31 kcal/mol
Surface area18910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.460, 116.600, 62.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-330-

ILE

21A-623-

HOH

31A-712-

HOH

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Components

#1: Protein Uridine 5'-monophosphate synthase / UMP synthase


Mass: 28231.695 Da / Num. of mol.: 1 / Mutation: K281R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UMPS, OK/SW-cl.21 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P11172, orotate phosphoribosyltransferase, orotidine-5'-phosphate decarboxylase
#2: Chemical ChemComp-OMP / OROTIDINE-5'-MONOPHOSPHATE


Mass: 368.191 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N2O11P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.48 Å3/Da / Density % sol: 50.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM Tris/HCl pH 7.0, 1.7 - 1.9 M Ammonium sulfate, 10 mM Glutathion pH 8.0, 5% (w/v) Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.6888 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: May 2, 2022
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6888 Å / Relative weight: 1
ReflectionResolution: 1.3→34.74 Å / Num. obs: 69096 / % possible obs: 99.8 % / Redundancy: 13.3 % / CC1/2: 1 / Rrim(I) all: 0.07064 / Net I/σ(I): 20.14
Reflection shellResolution: 1.3→1.346 Å / Num. unique obs: 6830 / CC1/2: 0.574

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→34.74 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1677 3454 5 %
Rwork0.1459 --
obs0.147 69056 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.3→34.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1969 0 24 258 2251
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142321
X-RAY DIFFRACTIONf_angle_d1.7423182
X-RAY DIFFRACTIONf_dihedral_angle_d16.774908
X-RAY DIFFRACTIONf_chiral_restr0.134353
X-RAY DIFFRACTIONf_plane_restr0.017423
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.320.33051380.31272609X-RAY DIFFRACTION99
1.32-1.340.33721350.28812566X-RAY DIFFRACTION100
1.34-1.360.27151380.27262618X-RAY DIFFRACTION100
1.36-1.380.31351370.26872592X-RAY DIFFRACTION100
1.38-1.40.29731360.25392586X-RAY DIFFRACTION100
1.4-1.420.26311350.24222599X-RAY DIFFRACTION100
1.42-1.450.27161370.21262590X-RAY DIFFRACTION100
1.45-1.480.23631370.19262598X-RAY DIFFRACTION100
1.48-1.510.21641370.16812601X-RAY DIFFRACTION100
1.51-1.540.17781360.15082588X-RAY DIFFRACTION99
1.54-1.580.17261390.14122632X-RAY DIFFRACTION100
1.58-1.620.16131360.12792595X-RAY DIFFRACTION99
1.62-1.660.19481360.13382577X-RAY DIFFRACTION100
1.66-1.710.14091390.132636X-RAY DIFFRACTION100
1.71-1.760.15451380.13232613X-RAY DIFFRACTION100
1.76-1.830.17241380.12272624X-RAY DIFFRACTION100
1.83-1.90.15721380.12062618X-RAY DIFFRACTION100
1.9-1.990.13511380.11682635X-RAY DIFFRACTION100
1.99-2.090.14791390.12542630X-RAY DIFFRACTION100
2.09-2.220.14681390.12352635X-RAY DIFFRACTION100
2.22-2.390.13981390.12492653X-RAY DIFFRACTION100
2.39-2.640.13211390.13212643X-RAY DIFFRACTION100
2.64-3.020.15681420.1462680X-RAY DIFFRACTION100
3.02-3.80.17951400.13892674X-RAY DIFFRACTION100
3.8-34.740.1641480.15592810X-RAY DIFFRACTION100

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