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- PDB-9hds: Variant T321N of Orotidine 5'-monophosphate decarboxylase-domain ... -

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Basic information

Entry
Database: PDB / ID: 9hds
TitleVariant T321N of Orotidine 5'-monophosphate decarboxylase-domain of human UMPS in complex with the product UMP and the nucleotide TMP at 0.86 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 / UDP biosynthetic process / orotidine-5'-phosphate decarboxylase activity / '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 / UDP biosynthetic process / orotidine-5'-phosphate decarboxylase activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / identical protein binding / nucleus / cytosol / cytoplasm
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
PROLINE / THYMIDINE-5'-PHOSPHATE / URIDINE-5'-MONOPHOSPHATE / Uridine 5'-monophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.86 Å
AuthorsKirck, L.L. / Tittmann, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochemistry / Year: 2025
Title: Expected and Unexpected "Guests" at the Active Site of Human Orotidine 5'-Monophosphate Decarboxylase.
Authors: Kirck, L.L. / Santagostino, E. / Brandhoff, L. / Simeth, N.A. / Tittmann, K.
History
DepositionNov 13, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 22, 2025Provider: 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)28,9784
Polymers28,2171
Non-polymers7623
Water5,891327
1
A: Uridine 5'-monophosphate synthase
hetero molecules

A: Uridine 5'-monophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9568
Polymers56,4332
Non-polymers1,5236
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area6220 Å2
ΔGint-43 kcal/mol
Surface area18580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.640, 117.320, 60.870
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-670-

HOH

21A-755-

HOH

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Components

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


Mass: 28216.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Asparagine inserted instead of Thr321 / 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-U5P / URIDINE-5'-MONOPHOSPHATE


Mass: 324.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N2O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO2
#4: Chemical ChemComp-TMP / THYMIDINE-5'-PHOSPHATE


Mass: 322.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N2O8P / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / 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: 2.71 Å3/Da / Density % sol: 54.6 %
Crystal growTemperature: 293.15 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: 0.7293 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Oct 22, 2020
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7293 Å / Relative weight: 1
ReflectionResolution: 0.86→30.43 Å / Num. obs: 251072 / % possible obs: 97.29 % / Redundancy: 11.9 % / CC1/2: 0.998 / Rrim(I) all: 0.05936 / Net I/σ(I): 19.01
Reflection shellResolution: 0.86→0.8907 Å / Num. unique obs: 21443 / CC1/2: 0.448

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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: 0.86→30.43 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 16.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1351 12540 5 %
Rwork0.127 --
obs0.1274 250741 97.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 0.86→30.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1968 0 50 327 2345
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092364
X-RAY DIFFRACTIONf_angle_d1.1713235
X-RAY DIFFRACTIONf_dihedral_angle_d14.828921
X-RAY DIFFRACTIONf_chiral_restr0.088355
X-RAY DIFFRACTIONf_plane_restr0.011429
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.86-0.870.36443340.37016285X-RAY DIFFRACTION77
0.87-0.880.30483510.34066658X-RAY DIFFRACTION83
0.88-0.890.36013780.33087194X-RAY DIFFRACTION89
0.89-0.90.30024050.31837704X-RAY DIFFRACTION95
0.9-0.910.29794070.29277737X-RAY DIFFRACTION95
0.91-0.930.29064100.26977769X-RAY DIFFRACTION96
0.93-0.940.264150.24637873X-RAY DIFFRACTION97
0.94-0.950.23414180.22727950X-RAY DIFFRACTION98
0.95-0.970.21894220.20198009X-RAY DIFFRACTION99
0.97-0.980.18184250.17398080X-RAY DIFFRACTION99
0.98-10.14864230.16128043X-RAY DIFFRACTION99
1-1.020.14914240.14258036X-RAY DIFFRACTION99
1.02-1.040.14094220.12718042X-RAY DIFFRACTION99
1.04-1.060.12584250.11088071X-RAY DIFFRACTION100
1.06-1.080.11024280.09958124X-RAY DIFFRACTION100
1.08-1.110.10444260.08768092X-RAY DIFFRACTION100
1.11-1.140.09584270.08368124X-RAY DIFFRACTION100
1.14-1.170.08924280.08298118X-RAY DIFFRACTION100
1.17-1.20.0984270.08478116X-RAY DIFFRACTION100
1.2-1.240.09144300.08788167X-RAY DIFFRACTION100
1.24-1.280.11914270.09418106X-RAY DIFFRACTION100
1.28-1.340.10724280.09298143X-RAY DIFFRACTION100
1.34-1.40.11084300.09488156X-RAY DIFFRACTION100
1.4-1.470.10034290.09598158X-RAY DIFFRACTION100
1.47-1.560.11194300.0998184X-RAY DIFFRACTION100
1.56-1.680.11124320.09958202X-RAY DIFFRACTION100
1.68-1.850.11784340.10868261X-RAY DIFFRACTION100
1.85-2.120.11954330.11298224X-RAY DIFFRACTION100
2.12-2.670.12794360.12418283X-RAY DIFFRACTION100
2.67-30.430.15944360.15398292X-RAY DIFFRACTION97

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