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- PDB-9hqy: Variant Q430N of Orotidine 5'-monophosphate decarboxylase-domain ... -

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Basic information

Entry
Database: PDB / ID: 9hqy
TitleVariant Q430N of Orotidine 5'-monophosphate decarboxylase-domain of human UMPS in complex with the product UMP at 1.07 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 / 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 / URIDINE-5'-MONOPHOSPHATE / Uridine 5'-monophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.07 Å
AuthorsKirck, L.L. / Tittmann, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Variant Q430N of Orotidine 5'-monophosphate decarboxylase-domain of human UMPS in complex with the product UMP at 1.07 Angstrom resolution
Authors: Kirck, L.L. / Tittmann, K.
History
DepositionDec 17, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 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
B: Uridine 5'-monophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1435
Polymers56,3792
Non-polymers7633
Water9,620534
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.960, 118.630, 61.850
Angle α, β, γ (deg.)90.00, 90.08, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-841-

HOH

21B-752-

HOH

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Components

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


Mass: 28189.652 Da / Num. of mol.: 2 / Mutation: Q430N
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-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO2
#3: Chemical ChemComp-U5P / URIDINE-5'-MONOPHOSPHATE


Mass: 324.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N2O9P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 534 / 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: 2.5 Å3/Da / Density % sol: 50.88 %
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: Oct 5, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6888 Å / Relative weight: 1
ReflectionResolution: 1.07→35.17 Å / Num. obs: 240461 / % possible obs: 98.86 % / Redundancy: 6.7 % / CC1/2: 0.997 / Rrim(I) all: 0.08674 / Net I/σ(I): 9.78
Reflection shellResolution: 1.07→1.108 Å / Num. unique obs: 23876 / CC1/2: 0.552

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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: 1.07→35.17 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.139 --
Rwork0.125 --
obs-240239 98.94 %
Refinement stepCycle: LAST / Resolution: 1.07→35.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3974 0 8 534 4516
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.07-1.080.35163950.36377478X-RAY DIFFRACTION98
1.08-1.090.34873990.32497586X-RAY DIFFRACTION99
1.09-1.110.32763980.30597568X-RAY DIFFRACTION98
1.11-1.120.29814000.27417611X-RAY DIFFRACTION98
1.12-1.140.27373950.25577494X-RAY DIFFRACTION99
1.14-1.150.25993990.24187553X-RAY DIFFRACTION99
1.15-1.170.23293990.22847598X-RAY DIFFRACTION98
1.17-1.190.22754000.21797599X-RAY DIFFRACTION99
1.19-1.210.22853990.2117574X-RAY DIFFRACTION98
1.21-1.220.22213990.20497579X-RAY DIFFRACTION99
1.22-1.250.21223990.18647569X-RAY DIFFRACTION99
1.25-1.270.20214010.17047612X-RAY DIFFRACTION99
1.27-1.290.18793990.16597571X-RAY DIFFRACTION99
1.29-1.320.1814010.14757610X-RAY DIFFRACTION98
1.32-1.350.17063980.13467580X-RAY DIFFRACTION99
1.35-1.380.17214020.12787628X-RAY DIFFRACTION99
1.38-1.410.15183990.11867569X-RAY DIFFRACTION99
1.41-1.450.14534010.11257633X-RAY DIFFRACTION99
1.45-1.490.15754020.12337629X-RAY DIFFRACTION99
1.49-1.540.14434040.11327672X-RAY DIFFRACTION99
1.54-1.60.13454000.10617596X-RAY DIFFRACTION99
1.6-1.660.13143990.10177593X-RAY DIFFRACTION99
1.66-1.740.13984030.10957638X-RAY DIFFRACTION99
1.74-1.830.15044020.11717638X-RAY DIFFRACTION99
1.83-1.940.14514010.11827616X-RAY DIFFRACTION99
1.94-2.090.1364030.11837668X-RAY DIFFRACTION99
2.09-2.30.14684010.12447627X-RAY DIFFRACTION99
2.3-2.640.16494040.1337658X-RAY DIFFRACTION99
2.64-3.320.16114070.14567740X-RAY DIFFRACTION100
3.32-35.170.16654080.14617735X-RAY DIFFRACTION99

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