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- PDB-9hom: Variant H283N of Orotidine 5'-monophosphate decarboxylase-domain ... -

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Basic information

Entry
Database: PDB / ID: 9hom
TitleVariant H283N of Orotidine 5'-monophosphate decarboxylase-domain of human UMPS in complex with the product UMP and carbon dioxide at 1.1 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
CARBON DIOXIDE / PROLINE / URIDINE-5'-MONOPHOSPHATE / Uridine 5'-monophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsKirck, L.L. / Tittmann, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Variant H283N of Orotidine 5'-monophosphate decarboxylase-domain of human UMPS in complex with the product UMP and carbon dioxide at 1.1 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,8556
Polymers28,1801
Non-polymers6755
Water5,441302
1
A: Uridine 5'-monophosphate synthase
hetero molecules

A: Uridine 5'-monophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,71012
Polymers56,3592
Non-polymers1,35110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area6060 Å2
ΔGint-74 kcal/mol
Surface area19270 Å2
Unit cell
Length a, b, c (Å)76.960, 115.960, 62.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 28179.637 Da / Num. of mol.: 1 / Mutation: H283N
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

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Non-polymers , 5 types, 307 molecules

#2: Chemical ChemComp-U5P / URIDINE-5'-MONOPHOSPHATE


Mass: 324.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N2O9P
#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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CO2 / CARBON DIOXIDE


Mass: 44.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.46 Å3/Da / Density % sol: 49.98 %
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: Aug 17, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6888 Å / Relative weight: 1
ReflectionResolution: 1.1→44.62 Å / Num. obs: 112399 / % possible obs: 99.9 % / Redundancy: 13.5 % / CC1/2: 1 / Rrim(I) all: 0.06987 / Net I/σ(I): 19.77
Reflection shellResolution: 1.1→1.139 Å / Num. unique obs: 11139 / CC1/2: 0.546

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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: 1.1→44.62 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 15.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1473 5619 5 %
Rwork0.1288 --
obs0.1298 112360 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.1→44.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1972 0 42 302 2316
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092269
X-RAY DIFFRACTIONf_angle_d1.1213098
X-RAY DIFFRACTIONf_dihedral_angle_d11.788343
X-RAY DIFFRACTIONf_chiral_restr0.082348
X-RAY DIFFRACTIONf_plane_restr0.01407
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.110.57361870.56123551X-RAY DIFFRACTION100
1.11-1.130.41151850.43783505X-RAY DIFFRACTION100
1.13-1.140.38881850.39293518X-RAY DIFFRACTION100
1.14-1.150.29621850.31873518X-RAY DIFFRACTION100
1.15-1.170.27881850.2653515X-RAY DIFFRACTION100
1.17-1.180.24451860.23373525X-RAY DIFFRACTION100
1.18-1.20.21441860.21053529X-RAY DIFFRACTION100
1.2-1.220.20071880.18623578X-RAY DIFFRACTION100
1.22-1.240.20621850.17973507X-RAY DIFFRACTION100
1.24-1.260.18551860.16673530X-RAY DIFFRACTION100
1.26-1.280.18261850.163514X-RAY DIFFRACTION100
1.28-1.30.18091840.16093531X-RAY DIFFRACTION100
1.3-1.330.18931870.16143551X-RAY DIFFRACTION100
1.33-1.360.18631860.16033531X-RAY DIFFRACTION100
1.36-1.390.20731860.15823518X-RAY DIFFRACTION100
1.39-1.420.13611870.11883555X-RAY DIFFRACTION100
1.42-1.450.141870.11123557X-RAY DIFFRACTION100
1.45-1.490.13161860.09753535X-RAY DIFFRACTION100
1.49-1.540.11591860.08213530X-RAY DIFFRACTION100
1.54-1.590.11051880.08253581X-RAY DIFFRACTION100
1.59-1.640.10521880.08413555X-RAY DIFFRACTION100
1.64-1.710.12161870.0923558X-RAY DIFFRACTION100
1.71-1.790.11471880.09133568X-RAY DIFFRACTION100
1.79-1.880.11481880.09293576X-RAY DIFFRACTION100
1.88-20.11331870.09793565X-RAY DIFFRACTION100
2-2.150.11071900.10153599X-RAY DIFFRACTION100
2.15-2.370.11091880.10593579X-RAY DIFFRACTION100
2.37-2.710.13061910.1153628X-RAY DIFFRACTION100
2.71-3.420.151920.13223651X-RAY DIFFRACTION100
3.42-44.620.16162000.13793783X-RAY DIFFRACTION100

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