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- PDB-7otu: Human OMPD-domain of UMPS in complex with 6-hydroxy-UMP at 0.95 A... -

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Basic information

Entry
Database: PDB / ID: 7otu
TitleHuman OMPD-domain of UMPS in complex with 6-hydroxy-UMP at 0.95 Angstroms resolution, crystal 2
ComponentsIsoform 2 of Uridine 5'-monophosphate synthase
KeywordsLYASE / OMPD / BMP / UMPS / Orotidine 5'-monophosphate decarboxylase
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 / 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
6-HYDROXYURIDINE-5'-PHOSPHATE / Uridine 5'-monophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.95 Å
AuthorsRindfleisch, S. / Rabe von Pappenheim, F. / Tittmann, K.
CitationJournal: Nat Catal / Year: 2022
Title: Ground-state destabilization by electrostatic repulsion is not a driving force in orotidine-5-monophosphate decarboxylase catalysis
Authors: Rindfleisch, S. / Krull, M. / Uranga, J. / Schmidt, T. / Rabe von Pappenheim, F. / Kirck, L.L. / Balouri, A. / Schneider, T. / Chari, A. / Kluger, R. / Bourenkov, G. / Diederichsen, U. / ...Authors: Rindfleisch, S. / Krull, M. / Uranga, J. / Schmidt, T. / Rabe von Pappenheim, F. / Kirck, L.L. / Balouri, A. / Schneider, T. / Chari, A. / Kluger, R. / Bourenkov, G. / Diederichsen, U. / Mata, R.A. / Tittmann, K.
History
DepositionJun 10, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1May 4, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isoform 2 of Uridine 5'-monophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8564
Polymers28,3321
Non-polymers5243
Water6,161342
1
A: Isoform 2 of Uridine 5'-monophosphate synthase
hetero molecules

A: Isoform 2 of Uridine 5'-monophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7128
Polymers56,6642
Non-polymers1,0496
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area5960 Å2
ΔGint-35 kcal/mol
Surface area18790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.893, 116.724, 61.898
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-710-

HOH

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Components

#1: Protein Isoform 2 of Uridine 5'-monophosphate synthase / UMP synthase


Mass: 28331.809 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UMPS, OK/SW-cl.21 / Production host: Escherichia coli (E. coli)
References: UniProt: P11172, orotate phosphoribosyltransferase, orotidine-5'-phosphate decarboxylase
#2: Chemical ChemComp-BMP / 6-HYDROXYURIDINE-5'-PHOSPHATE


Type: RNA linking / Mass: 340.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N2O10P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / 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: 50.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.8 / Details: Ammonium sulfate, Tris/HCl, Glutathion, 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: 0.7653 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7653 Å / Relative weight: 1
ReflectionResolution: 0.95→42.46 Å / Num. obs: 175866 / % possible obs: 99.7 % / Redundancy: 13.383 % / Biso Wilson estimate: 11.613 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.052 / Rrim(I) all: 0.054 / Χ2: 0.874 / Net I/σ(I): 23.58 / Num. measured all: 2353528 / Scaling rejects: 149
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
0.95-0.9712.611.4482.3416201412973128480.7851.50799
0.97-113.4191.1442.9916725912592124640.8641.18899
1-1.0313.6360.8354.116685112310122360.9250.86799.4
1.03-1.0613.6930.5935.6616253211922118700.9590.61699.6
1.06-1.113.7090.4197.7715836711577115520.9780.43599.8
1.1-1.1413.6480.3129.9815218411180111510.9880.32499.7
1.14-1.1813.5870.24812.0814660210810107900.9920.25799.8
1.18-1.2313.5440.21213.9114107610436104160.9940.2299.8
1.23-1.2813.4680.17815.951346571002899980.9950.18599.7
1.28-1.3413.3980.14818.44127839957495420.9960.15499.7
1.34-1.4213.2320.12122.15120235908990870.9970.125100
1.42-1.513.8620.09727.28119613862986290.9980.101100
1.5-1.6113.820.07335.92111900809780970.9990.075100
1.61-1.7313.60.05843.43103279759475940.9990.06100
1.73-1.913.2150.04552.3392492700069990.9990.047100
1.9-2.1212.8630.03564.95816056344634410.036100
2.12-2.4512.4790.0372.19697855596559210.03199.9
2.45-313.0410.02681.59625054793479310.027100
3-4.2512.8430.02289.77480073738373810.023100
4.25-42.4611.630.02186.81247262153212610.02298.7

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
REFMAC5.8.0258phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QCD

2qcd


Resolution: 0.95→42.46 Å / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 10.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1062 8677 4.93 %
Rwork0.0961 167160 -
obs0.0966 175837 99.66 %
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.65 Å2 / Biso mean: 13.133 Å2 / Biso min: 4.12 Å2
Refinement stepCycle: final / Resolution: 0.95→42.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1967 0 59 363 2389
Biso mean--21.31 27.37 -
Num. residues----257
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
0.95-0.960.28012670.26565463573099
0.96-0.970.2472880.23565495578399
0.97-0.980.21833030.21575491579499
0.98-10.20622830.19545503578699
1-1.010.19212860.17985463574999
1.01-1.020.16452910.15975513580499
1.02-1.040.17172900.141855385828100
1.04-1.050.14382970.129655255822100
1.05-1.070.12592920.118755105802100
1.07-1.090.11633060.109855265832100
1.09-1.110.11532870.097555475834100
1.11-1.130.11052730.089455485821100
1.13-1.150.08882900.083555955885100
1.15-1.170.09092760.078355445820100
1.17-1.20.08033070.075755365843100
1.2-1.220.09053000.074655385838100
1.22-1.260.08933010.070555445845100
1.26-1.290.07882790.070355555834100
1.29-1.330.08372870.068455655852100
1.33-1.370.08862910.068255885879100
1.37-1.420.08532820.070656095891100
1.42-1.480.08892870.07155675854100
1.48-1.540.08442670.068956055872100
1.54-1.620.08912870.068856425929100
1.62-1.730.08683180.077655885906100
1.73-1.860.0962780.08456375915100
1.86-2.050.0812760.08356615937100
2.05-2.340.09942890.087856815970100
2.34-2.950.10953060.097857016007100
2.95-42.460.11962930.116158826175100

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