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- PDB-7ov0: Orotidine 5'-monophosphate decarboxylase-domain of human UMPS in ... -

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Basic information

Entry
Database: PDB / ID: 7ov0
TitleOrotidine 5'-monophosphate decarboxylase-domain of human UMPS in resting state at 0.95 Angstrom resolution
ComponentsUridine 5'-monophosphate synthase
KeywordsLYASE / OMPD / UMPS / UMP
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
PROLINE / 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.
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 14, 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 6, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,8297
Polymers28,2041
Non-polymers6266
Water6,269348
1
A: Uridine 5'-monophosphate synthase
hetero molecules

A: Uridine 5'-monophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,65914
Polymers56,4072
Non-polymers1,25112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area5350 Å2
ΔGint-63 kcal/mol
Surface area19490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.396, 116.562, 61.958
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-755-

HOH

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Components

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


Mass: 28203.680 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H9NO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 348 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 50.35 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / 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: Apr 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7653 Å / Relative weight: 1
ReflectionResolution: 0.95→42.45 Å / Num. obs: 172156 / % possible obs: 98.2 % / Redundancy: 4.279 % / Biso Wilson estimate: 12.276 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.033 / Rrim(I) all: 0.037 / Χ2: 0.945 / Net I/σ(I): 18.05 / Num. measured all: 736718 / Scaling rejects: 9
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
0.95-0.973.3160.6391.784246912886128060.6810.7699.4
0.97-13.5940.4912.494485212549124800.7860.57499.5
1-1.034.1970.3693.645098612212121480.8970.4299.5
1.03-1.064.3790.2585.175158411864117810.9510.29299.3
1.06-1.14.4420.187.345057211442113860.9760.20399.5
1.1-1.144.4690.1339.874958311138110940.9860.1599.6
1.14-1.184.4780.109124797610758107140.9910.12399.6
1.18-1.234.4490.09413.894582410368102990.9930.10699.3
1.23-1.284.450.0815.9243686991398170.9950.0999
1.28-1.344.4240.06818.3341493951993790.9960.07698.5
1.34-1.424.4140.05821.2339220903588860.9970.06598.4
1.42-1.54.3510.05224.1236536858083970.9980.05897.9
1.5-1.614.4780.0430.7535249805378720.9980.04597.8
1.61-1.734.5380.03535.133162753473080.9990.03997
1.73-1.94.4680.03139.629840693866780.9990.03496.3
1.9-2.124.4390.02644.2926596631159910.9990.0394.9
2.12-2.454.3590.02546.2422971557852700.9990.02894.5
2.45-34.4880.02348.820053474144680.9990.02594.2
3-4.254.5940.02151.5716001371834830.9990.02493.7
4.25-42.454.2470.02250.058065213818990.9980.02588.8

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QCD

2qcd


Resolution: 0.95→42.45 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 10.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1175 8501 4.94 %
Rwork0.105 163627 -
obs0.1056 172128 98.21 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.74 Å2 / Biso mean: 14.1161 Å2 / Biso min: 5.96 Å2
Refinement stepCycle: final / Resolution: 0.95→42.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1975 0 92 353 2420
Biso mean--20.08 28.28 -
Num. residues----258
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 (%)
0.95-0.960.39472680.36545464573299
0.96-0.970.31672920.30795506579899
0.97-0.980.27882980.26785451574999
0.98-10.24652920.231554535745100
1-1.010.21342650.20195477574299
1.01-1.020.22033050.1755487579299
1.02-1.040.15362760.1535482575899
1.04-1.050.15522950.13845456575199
1.05-1.070.13752940.124355115805100
1.07-1.090.12413110.11485459577099
1.09-1.110.11432860.105654695755100
1.11-1.130.11252570.099355595816100
1.13-1.150.11632920.098654925784100
1.15-1.170.10482730.09554935766100
1.17-1.20.09393120.08315484579699
1.2-1.220.10163010.08285479578099
1.22-1.260.09322830.08065471575499
1.26-1.290.09982880.08075485577399
1.29-1.330.1022750.07835467574299
1.33-1.370.09532810.07765468574998
1.37-1.420.09732720.07745469574198
1.42-1.480.10032830.08155413569698
1.48-1.540.09822630.07855462572598
1.54-1.620.08682730.0765458573198
1.62-1.730.0923090.0825363567297
1.73-1.860.09092690.08665402567196
1.86-2.050.10082590.09035353561295
2.05-2.340.10632690.0975350561995
2.34-2.950.12552900.1095336562694
2.95-42.450.13142700.12365408567892

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