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- PDB-7ouz: Human OMPD-domain of UMPS in complex with 6-hydroxy-UMP at 0.9 An... -

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Basic information

Entry
Database: PDB / ID: 7ouz
TitleHuman OMPD-domain of UMPS in complex with 6-hydroxy-UMP at 0.9 Angstroms resolution, crystal 1
ComponentsUridine 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 / 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
6-HYDROXYURIDINE-5'-PHOSPHATE / PROLINE / Uridine 5'-monophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.9 Å
AuthorsRindfleisch, S. / 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 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)28,6524
Polymers28,1051
Non-polymers5473
Water5,783321
1
A: Uridine 5'-monophosphate synthase
hetero molecules

A: Uridine 5'-monophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3048
Polymers56,2092
Non-polymers1,0956
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area5500 Å2
ΔGint-36 kcal/mol
Surface area19040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.896, 116.425, 61.968
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-721-

HOH

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Components

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


Mass: 28104.551 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-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / 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: 50.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: Tris/HCl, ammonium sulfate, glutathione

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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 PILATUS 6M / Detector: PIXEL / Date: Apr 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7653 Å / Relative weight: 1
ReflectionResolution: 0.9→30.3 Å / Num. obs: 200348 / % possible obs: 96.8 % / Redundancy: 3.499 % / Biso Wilson estimate: 11.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.036 / Rrim(I) all: 0.042 / Χ2: 0.949 / Net I/σ(I): 15.25 / Num. measured all: 701093 / Scaling rejects: 288
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
0.9-0.922.6580.8561.233661815204137750.531.05690.6
0.92-0.952.9750.691.684351914801146280.6080.83998.8
0.95-0.983.040.5192.294312514427141880.7530.62898.3
0.98-1.013.1080.3793.184257013995136990.8540.45597.9
1.01-1.043.2630.2574.544370513605133940.9320.30498.4
1.04-1.083.4390.186.64450113121129390.970.21198.6
1.08-1.123.7620.1259.564734412688125860.9870.14399.2
1.12-1.163.7870.112.074550612224120160.9910.11598.3
1.16-1.213.7930.0814.424395611746115900.9940.09298.7
1.21-1.273.7920.07116.284167911210109920.9950.08198.1
1.27-1.343.7670.06218.573913910708103910.9960.07197
1.34-1.423.7470.05421.09365801010097620.9970.06296.7
1.42-1.523.7480.04624.9234426952391860.9970.05396.5
1.52-1.643.9360.03630.6333876887886060.9980.04196.9
1.64-1.83.90.03234.3930812820779000.9980.03796.3
1.8-2.013.8390.02938.2627255743070990.9990.03395.5
2.01-2.323.7870.02740.923612658262350.9990.03194.7
2.32-2.853.9040.02343.0120547560152630.9990.02694
2.85-4.023.8380.02344.4415631437740730.9980.02693.1
4.02-30.33.3030.02441.486692251820260.9960.02980.5

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Processing

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

2qcc


Resolution: 0.9→30.3 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 12.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1196 9875 4.93 %
Rwork0.1096 190404 -
obs0.11 200279 96.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 59.35 Å2 / Biso mean: 12.8889 Å2 / Biso min: 4.78 Å2
Refinement stepCycle: final / Resolution: 0.9→30.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1967 0 67 326 2360
Biso mean--12.78 24.3 -
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 (%)
0.9-0.910.35012790.3415659593887
0.91-0.920.30543200.31946000632093
0.92-0.930.29263000.29266454675498
0.93-0.940.26433610.26776357671899
0.94-0.960.2563110.25036482679399
0.96-0.970.28223230.28266365668898
0.97-0.980.2873570.27816439679699
0.98-10.26533320.25286264659697
1-1.010.16753270.16216474680199
1.01-1.030.15343620.14156428679099
1.03-1.050.16263370.15166336667398
1.05-1.070.12593360.11446434677099
1.07-1.090.10733580.09766484684299
1.09-1.110.10063230.08526470679399
1.11-1.130.10253300.0916381671198
1.13-1.160.09453290.08226435676499
1.16-1.190.09013370.07876486682399
1.19-1.220.08643450.07426418676399
1.22-1.260.08873480.07536419676798
1.26-1.30.08943390.07796376671597
1.3-1.340.09453240.07316376670097
1.34-1.40.08613340.07246334666897
1.4-1.460.0893170.07726341665896
1.46-1.540.09483100.07656352666297
1.54-1.640.09183230.07636417674097
1.64-1.760.09833520.0826335668796
1.76-1.940.09923010.09016357665896
1.94-2.220.09753200.09226316663695
2.22-2.80.11523290.10736281661094
2.8-30.30.1493110.14266134644589

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