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- PDB-7oqk: Human OMPD-domain of UMPS in complex with substrate OMP at 1.10 A... -

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Basic information

Entry
Database: PDB / ID: 7oqk
TitleHuman OMPD-domain of UMPS in complex with substrate OMP at 1.10 Angstroms resolution, 15 minutes soaking
Components(Uridine 5'-monophosphate ...) x 2
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
OROTIDINE-5'-MONOPHOSPHATE / URIDINE-5'-MONOPHOSPHATE / Uridine 5'-monophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 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 3, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 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: Uridine 5'-monophosphate synthase
B: Uridine 5'-monophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,78011
Polymers56,1952
Non-polymers1,5859
Water12,719706
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint-65 kcal/mol
Surface area18780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.016, 61.916, 70.159
Angle α, β, γ (deg.)90.000, 112.950, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Uridine 5'-monophosphate ... , 2 types, 2 molecules AB

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


Mass: 28113.516 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 BL21(DE3) (bacteria)
References: UniProt: P11172, orotate phosphoribosyltransferase, orotidine-5'-phosphate decarboxylase
#2: Protein Uridine 5'-monophosphate synthase / UMP synthase


Mass: 28081.451 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 BL21(DE3) (bacteria)
References: UniProt: P11172, orotate phosphoribosyltransferase, orotidine-5'-phosphate decarboxylase

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Non-polymers , 5 types, 715 molecules

#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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-OMP / OROTIDINE-5'-MONOPHOSPHATE


Mass: 368.191 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N2O11P / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-U / URIDINE-5'-MONOPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 706 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 50.39 %
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: 0.827 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.827 Å / Relative weight: 1
ReflectionResolution: 1.1→34.85 Å / Num. obs: 220012 / % possible obs: 98.4 % / Redundancy: 3.459 % / Biso Wilson estimate: 14.315 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rrim(I) all: 0.062 / Χ2: 0.869 / Net I/σ(I): 12.21 / Num. measured all: 760933 / Scaling rejects: 165
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
1.1-1.133.370.8651.85455516519161870.6931.0398
1.13-1.163.4050.7022.25373615980157830.7730.83498.8
1.16-1.193.4590.5432.855328415625154050.8370.64398.6
1.19-1.233.4690.4743.25206515200150070.8610.56198.7
1.23-1.273.4660.4043.765009114685144510.9020.47898.4
1.27-1.313.460.3394.354842014227139960.9230.40298.4
1.31-1.363.460.2735.224656313699134580.9470.32398.2
1.36-1.423.4340.2266.254489613240130740.9570.26998.7
1.42-1.483.4310.1887.184308012750125560.9710.22498.5
1.48-1.563.3910.139.664055512127119600.9850.15598.6
1.56-1.643.3990.09412.683866711519113760.9920.11298.8
1.64-1.743.5880.07216.183870210918107870.9950.08598.8
1.74-1.863.580.056203615110242100980.9960.06698.6
1.86-2.013.5140.04724.1633154961794350.9970.05598.1
2.01-2.23.510.03828.4730302882286330.9980.04497.9
2.2-2.463.4240.03331.4826687799077930.9980.0497.5
2.46-2.843.4450.02636.1823998708469660.9980.03198.3
2.84-3.483.6230.02342.2321540599059460.9990.02899.3
3.48-4.923.5450.02444.8616285465345940.9980.02998.7
4.92-34.853.2720.02543.538202261825070.9970.0395.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ZWY

6zwy


Resolution: 1.1→34.85 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.98 / SU B: 1.118 / SU ML: 0.022 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.026 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1456 10880 4.9 %RANDOM
Rwork0.1297 ---
obs0.1305 209142 98.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 77.27 Å2 / Biso mean: 14.905 Å2 / Biso min: 8.25 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20.49 Å2
2---0.82 Å20 Å2
3---0.28 Å2
Refinement stepCycle: final / Resolution: 1.1→34.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3923 0 53 712 4688
Biso mean--26.68 32.89 -
Num. residues----514
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0134565
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174329
X-RAY DIFFRACTIONr_angle_refined_deg1.4581.6356245
X-RAY DIFFRACTIONr_angle_other_deg1.5211.59210084
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7555615
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.68522.238210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.46315814
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4311529
X-RAY DIFFRACTIONr_chiral_restr0.0810.2589
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025286
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021935
X-RAY DIFFRACTIONr_rigid_bond_restr1.00738894
LS refinement shellResolution: 1.1→1.129 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 802 -
Rwork0.283 15381 -
all-16183 -
obs--98.09 %

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