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- PDB-6ywu: Human OMPD-domain of UMPS (K314AcK) in complex with UMP at 1.1 An... -

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Basic information

Entry
Database: PDB / ID: 6ywu
TitleHuman OMPD-domain of UMPS (K314AcK) in complex with UMP at 1.1 Angstroms resolution
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 / lactation / female pregnancy / cellular response to xenobiotic stimulus / 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
URIDINE-5'-MONOPHOSPHATE / Uridine 5'-monophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.1 Å
AuthorsTittmann, K. / Rindfleisch, S. / Krull, M.
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
DepositionApr 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 23, 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 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 9, 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)28,8854
Polymers28,3731
Non-polymers5123
Water5,693316
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-13 kcal/mol
Surface area11340 Å2
Unit cell
Length a, b, c (Å)77.080, 116.940, 61.900
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-766-

HOH

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Components

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


Mass: 28372.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Cysteine modification on position 304 UAG stop-codon mediated introduction of acetylated lysine residue (AcK314)
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-U5P / URIDINE-5'-MONOPHOSPHATE


Mass: 324.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N2O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / 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: 2.46 Å3/Da / Density % sol: 49.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Crystallization: 100 mM Tris/HCl pH 7.8, 1.8 - 2.0 M Ammonium sulfate, 10 mM Glutathion, 5% (v/v) Glycerol, 12.5 mM UMP Cryo-protection: 100 mM Tris/HCl pH 7.8, 2.0 M Ammonium sulfate, 10 mM ...Details: Crystallization: 100 mM Tris/HCl pH 7.8, 1.8 - 2.0 M Ammonium sulfate, 10 mM Glutathion, 5% (v/v) Glycerol, 12.5 mM UMP Cryo-protection: 100 mM Tris/HCl pH 7.8, 2.0 M Ammonium sulfate, 10 mM Glutathion, 5% (v/v) Glycerol, 12.5 mM UMP, 2 M L-proline

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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: 0.8266 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: 0.8266 Å / Relative weight: 1
ReflectionResolution: 1.1→19.66 Å / Num. obs: 112207 / % possible obs: 99.2 % / Redundancy: 6.703 % / Biso Wilson estimate: 14.116 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Rrim(I) all: 0.067 / Χ2: 0.866 / Net I/σ(I): 15.55 / Num. measured all: 752166 / Scaling rejects: 4319
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.1-1.156.6720.8992.58138640.8540.97399.1
1.15-1.26.7170.643.43116670.9140.69299.5
1.2-1.56.7740.3316.46419290.9730.35899.1
1.5-56.6570.03930.424345110.04299.2
5-106.3190.02259.1211480.9990.02499.8
10-205.1490.02156.161480.9990.02394.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QCD

2qcd


Resolution: 1.1→19.66 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.977 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.027 / ESU R Free: 0.028
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1584 5501 4.9 %RANDOM
Rwork0.138 ---
obs0.139 106706 99.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 58.94 Å2 / Biso mean: 13.673 Å2 / Biso min: 7.31 Å2
Baniso -1Baniso -2Baniso -3
1-1.42 Å20 Å2-0 Å2
2---0.63 Å20 Å2
3----0.79 Å2
Refinement stepCycle: final / Resolution: 1.1→19.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1962 0 32 317 2311
Biso mean--18.12 28.06 -
Num. residues----256
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132347
X-RAY DIFFRACTIONr_bond_other_d0.0350.0172228
X-RAY DIFFRACTIONr_angle_refined_deg1.631.6293213
X-RAY DIFFRACTIONr_angle_other_deg2.2811.5845192
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7285319
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.17622.054112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.47315420
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7491516
X-RAY DIFFRACTIONr_chiral_restr0.0960.2303
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022745
X-RAY DIFFRACTIONr_gen_planes_other0.0130.02492
X-RAY DIFFRACTIONr_rigid_bond_restr8.03734574
LS refinement shellResolution: 1.1→1.129 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 383 -
Rwork0.344 7801 -
all-8184 -
obs--98.73 %

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