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- PDB-2qch: Crystal structure of the orotidine-5'-monophosphate decarboxylase... -

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Basic information

Entry
Database: PDB / ID: 2qch
TitleCrystal structure of the orotidine-5'-monophosphate decarboxylase domain of human UMP synthase bound to 5-iodo-UMP
ComponentsUridine 5'-monophosphate synthase (UMP synthase)
KeywordsLYASE / UMP synthase / decarboxylase / catalytic proficiency
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 class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE / IODIDE ION / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / Uridine 5'-monophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsWittmann, J. / Rudolph, M.
CitationJournal: Structure / Year: 2008
Title: Structures of the human orotidine-5'-monophosphate decarboxylase support a covalent mechanism and provide a framework for drug design.
Authors: Wittmann, J.G. / Heinrich, D. / Gasow, K. / Frey, A. / Diederichsen, U. / Rudolph, M.G.
History
DepositionJun 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uridine 5'-monophosphate synthase (UMP synthase)
B: Uridine 5'-monophosphate synthase (UMP synthase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3388
Polymers56,5992
Non-polymers1,7386
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6610 Å2
ΔGint-25 kcal/mol
Surface area17900 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)69.580, 61.998, 70.565
Angle α, β, γ (deg.)90.00, 113.27, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Uridine 5'-monophosphate synthase (UMP synthase)


Mass: 28299.742 Da / Num. of mol.: 2 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UMPS / Plasmid: pETM-30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta 2(DE3)
References: UniProt: P11172, orotidine-5'-phosphate decarboxylase
#2: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-5IU / 5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE


Type: DNA linking / Mass: 434.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H12IN2O8P
#4: Chemical ChemComp-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP


Mass: 308.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N2O8P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / Source method: isolated from a natural source / Formula: H2O

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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: 2.47 Å3/Da / Density % sol: 50.2 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5419 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 26, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 1.95→40 Å / Num. obs: 37157 / % possible obs: 92.1 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rsym value: 0.101 / Net I/σ(I): 10.3
Reflection shellResolution: 1.95→2 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 2610 / Rsym value: 0.382 / % possible all: 65.4

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→40 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.898 / SU B: 5.843 / SU ML: 0.163 / Cross valid method: THROUGHOUT / ESU R: 0.22 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The atoms that are in close contact have occupancy less than 1 and are mutually exclusive.
RfactorNum. reflection% reflectionSelection details
Rfree0.26819 1868 5 %RANDOM
Rwork0.22061 ---
obs0.22305 35268 91.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.961 Å2
Baniso -1Baniso -2Baniso -3
1-1.47 Å20 Å23.6 Å2
2---2.27 Å20 Å2
3---3.64 Å2
Refinement stepCycle: LAST / Resolution: 1.95→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3908 0 84 229 4221
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224137
X-RAY DIFFRACTIONr_bond_other_d0.0010.022831
X-RAY DIFFRACTIONr_angle_refined_deg1.25125608
X-RAY DIFFRACTIONr_angle_other_deg0.89736927
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.045530
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.05423.757173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.20615742
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9241531
X-RAY DIFFRACTIONr_chiral_restr0.0650.2640
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024556
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02809
X-RAY DIFFRACTIONr_nbd_refined0.2050.2923
X-RAY DIFFRACTIONr_nbd_other0.1930.23047
X-RAY DIFFRACTIONr_nbtor_refined0.1730.21939
X-RAY DIFFRACTIONr_nbtor_other0.0840.22201
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2234
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.170.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2510.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1970.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5081.52573
X-RAY DIFFRACTIONr_mcbond_other0.0951.51057
X-RAY DIFFRACTIONr_mcangle_it0.90224093
X-RAY DIFFRACTIONr_scbond_it1.23731690
X-RAY DIFFRACTIONr_scangle_it2.0394.51504
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 91 -
Rwork0.274 1763 -
obs--62.55 %

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