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

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Basic information

Entry
Database: PDB / ID: 2qcd
TitleCrystal structure of the orotidine-5'-monophosphate decarboxylase domain of human UMP synthase bound to UMP
Components(Uridine 5'-monophosphate synthase (UMP synthase)) x 2
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 / 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 class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
URIDINE-5'-MONOPHOSPHATE / Uridine 5'-monophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.03 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: Version format compliance
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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)57,2804
Polymers56,6322
Non-polymers6482
Water6,269348
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5160 Å2
ΔGint-34 kcal/mol
Surface area18450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.394, 61.643, 69.970
Angle α, β, γ (deg.)90.00, 112.71, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 28331.809 Da / Num. of mol.: 1 / 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: Protein Uridine 5'-monophosphate synthase (UMP synthase)


Mass: 28299.742 Da / Num. of mol.: 1
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
#3: Chemical ChemComp-U5P / URIDINE-5'-MONOPHOSPHATE


Mass: 324.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N2O9P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 348 / Source method: isolated from a natural source / Formula: H2O
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: 2.44 Å3/Da / Density % sol: 49.56 %

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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 15, 2006 / Details: mirors
RadiationMonochromator: filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 2.03→42.3 Å / Num. obs: 34716 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rsym value: 0.095 / Net I/σ(I): 18.6
Reflection shellResolution: 2.03→2.08 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 3.9 / Num. unique all: 2961 / Rsym value: 0.344 / % possible all: 83.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
COMOphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.03→42.26 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.696 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1946 1733 5 %RANDOM
Rwork0.14947 ---
obs0.15174 32963 98.49 %-
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: 20.797 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å21.47 Å2
2---1.18 Å20 Å2
3---2.38 Å2
Refinement stepCycle: LAST / Resolution: 2.03→42.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3943 0 42 348 4333
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224135
X-RAY DIFFRACTIONr_bond_other_d0.0010.022827
X-RAY DIFFRACTIONr_angle_refined_deg1.3881.995606
X-RAY DIFFRACTIONr_angle_other_deg0.9336927
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1895542
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.24623.765170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.81715748
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6651530
X-RAY DIFFRACTIONr_chiral_restr0.080.2647
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024584
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02816
X-RAY DIFFRACTIONr_nbd_refined0.2180.2871
X-RAY DIFFRACTIONr_nbd_other0.20.23053
X-RAY DIFFRACTIONr_nbtor_refined0.1740.21984
X-RAY DIFFRACTIONr_nbtor_other0.0830.22182
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2310
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1820.227
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2920.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.180.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1751.53385
X-RAY DIFFRACTIONr_mcbond_other0.1821.51074
X-RAY DIFFRACTIONr_mcangle_it1.25824154
X-RAY DIFFRACTIONr_scbond_it2.3831729
X-RAY DIFFRACTIONr_scangle_it3.424.51438
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.03→2.086 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 103 -
Rwork0.191 2120 -
obs--86.3 %

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