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- PDB-2qcn: Covalent complex of the orotidine-5'-monophosphate decarboxylase ... -

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Basic information

Entry
Database: PDB / ID: 2qcn
TitleCovalent complex of the orotidine-5'-monophosphate decarboxylase domain of human UMP synthase with 6-iodo-UMP
ComponentsUridine 5'-monophosphate synthase
KeywordsLYASE / UMP synthase / decarboxylase / catalytic proficiency / Disease mutation / Glycosyltransferase / Multifunctional enzyme / Pyrimidine biosynthesis / Transferase
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: 1.85 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 13, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / 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
B: Uridine 5'-monophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5287
Polymers56,5992
Non-polymers9295
Water7,386410
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.448, 61.912, 70.280
Angle α, β, γ (deg.)90.00, 114.06, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Uridine 5'-monophosphate synthase / UMP synthase [Includes: Orotate phosphoribosyltransferase (E.C. 2.4.2.10) (OPRTase) / and Orotidine ...UMP synthase [Includes: Orotate phosphoribosyltransferase (E.C. 2.4.2.10) (OPRTase) / and Orotidine 5'-phosphate decarboxylase (E.C. 4.1.1.23) (OMPdecase)]


Mass: 28299.742 Da / Num. of mol.: 2
Fragment: C-terminal domain: Orotidine 5'- phosphate decarboxylase: Residues 224-480
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-U5P / URIDINE-5'-MONOPHOSPHATE


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 410 / 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: 49.54 %
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: Apr 6, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 1.85→34.94 Å / Num. obs: 46040 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rsym value: 0.053 / Net I/σ(I): 17.6
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 1575 / Rsym value: 0.271 / % possible all: 79.9

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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: 1.85→34.94 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.669 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18843 2306 5 %RANDOM
Rwork0.15634 ---
obs0.15795 43717 99.25 %-
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: 25.916 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20 Å22.01 Å2
2---1.06 Å20 Å2
3---2.29 Å2
Refinement stepCycle: LAST / Resolution: 1.85→34.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3929 0 59 410 4398
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224171
X-RAY DIFFRACTIONr_bond_other_d0.0010.022865
X-RAY DIFFRACTIONr_angle_refined_deg1.4741.9925650
X-RAY DIFFRACTIONr_angle_other_deg0.94337009
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7255545
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.4223.563174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.95715761
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9251533
X-RAY DIFFRACTIONr_chiral_restr0.0910.2648
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024612
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02823
X-RAY DIFFRACTIONr_nbd_refined0.2160.2834
X-RAY DIFFRACTIONr_nbd_other0.2010.23082
X-RAY DIFFRACTIONr_nbtor_refined0.1760.21955
X-RAY DIFFRACTIONr_nbtor_other0.0860.22232
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2317
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2710.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2620.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1330.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3751.53390
X-RAY DIFFRACTIONr_mcbond_other0.2331.51071
X-RAY DIFFRACTIONr_mcangle_it1.44124158
X-RAY DIFFRACTIONr_scbond_it2.64931778
X-RAY DIFFRACTIONr_scangle_it3.7754.51475
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.9 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 153 -
Rwork0.22 2913 -
obs--90.18 %

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