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

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Basic information

Entry
Database: PDB / ID: 2qce
TitleCrystal structure of the orotidine-5'-monophosphate decarboxylase domain of human UMP synthase bound to sulfate, glycerol, and chloride
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 / 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 synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 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: Non-polymer description / Version format compliance
Revision 1.2Nov 13, 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 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6485
Polymers28,3321
Non-polymers3164
Water6,431357
1
A: Uridine 5'-monophosphate synthase (UMP synthase)
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)57,29510
Polymers56,6642
Non-polymers6318
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area5620 Å2
ΔGint-91 kcal/mol
Surface area18450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.224, 116.912, 61.965
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-505-

HOH

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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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#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.: 357 / 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: 2.47 Å3/Da / Density % sol: 50.21 %
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: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13
DetectorType: MAR CCD 165 mm / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.42→34.8 Å / Num. obs: 45102 / % possible obs: 84.4 % / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rsym value: 0.079 / Net I/σ(I): 21
Reflection shellResolution: 1.42→1.47 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.263 / Mean I/σ(I) obs: 1.7 / Num. unique all: 1381 / Rsym value: 0.492 / % possible all: 26.3

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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: 1.43→34.79 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.967 / SU B: 0.922 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16485 2295 5.1 %RANDOM
Rwork0.14504 ---
obs0.14603 42806 86.41 %-
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: 10.86 Å2
Baniso -1Baniso -2Baniso -3
1-1.23 Å20 Å20 Å2
2---0.6 Å20 Å2
3----0.64 Å2
Refinement stepCycle: LAST / Resolution: 1.43→34.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1964 0 18 357 2339
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222221
X-RAY DIFFRACTIONr_bond_other_d0.0020.021558
X-RAY DIFFRACTIONr_angle_refined_deg1.2381.9913040
X-RAY DIFFRACTIONr_angle_other_deg0.8833857
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5915315
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.8792495
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.67315434
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8221517
X-RAY DIFFRACTIONr_chiral_restr0.0720.2353
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022494
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02437
X-RAY DIFFRACTIONr_nbd_refined0.2250.2446
X-RAY DIFFRACTIONr_nbd_other0.1970.21676
X-RAY DIFFRACTIONr_nbtor_refined0.1760.21069
X-RAY DIFFRACTIONr_nbtor_other0.0820.21183
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2250
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2550.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.241
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9341.51837
X-RAY DIFFRACTIONr_mcbond_other0.1561.5560
X-RAY DIFFRACTIONr_mcangle_it0.99122231
X-RAY DIFFRACTIONr_scbond_it1.9913950
X-RAY DIFFRACTIONr_scangle_it2.8564.5777
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.429→1.466 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 65 -
Rwork0.308 1186 -
obs--32.96 %

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