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

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Basic information

Entry
Database: PDB / ID: 2qcf
TitleCrystal structure of the orotidine-5'-monophosphate decarboxylase domain (Asp312Asn mutant) of human UMP synthase bound to 5-fluoro-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 / 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
5-FLUORO-URIDINE-5'-MONOPHOSPHATE / Uridine 5'-monophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22 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 1.2Oct 20, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / 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
Revision 1.3Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,7653
Polymers28,3311
Non-polymers4342
Water6,882382
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)57,5306
Polymers56,6622
Non-polymers8694
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area5430 Å2
ΔGint-35 kcal/mol
Surface area18050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.815, 115.512, 61.370
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-560-

HOH

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Components

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


Mass: 28330.824 Da / Num. of mol.: 1 / Fragment: C-terminal domain / Mutation: y
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-5FU / 5-FLUORO-URIDINE-5'-MONOPHOSPHATE


Type: RNA linking / Mass: 342.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H12FN2O9P
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / 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: 2.4 Å3/Da / Density % sol: 48.85 %
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 / Wavelength: 0.8 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 28, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.22→22.14 Å / Num. obs: 81404 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rsym value: 0.083 / Net I/σ(I): 21.4
Reflection shellResolution: 1.22→1.24 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 3900 / Rsym value: 0.594

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.22→22.14 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.977 / SU B: 1.171 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.034 / 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
Rfree0.14838 4111 5.1 %RANDOM
Rwork0.12128 ---
obs0.12264 77246 99.69 %-
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: 9.11 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å20 Å20 Å2
2---0.44 Å20 Å2
3----0.52 Å2
Refinement stepCycle: LAST / Resolution: 1.22→22.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1967 0 28 382 2377
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222344
X-RAY DIFFRACTIONr_bond_other_d0.0020.021659
X-RAY DIFFRACTIONr_angle_refined_deg1.841.9983230
X-RAY DIFFRACTIONr_angle_other_deg1.04734124
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2295345
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.14124.02102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.11815469
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0471519
X-RAY DIFFRACTIONr_chiral_restr0.1250.2373
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022667
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02465
X-RAY DIFFRACTIONr_nbd_refined0.2540.2537
X-RAY DIFFRACTIONr_nbd_other0.2150.22070
X-RAY DIFFRACTIONr_nbtor_refined0.1980.21193
X-RAY DIFFRACTIONr_nbtor_other0.0940.21510
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2110.2343
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2820.228
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3310.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3170.254
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9241.51796
X-RAY DIFFRACTIONr_mcbond_other0.6721.5581
X-RAY DIFFRACTIONr_mcangle_it2.0922338
X-RAY DIFFRACTIONr_scbond_it3.47231016
X-RAY DIFFRACTIONr_scangle_it4.6664.5849
X-RAY DIFFRACTIONr_rigid_bond_restr1.73534714
X-RAY DIFFRACTIONr_sphericity_free9.4323383
X-RAY DIFFRACTIONr_sphericity_bonded2.9233924
LS refinement shellResolution: 1.22→1.25 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 310 -
Rwork0.261 5410 -
obs--96.25 %

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