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

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Basic information

Entry
Database: PDB / ID: 2qcm
TitleCrystal structure of the orotidine-5'-monophosphate decarboxylase domain (Asp312Asn mutant) of human UMP synthase bound to 6-hydroxymethyl-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
Chem-JW5 / Uridine 5'-monophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.67 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 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6852
Polymers28,3311
Non-polymers3541
Water5,567309
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)57,3704
Polymers56,6622
Non-polymers7082
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area5290 Å2
ΔGint-33 kcal/mol
Surface area18370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.378, 116.607, 61.910
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-485-

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
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-JW5 / 6-(HYDROXYMETHYL)URIDINE 5'-(DIHYDROGEN PHOSPHATE)


Type: RNA linking / Mass: 354.207 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N2O10P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / 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: 50.14 %
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 13, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 1.66→32.24 Å / Num. obs: 32717 / % possible obs: 97.3 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rsym value: 0.05 / Net I/σ(I): 26
Reflection shellResolution: 1.66→1.72 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 4.3 / Num. unique all: 2466 / Rsym value: 0.243 / % possible all: 73.9

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.67→32.24 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.426 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.076 / 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
Rfree0.15927 1640 5 %RANDOM
Rwork0.14123 ---
obs0.14213 31057 98.62 %-
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: 20.58 Å2
Baniso -1Baniso -2Baniso -3
1-1.98 Å20 Å20 Å2
2---0.9 Å20 Å2
3----1.08 Å2
Refinement stepCycle: LAST / Resolution: 1.67→32.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2125 0 24 309 2458
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222209
X-RAY DIFFRACTIONr_bond_other_d0.0020.021536
X-RAY DIFFRACTIONr_angle_refined_deg1.4212.0053023
X-RAY DIFFRACTIONr_angle_other_deg0.91933797
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7445309
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.34524.06296
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.07315425
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2621517
X-RAY DIFFRACTIONr_chiral_restr0.0820.2349
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022479
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02434
X-RAY DIFFRACTIONr_nbd_refined0.2260.2462
X-RAY DIFFRACTIONr_nbd_other0.2060.21674
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21071
X-RAY DIFFRACTIONr_nbtor_other0.0830.21162
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2239
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3210.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1660.234
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1421.51808
X-RAY DIFFRACTIONr_mcbond_other0.2051.5556
X-RAY DIFFRACTIONr_mcangle_it1.11322203
X-RAY DIFFRACTIONr_scbond_it2.1913954
X-RAY DIFFRACTIONr_scangle_it3.2084.5792
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.67→1.71 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.196 105 -
Rwork0.191 1929 -
obs--83.84 %

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