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

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Basic information

Entry
Database: PDB / ID: 2qcc
TitleCrystal structure of the orotidine-5'-monophosphate decarboxylase domain of human UMP synthase, apo form
ComponentsOrotidine 5'- phosphate decarboxylase (OMPdecase)
KeywordsLYASE / UMP synthase / decarboxylase / TIM barrel / 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 / 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 6, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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: Orotidine 5'- phosphate decarboxylase (OMPdecase)
B: Orotidine 5'- phosphate decarboxylase (OMPdecase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9766
Polymers56,5992
Non-polymers3764
Water5,495305
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-57 kcal/mol
Surface area19130 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)62.019, 75.912, 119.545
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Orotidine 5'- phosphate decarboxylase (OMPdecase)


Mass: 28299.742 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 305 / 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: 2.49 Å3/Da / Density % sol: 50.51 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: ammonium sulfate, 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: Aug 15, 2006 / Details: mirrors
RadiationMonochromator: filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 1.85→47 Å / Num. obs: 46969 / % possible obs: 94.3 % / Observed criterion σ(I): 0 / Redundancy: 10.8 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 28.5
Reflection shellResolution: 1.84→1.91 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 2 / Num. unique all: 2878 / Rsym value: 0.619 / % possible all: 58.8

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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: 1.85→46.96 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.926 / SU B: 8.308 / SU ML: 0.126 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.147 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25755 2352 5 %RANDOM
Rwork0.19705 ---
obs0.2 44555 96.01 %-
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: 34.791 Å2
Baniso -1Baniso -2Baniso -3
1--1.28 Å20 Å20 Å2
2--2.54 Å20 Å2
3----1.26 Å2
Refinement stepCycle: LAST / Resolution: 1.85→46.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3814 0 22 305 4141
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223978
X-RAY DIFFRACTIONr_bond_other_d0.0010.022740
X-RAY DIFFRACTIONr_angle_refined_deg1.2811.9835385
X-RAY DIFFRACTIONr_angle_other_deg0.88636706
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8625520
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.31723.58162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.82915730
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.2711529
X-RAY DIFFRACTIONr_chiral_restr0.0730.2622
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024393
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02784
X-RAY DIFFRACTIONr_nbd_refined0.210.2881
X-RAY DIFFRACTIONr_nbd_other0.1920.23002
X-RAY DIFFRACTIONr_nbtor_refined0.1720.21945
X-RAY DIFFRACTIONr_nbtor_other0.0860.22117
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2297
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0520.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.225
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2980.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.180.217
X-RAY DIFFRACTIONr_mcbond_it0.6961.52575
X-RAY DIFFRACTIONr_mcbond_other0.181.51031
X-RAY DIFFRACTIONr_mcangle_it1.0824015
X-RAY DIFFRACTIONr_scbond_it1.90831564
X-RAY DIFFRACTIONr_scangle_it2.7754.51356
LS refinement shellResolution: 1.851→1.899 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 158 -
Rwork0.261 2373 -
obs--70.86 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.0949-0.0519-0.08711.67390.17992.2421-0.022-0.631-0.48590.1427-0.08160.12070.1160.04560.1036-0.1977-0.027-0.0152-0.06610.1263-0.0852.277.39516.201
22.8471-0.31920.09651.6492-0.00452.16340.06290.617-0.4674-0.1367-0.1478-0.04620.1046-0.01460.0849-0.19420.037-0.0224-0.0629-0.1338-0.0862-1.7796.374-15.35
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA224 - 4794 - 259
2X-RAY DIFFRACTION2BB223 - 4803 - 260

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