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- PDB-3gdk: Crystal structure of the orotidine 5'-monophosphate decarboxylase... -

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Basic information

Entry
Database: PDB / ID: 3gdk
TitleCrystal structure of the orotidine 5'-monophosphate decarboxylase from Saccharomyces cerevisiae
ComponentsOrotidine 5'-phosphate decarboxylase
KeywordsLYASE / orotidine 5'-monophosphate decarboxylase / Saccharomyces cerevisiae / Decarboxylase / Phosphoprotein / Pyrimidine biosynthesis / Ubl conjugation
Function / homology
Function and homology information


UMP biosynthetic process / orotidine-5'-phosphate decarboxylase / orotidine-5'-phosphate decarboxylase activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / cytosol
Similarity search - Function
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 / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel ...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 / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Orotidine 5'-phosphate decarboxylase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Wood, B.M. / Gerlt, J.A. / Almo, S.C.
CitationJournal: Biochemistry / Year: 2009
Title: Mechanism of the orotidine 5'-monophosphate decarboxylase-catalyzed reaction: evidence for substrate destabilization.
Authors: Chan, K.K. / Wood, B.M. / Fedorov, A.A. / Fedorov, E.V. / Imker, H.J. / Amyes, T.L. / Richard, J.P. / Almo, S.C. / Gerlt, J.A.
History
DepositionFeb 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Orotidine 5'-phosphate decarboxylase
B: Orotidine 5'-phosphate decarboxylase
C: Orotidine 5'-phosphate decarboxylase
D: Orotidine 5'-phosphate decarboxylase


Theoretical massNumber of molelcules
Total (without water)117,1184
Polymers117,1184
Non-polymers00
Water7,674426
1
A: Orotidine 5'-phosphate decarboxylase
D: Orotidine 5'-phosphate decarboxylase


Theoretical massNumber of molelcules
Total (without water)58,5592
Polymers58,5592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-20.1 kcal/mol
Surface area20140 Å2
MethodPISA
2
B: Orotidine 5'-phosphate decarboxylase
C: Orotidine 5'-phosphate decarboxylase


Theoretical massNumber of molelcules
Total (without water)58,5592
Polymers58,5592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-20.6 kcal/mol
Surface area20240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.134, 98.371, 127.100
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 / OMP decarboxylase / OMPdecase / OMPDCase / Uridine 5'-monophosphate synthase / UMP synthase


Mass: 29279.531 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: URA3, YEL021W / Production host: Escherichia coli (E. coli)
References: UniProt: P03962, orotidine-5'-phosphate decarboxylase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 426 / 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: 2.25 Å3/Da / Density % sol: 45.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% PEG 4000, 0.1M Tris-HCl, 0.2M Sodium acetate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 28, 2007
RadiationMonochromator: Si(111) CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. all: 71799 / Num. obs: 71799 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 15.5 Å2 / Rmerge(I) obs: 0.053

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
BALBESphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1DQW

1dqw


Resolution: 2→24.83 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2023340.44 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.28 3627 5.1 %RANDOM
Rwork0.249 ---
all0.25 71799 --
obs0.25 71799 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.404 Å2 / ksol: 0.349067 e/Å3
Displacement parametersBiso mean: 28.6 Å2
Baniso -1Baniso -2Baniso -3
1-21.58 Å20 Å20 Å2
2---7.57 Å20 Å2
3----14 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2→24.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7884 0 0 426 8310
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_mcbond_it1.171.5
X-RAY DIFFRACTIONc_mcangle_it1.662
X-RAY DIFFRACTIONc_scbond_it1.992
X-RAY DIFFRACTIONc_scangle_it2.792.5
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.363 348 4.9 %
Rwork0.315 6718 -
obs-6718 99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4&_1_PARAMETER_INFILE_4&_1_TOPOLOGY_INFILE_4
X-RAY DIFFRACTION5&_1_PARAMETER_INFILE_5&_1_TOPOLOGY_INFILE_5

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