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- PDB-1dqw: CRYSTAL STRUCTURE OF OROTIDINE 5'-PHOSPHATE DECARBOXYLASE -

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Basic information

Entry
Database: PDB / ID: 1dqw
TitleCRYSTAL STRUCTURE OF OROTIDINE 5'-PHOSPHATE DECARBOXYLASE
ComponentsOROTIDINE 5'-PHOSPHATE DECARBOXYLASE
KeywordsLYASE / TIM barrel / orotidine 5'-phosphate / uridine 5'-phosphate / decarboxylase
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 / Resolution: 2.1 Å
AuthorsMilburn, M.V. / Miller, B.G. / Hassell, A.M. / Wolfenden, R. / Short, S.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Anatomy of a proficient enzyme: the structure of orotidine 5'-monophosphate decarboxylase in the presence and absence of a potential transition state analog.
Authors: Miller, B.G. / Hassell, A.M. / Wolfenden, R. / Milburn, M.V. / Short, S.A.
History
DepositionJan 5, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)117,3904
Polymers117,3904
Non-polymers00
Water15,745874
1
A: OROTIDINE 5'-PHOSPHATE DECARBOXYLASE
B: OROTIDINE 5'-PHOSPHATE DECARBOXYLASE


Theoretical massNumber of molelcules
Total (without water)58,6952
Polymers58,6952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-21 kcal/mol
Surface area20570 Å2
MethodPISA
2
C: OROTIDINE 5'-PHOSPHATE DECARBOXYLASE
D: OROTIDINE 5'-PHOSPHATE DECARBOXYLASE


Theoretical massNumber of molelcules
Total (without water)58,6952
Polymers58,6952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-21 kcal/mol
Surface area20560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.060, 116.217, 116.979
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a dimer of molecule A related by a two-fold symmetry axis to molecule B, or molecule C related by a two-fold symmetry axis to molecule D.

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Components

#1: Protein
OROTIDINE 5'-PHOSPHATE DECARBOXYLASE


Mass: 29347.586 Da / Num. of mol.: 4 / Mutation: S2H, N267D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: PCDA6022 / 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.: 874 / 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: 2.61 Å3/Da / Density % sol: 52.82 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7
Details: sodium-HEPES, isopropanol, polyethylene glycol 4000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 278.0K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.1 Msodium HEPES1reservoirpH7.0
210 %isopropanol1reservoir
320 %(w/v)PEG40001reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Type: APS / Wavelength: 1.0281
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 18, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0281 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 72247 / Num. obs: 70148 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.1 % / Biso Wilson estimate: 12.4 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 22.5
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 9 % / Rmerge(I) obs: 0.113 / % possible all: 93.4

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Processing

Software
NameClassification
CNSrefinement
MAR345data collection
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 2.1→50 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2473075.21 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.255 5311 8.2 %RANDOM
Rwork0.218 ---
all0.222 72247 --
obs0.218 65044 90.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 85.65 Å2 / ksol: 0.355 e/Å3
Displacement parametersBiso mean: 31.5 Å2
Baniso -1Baniso -2Baniso -3
1-3.44 Å20 Å20 Å2
2---0.35 Å20 Å2
3----3.09 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.27 Å
Luzzati d res low-10 Å
Luzzati sigma a0.21 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8236 0 0 874 9110
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg2.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_improper_angle_d0.93
X-RAY DIFFRACTIONc_mcbond_it1.181.5
X-RAY DIFFRACTIONc_mcangle_it1.942
X-RAY DIFFRACTIONc_scbond_it1.882
X-RAY DIFFRACTIONc_scangle_it2.82.5
Refine LS restraints NCSNCS model details: CONSTRAINED
LS refinement shellResolution: 2.1→2.18 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.278 452 8.5 %
Rwork0.244 4889 -
obs--75.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAM
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 8.2 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 31.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg2.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.93
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.278 / % reflection Rfree: 8.5 % / Rfactor Rwork: 0.244 / Rfactor obs: 0.233

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