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- PDB-2za1: Crystal Structure of orotidine 5'-monophosphate decarboxylase com... -

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Basic information

Entry
Database: PDB / ID: 2za1
TitleCrystal Structure of orotidine 5'-monophosphate decarboxylase complexed with orotidine 5'-monophosphate from P.falciparum
ComponentsOrotidine 5'-phosphate decarboxylase
KeywordsLYASE / orotidine 5'-monophosphate decarboxylase / Plasmodium falciparum / orotidine 5'-monophosphate / Pyrimidine biosynthesis
Function / homology
Function and homology information


orotidine-5'-phosphate decarboxylase / orotidine-5'-phosphate decarboxylase activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process
Similarity search - Function
Orotidine 5'-phosphate decarboxylase, type 2 / 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, type 2 / 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'-MONOPHOSPHATE / orotidine-5'-phosphate decarboxylase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsTokuoka, K. / Inoue, T.
CitationJournal: J.BIOCHEM.(TOKYO) / Year: 2008
Title: Structural Basis for the Decarboxylation of Orotidine 5'-Monophosphate (OMP) by Plasmodium Falciparum OMP Decarboxylase
Authors: Tokuoka, K. / Kusakari, Y. / Krungkrai, S.R. / Matsumura, H. / Kai, Y. / Krungkrai, J. / Horii, T. / Inoue, T.
History
DepositionSep 26, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Orotidine 5'-phosphate decarboxylase
B: Orotidine 5'-phosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,4694
Polymers75,7322
Non-polymers7362
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)201.800, 201.800, 44.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Orotidine 5'-phosphate decarboxylase /


Mass: 37866.246 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Plasmid: pTrcHis-TOPO / Production host: Escherichia coli (E. coli)
References: UniProt: Q8T6J6, orotidine-5'-phosphate decarboxylase
#2: Chemical ChemComp-OMP / OROTIDINE-5'-MONOPHOSPHATE / Orotidine 5'-monophosphate


Mass: 368.191 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N2O11P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.29 Å3/Da / Density % sol: 46.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 23% PEG 3000, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 18, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 20677 / % possible obs: 98.8 % / Biso Wilson estimate: 61.8 Å2 / Rsym value: 0.086
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.339 / % possible all: 99.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZA2

2za2


Resolution: 2.65→38.14 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2228635.27 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.292 1877 9.7 %RANDOM
Rwork0.21 ---
obs0.21 19268 98.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.407 Å2 / ksol: 0.337174 e/Å3
Displacement parametersBiso mean: 53.9 Å2
Baniso -1Baniso -2Baniso -3
1-2.92 Å28.36 Å20 Å2
2--2.92 Å20 Å2
3----5.83 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.54 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.65→38.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5109 0 48 118 5275
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d1
LS refinement shellResolution: 2.65→2.82 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.439 312 9.8 %
Rwork0.315 2872 -
obs--98.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3omp.paramomp.top

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