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- PDB-2dx7: Crystal structure of Pyrococcus horikoshii OT3 aspartate racemase... -

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Basic information

Entry
Database: PDB / ID: 2dx7
TitleCrystal structure of Pyrococcus horikoshii OT3 aspartate racemase complex with citric acid
Componentsaspartate racemase
KeywordsISOMERASE / aspartate racemase
Function / homology
Function and homology information


aspartate racemase / aspartate racemase activity
Similarity search - Function
Aspartate racemase / Asp/Glu racemase, active site 1 / Aspartate and glutamate racemases signature 1. / Aspartate and glutamate racemases signature 2. / Rossmann fold - #1860 / Asp/Glu racemase / Asp/Glu/hydantoin racemase / Asp/Glu/Hydantoin racemase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / Aspartate racemase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsOhtaki, A. / Arakawa, T. / Iizuka, R. / Odaka, M. / Yohda, M.
CitationJournal: Proteins / Year: 2008
Title: Structure of aspartate racemase complexed with a dual substrate analogue, citric acid, and implications for the reaction mechanism.
Authors: Ohtaki, A. / Nakano, Y. / Iizuka, R. / Arakawa, T. / Yamada, K. / Odaka, M. / Yohda, M.
History
DepositionAug 24, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 28, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: aspartate racemase
B: aspartate racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7084
Polymers50,3232
Non-polymers3842
Water4,396244
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-15 kcal/mol
Surface area18580 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)43.394, 80.571, 66.943
Angle α, β, γ (deg.)90.00, 106.90, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein aspartate racemase


Mass: 25161.664 Da / Num. of mol.: 2 / Mutation: C82A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Plasmid: PET23C / Production host: Escherichia coli (E. coli) / References: UniProt: O58403, aspartate racemase
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 2.22 Å3/Da / Density % sol: 44.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.1
Details: 16% PEG4000, 100mM citric asid, pH 4.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 9, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 31250

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JFL

1jfl


Resolution: 2→50 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.219 2835 -
Rwork0.185 --
all-31250 -
obs-29879 94.6 %
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3522 0 26 244 3792

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