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- PDB-1jfl: CRYSTAL STRUCTURE DETERMINATION OF ASPARTATE RACEMASE FROM AN ARCHAEA -

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Basic information

Entry
Database: PDB / ID: 1jfl
TitleCRYSTAL STRUCTURE DETERMINATION OF ASPARTATE RACEMASE FROM AN ARCHAEA
ComponentsASPARTATE RACEMASE
KeywordsISOMERASE / ALPHA-BETA STRUCTURE / HOMO-DIMER / HOMOLOGOUS DOMAINS
Function / homology
Function and homology information


aspartate racemase activity / aspartate racemase
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
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.9 Å
AuthorsLiu, L.J. / Iwata, K. / Kita, A. / Kawarabayasi, Y. / Yohda, M. / Miki, K.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Crystal structure of aspartate racemase from Pyrococcus horikoshii OT3 and its implications for molecular mechanism of PLP-independent racemization.
Authors: Liu, L. / Iwata, K. / Kita, A. / Kawarabayasi, Y. / Yohda, M. / Miki, K.
History
DepositionJun 21, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 5, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: ASPARTATE RACEMASE
B: ASPARTATE RACEMASE


Theoretical massNumber of molelcules
Total (without water)50,3872
Polymers50,3872
Non-polymers00
Water5,675315
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-14 kcal/mol
Surface area19450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.481, 58.685, 67.035
Angle α, β, γ (deg.)90.00, 109.62, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ASPARTATE RACEMASE


Mass: 25193.729 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: PH0670 / Plasmid: PET23C / Production host: Escherichia coli (E. coli) / References: UniProt: O58403, aspartate racemase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.41 Å3/Da / Density % sol: 48.89 %
Crystal growTemperature: 293.2 K / Method: vapor diffusion, sitting drop / pH: 4
Details: PEG6000, sodium citrate, calcium chloride, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.2K
Crystal grow
*PLUS
Temperature: 293 K / Details: Liu, L., (2001) Acta Crystallogr., D57, 1674.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
116.5 %(w/v)PEG60001reservoir
20.10 Msodium citrate1reservoirpH4.0
330 mg/mlprotein1drop

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
2901
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-6A11
SYNCHROTRONSPring-8 BL44B221
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDMay 18, 2000
MARRESEARCH2CCDOct 10, 2000
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 channelSINGLE WAVELENGTHMx-ray1
2a fixed-exit double crystal monochromatorSINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 37943 / Num. obs: 37256 / % possible obs: 98.2 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 5.1 % / Biso Wilson estimate: 19.4 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.055 / Net I/σ(I): 8.9
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.176 / Mean I/σ(I) obs: 4.6 / Num. unique all: 5352 / Rsym value: 0.15 / % possible all: 98.4
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 20 Å / Num. measured all: 191528
Reflection shell
*PLUS
% possible obs: 99.2 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
DENZOdata reduction
SCALAdata scaling
SCALEPACKdata scaling
MLPHAREphasing
DMmodel building
CNS1refinement
CCP4(SCALA)data scaling
DMphasing
RefinementMethod to determine structure: MIR / Resolution: 1.9→20 Å / Isotropic thermal model: ISOTROPIC / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1852 -RANDOM
Rwork0.194 ---
all-37904 --
obs-37184 98.1 %-
Displacement parametersBiso mean: 21.1 Å2
Baniso -1Baniso -2Baniso -3
1-2.228 Å20 Å20.737 Å2
2--1.374 Å20 Å2
3----3.602 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3524 0 0 315 3839
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.254
X-RAY DIFFRACTIONc_dihedral_angle_d21.2
X-RAY DIFFRACTIONc_improper_angle_d0.85
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor obs: 0.194
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.25
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.85

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