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- PDB-5b19: Picrophilus torridus aspartate racemase -

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Basic information

Entry
Database: PDB / ID: 5b19
TitlePicrophilus torridus aspartate racemase
ComponentsAspartate racemase
KeywordsISOMERASE / Aspartate racemase / Picrophilus torridus / Archaea / D-amino acid
Function / homologyaspartate racemase activity / aspartate racemase / Aspartate racemase / Asp/Glu racemase / Asp/Glu/hydantoin racemase / Asp/Glu/Hydantoin racemase / L(+)-TARTARIC ACID / Aspartate racemase
Function and homology information
Biological speciesPicrophilus torridus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.851 Å
AuthorsAihara, T. / Ito, T. / Yamanaka, Y. / Noguchi, K. / Odaka, M. / Sekine, M. / Homma, H. / Yohda, M.
CitationJournal: Extremophiles / Year: 2016
Title: Structural and functional characterization of aspartate racemase from the acidothermophilic archaeon Picrophilus torridus
Authors: Aihara, T. / Ito, T. / Yamanaka, Y. / Noguchi, K. / Odaka, M. / Sekine, M. / Homma, H. / Yohda, M.
History
DepositionNov 30, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2016Group: Database references
Revision 1.2Feb 26, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 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: Aspartate racemase
B: Aspartate racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0683
Polymers51,9182
Non-polymers1501
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-12 kcal/mol
Surface area17220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.506, 111.506, 111.506
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: Protein Aspartate racemase


Mass: 25958.973 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Picrophilus torridus (strain ATCC 700027 / DSM 9790 / JCM 10055 / NBRC 100828) (archaea)
Strain: ATCC 700027 / DSM 9790 / JCM 10055 / NBRC 100828 / Gene: PTO0149 / Plasmid: pET23b / Production host: Escherichia coli (E. coli) / References: UniProt: Q6L2R8, aspartate racemase
#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.23 Å3/Da / Density % sol: 44.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: polyethylene glycol 3400, potassium/sodium tartrate, L-aspartate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 38749 / % possible obs: 97.3 % / Redundancy: 21 % / Rmerge(I) obs: 0.146 / Net I/σ(I): 40.2
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 20.3 % / Rmerge(I) obs: 0.843 / Mean I/σ(I) obs: 5.2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3S81

3s81


Resolution: 1.851→33.62 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2686 1890 4.94 %Random selection
Rwork0.2387 ---
obs0.2403 38234 96.61 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.851→33.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2959 0 10 75 3044
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083015
X-RAY DIFFRACTIONf_angle_d1.1134074
X-RAY DIFFRACTIONf_dihedral_angle_d13.3141120
X-RAY DIFFRACTIONf_chiral_restr0.046479
X-RAY DIFFRACTIONf_plane_restr0.005512
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8512-1.89750.40821340.362530X-RAY DIFFRACTION95
1.8975-1.94880.42731350.37242649X-RAY DIFFRACTION99
1.9488-2.00620.26521340.24882637X-RAY DIFFRACTION100
2.0062-2.07090.33071210.23252681X-RAY DIFFRACTION100
2.0709-2.14490.27721200.23842674X-RAY DIFFRACTION100
2.1449-2.23080.35691210.24852425X-RAY DIFFRACTION90
2.2308-2.33230.35541240.27922312X-RAY DIFFRACTION87
2.3323-2.45520.25761540.22782646X-RAY DIFFRACTION100
2.4552-2.6090.28151520.2352670X-RAY DIFFRACTION100
2.609-2.81030.27131390.23822673X-RAY DIFFRACTION100
2.8103-3.0930.26091410.23742723X-RAY DIFFRACTION100
3.093-3.54010.26151610.2292650X-RAY DIFFRACTION100
3.5401-4.45850.23241160.21562376X-RAY DIFFRACTION86
4.4585-33.62590.23811380.2332698X-RAY DIFFRACTION96

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