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- PDB-5ybw: Crystal structure of pyridoxal 5'-phosphate-dependent aspartate r... -

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Basic information

Entry
Database: PDB / ID: 5ybw
TitleCrystal structure of pyridoxal 5'-phosphate-dependent aspartate racemase
ComponentsAspartate racemase
KeywordsISOMERASE / pyridoxal 5'-phosphate / aspartate racemase / Scapharca broughtonii / serine racemase
Function / homology
Function and homology information


L-serine ammonia-lyase / L-serine ammonia-lyase activity / amino acid metabolic process / isomerase activity / pyridoxal phosphate binding
Similarity search - Function
Serine/threonine dehydratase, pyridoxal-phosphate-binding site / Serine/threonine dehydratases pyridoxal-phosphate attachment site. / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
L-serine ammonia-lyase
Similarity search - Component
Biological speciesScapharca broughtonii (blood clam)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMizobuchi, T. / Nonaka, R. / Yoshimura, M. / Abe, K. / Takahashi, S. / Kera, Y. / Goto, M.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2017
Title: Crystal structure of a pyridoxal 5'-phosphate-dependent aspartate racemase derived from the bivalve mollusc Scapharca broughtonii
Authors: Mizobuchi, T. / Nonaka, R. / Yoshimura, M. / Abe, K. / Takahashi, S. / Kera, Y. / Goto, M.
History
DepositionSep 5, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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


Theoretical massNumber of molelcules
Total (without water)72,6972
Polymers72,6972
Non-polymers00
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-10 kcal/mol
Surface area23410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.181, 80.708, 87.991
Angle α, β, γ (deg.)90.000, 116.220, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-495-

HOH

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Components

#1: Protein Aspartate racemase


Mass: 36348.727 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Scapharca broughtonii (blood clam) / Gene: Asr / Plasmid: pET25b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q2L695, aspartate racemase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.06 Å3/Da / Density % sol: 40.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG 4000, sodium acetate, ammonium acetate, glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 20, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→78.936 Å / Num. all: 46230 / Num. obs: 46230 / % possible obs: 99.2 % / Redundancy: 4 % / Rpim(I) all: 0.025 / Rrim(I) all: 0.05 / Rsym value: 0.037 / Net I/av σ(I): 13.8 / Net I/σ(I): 17.9 / Num. measured all: 186532
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.9-23.20.3382.364390.2750.5020.33895.1
2-2.124.20.259364170.1660.340.259100
2.12-2.274.20.1564.960000.10.2070.156100
2.27-2.454.20.0987.856310.0630.130.098100
2.45-2.694.20.06711.451970.0430.0890.067100
2.69-34.20.04416.746710.0280.0580.044100
3-3.474.20.02922.741430.0180.0380.02999.9
3.47-4.254.20.02324.935080.0140.0290.02399.9
4.25-6.014.10.02324.327200.0140.0290.02399.7
6.01-46.8383.90.02126.315040.0150.0290.02198.4

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
REFMAC5.8.0131refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1V71

1v71


Resolution: 1.9→50.01 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.938 / SU B: 5.536 / SU ML: 0.152 / SU R Cruickshank DPI: 0.1871 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.187 / ESU R Free: 0.167 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2515 2224 4.8 %RANDOM
Rwork0.2053 ---
obs0.2075 44006 99.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 88.31 Å2 / Biso mean: 36.781 Å2 / Biso min: 17.64 Å2
Baniso -1Baniso -2Baniso -3
1--1.16 Å2-0 Å2-0.19 Å2
2--4.03 Å20 Å2
3----1.8 Å2
Refinement stepCycle: final / Resolution: 1.9→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4963 0 0 206 5169
Biso mean---37.97 -
Num. residues----654
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195058
X-RAY DIFFRACTIONr_angle_refined_deg1.3741.976871
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0385650
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.61824.876201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.67215826
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5531523
X-RAY DIFFRACTIONr_chiral_restr0.0930.2790
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213777
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 152 -
Rwork0.327 3003 -
all-3155 -
obs--92.49 %

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