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- PDB-8ywo: Crystal structure of L-azetidine-2-carboxylate hydrolase soaked i... -

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Entry
Database: PDB / ID: 8ywo
TitleCrystal structure of L-azetidine-2-carboxylate hydrolase soaked in (S)-azetidine-2-carboxylic acid
Components(S)-2-haloacid dehalogenase
KeywordsHYDROLASE / azetidine-2-carboxylate / dehalogenase / alpha/beta hydrolase
Function / homology
Function and homology information


hydrolase activity, acting on halide bonds, in C-halide compounds / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds / response to toxic substance / periplasmic space
Similarity search - Function
L-2-Haloacid dehalogenase / : / HAD hydrolase, subfamily IA / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
(2S)-azetidine-2-carboxylic acid / L-azetidine-2-carboxylate hydrolase
Similarity search - Component
Biological speciesPseudomonas sp. A2C (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsToyoda, M. / Mizutani, K. / Mikami, B. / Wackett, L.P. / Esaki, N. / Kurihara, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Research for the crystal structure of L-azetidine-2-carboxylate hydrolase
Authors: Toyoda, M. / Jitsumori, K. / Mikami, B. / Mizutani, K. / Esaki, N. / Wackett, L.P. / Kurihara, T.
History
DepositionMar 31, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 8, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: (S)-2-haloacid dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2482
Polymers27,1471
Non-polymers1011
Water5,837324
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.105, 64.419, 54.307
Angle α, β, γ (deg.)90.000, 106.990, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein (S)-2-haloacid dehalogenase / 2-haloalkanoic acid dehalogenase / Halocarboxylic acid halidohydrolase / L-2-haloacid dehalogenase ...2-haloalkanoic acid dehalogenase / Halocarboxylic acid halidohydrolase / L-2-haloacid dehalogenase / L-azetidine-2-carboxylate hydrolase


Mass: 27146.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. A2C (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): BLR / References: UniProt: B2Z3V8, (S)-2-haloacid dehalogenase
#2: Chemical ChemComp-02A / (2S)-azetidine-2-carboxylic acid


Type: L-peptide linking / Mass: 101.104 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H7NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 44.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Precipitant: 20% PEG 3350, 0.15 M Magnesium acetate, 0.1 M imidazole/HCl buffer; Soaking: the precipitant above with 50 mM L-azetidine-2-carboxylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Feb 20, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.58→40.43 Å / Num. obs: 32195 / % possible obs: 97.9 % / Redundancy: 3.3 % / Biso Wilson estimate: 13.53 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.05 / Net I/σ(I): 20.6
Reflection shellResolution: 1.58→1.67 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.98 / Num. unique obs: 4744 / CC1/2: 0.869 / Rrim(I) all: 0.394 / % possible all: 90

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SMV

3smv


Resolution: 1.58→25.52 Å / SU ML: 0.1686 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.9539
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1832 1609 5 %
Rwork0.1315 30583 -
obs0.134 32192 98.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.13 Å2
Refinement stepCycle: LAST / Resolution: 1.58→25.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1915 0 7 324 2246
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00562104
X-RAY DIFFRACTIONf_angle_d0.78062875
X-RAY DIFFRACTIONf_chiral_restr0.0522303
X-RAY DIFFRACTIONf_plane_restr0.0059385
X-RAY DIFFRACTIONf_dihedral_angle_d14.2287816
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.630.28231250.20962387X-RAY DIFFRACTION84.75
1.63-1.690.22711440.15972733X-RAY DIFFRACTION97.33
1.69-1.750.23171490.142833X-RAY DIFFRACTION99.7
1.75-1.830.20821480.13852800X-RAY DIFFRACTION99.73
1.83-1.930.22631480.14172825X-RAY DIFFRACTION99.63
1.93-2.050.19591490.12352826X-RAY DIFFRACTION99.87
2.05-2.210.16351480.11452813X-RAY DIFFRACTION99.56
2.21-2.430.18081490.11892829X-RAY DIFFRACTION99.47
2.43-2.780.18031490.12672829X-RAY DIFFRACTION99.6
2.78-3.50.16791500.12962845X-RAY DIFFRACTION99.57
3.5-25.520.15691500.13052863X-RAY DIFFRACTION98.88

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