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- PDB-8yvw: Crystal structure of D12N mutant of L-azetidine-2-carboxylate hyd... -

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Basic information

Entry
Database: PDB / ID: 8yvw
TitleCrystal structure of D12N mutant of L-azetidine-2-carboxylate hydrolase
Components(S)-2-haloacid dehalogenase(S)-2-haloacid dehalogenase
KeywordsHYDROLASE / azetidine-2-carboxylate / dehalogenase / alpha/beta hydrolase
Function / homology
Function and homology information


(S)-2-haloacid dehalogenase / (S)-2-haloacid dehalogenase activity
Similarity search - Function
L-2-Haloacid dehalogenase / HAD hydrolase, subfamily IA / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
FORMIC ACID / IMIDAZOLE / (S)-2-haloacid dehalogenase
Similarity search - Component
Biological speciesPseudomonas sp. A2C (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.19 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 29, 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)27,3315
Polymers27,1461
Non-polymers1854
Water8,737485
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area590 Å2
ΔGint-1 kcal/mol
Surface area10690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.176, 71.361, 72.349
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein (S)-2-haloacid dehalogenase / (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: 27145.578 Da / Num. of mol.: 1 / Mutation: D12N
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-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 485 / 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: 2.24 Å3/Da / Density % sol: 45.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 25% PEG 3350, 0.1M magnesium formate, 0.1 M imidazole/HCl buffer, pH8.0, 5 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: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Mar 8, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.19→39.52 Å / Num. obs: 76136 / % possible obs: 95.4 % / Redundancy: 9 % / Biso Wilson estimate: 9.54 Å2 / CC1/2: 1 / Rrim(I) all: 0.037 / Net I/σ(I): 37.06
Reflection shellResolution: 1.19→1.26 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 5.26 / Num. unique obs: 10019 / CC1/2: 0.946 / Rrim(I) all: 0.334 / % possible all: 78.7

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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: 1.19→20.38 Å / SU ML: 0.1008 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 12.5303
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.145 3807 5 %
Rwork0.1186 72318 -
obs0.1199 76125 95.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.63 Å2
Refinement stepCycle: LAST / Resolution: 1.19→20.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1915 0 12 485 2412
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00852125
X-RAY DIFFRACTIONf_angle_d1.13312898
X-RAY DIFFRACTIONf_chiral_restr0.0945306
X-RAY DIFFRACTIONf_plane_restr0.011384
X-RAY DIFFRACTIONf_dihedral_angle_d13.0028827
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.19-1.20.2683980.23881849X-RAY DIFFRACTION67.28
1.2-1.220.22471070.20852048X-RAY DIFFRACTION73.17
1.22-1.230.21331170.15652208X-RAY DIFFRACTION79.81
1.23-1.250.19631280.15052446X-RAY DIFFRACTION88.58
1.25-1.270.16281400.13072662X-RAY DIFFRACTION95.24
1.27-1.290.18341420.13112689X-RAY DIFFRACTION97.52
1.29-1.310.14321440.11812726X-RAY DIFFRACTION97.35
1.31-1.330.14811420.11222701X-RAY DIFFRACTION97.56
1.33-1.360.1471430.10682714X-RAY DIFFRACTION97.44
1.36-1.380.13621430.10382719X-RAY DIFFRACTION97.78
1.38-1.410.14191430.10932714X-RAY DIFFRACTION98.01
1.41-1.440.14271430.11412730X-RAY DIFFRACTION97.85
1.44-1.480.14931470.11682782X-RAY DIFFRACTION98.22
1.48-1.510.14381430.10712723X-RAY DIFFRACTION98.49
1.51-1.550.13131440.08992742X-RAY DIFFRACTION98.6
1.55-1.60.13211460.0922764X-RAY DIFFRACTION98.54
1.6-1.650.13171450.09212765X-RAY DIFFRACTION98.68
1.65-1.710.12951460.09632770X-RAY DIFFRACTION99.32
1.71-1.780.12031460.10212781X-RAY DIFFRACTION98.95
1.78-1.860.14151470.11082783X-RAY DIFFRACTION99.09
1.86-1.960.16341480.12492812X-RAY DIFFRACTION99.13
1.96-2.080.1651470.11262790X-RAY DIFFRACTION99.36
2.08-2.240.14241490.11482835X-RAY DIFFRACTION99.53
2.24-2.460.13991490.12842833X-RAY DIFFRACTION99.73
2.46-2.820.14151500.12672845X-RAY DIFFRACTION99.47
2.82-3.550.14081510.12372880X-RAY DIFFRACTION99.64
3.55-20.380.13041590.1223007X-RAY DIFFRACTION99.28

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