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- PDB-9v14: crystal structure of the enzyme-product complex of L-azetidine-2-... -

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Basic information

Entry
Database: PDB / ID: 9v14
Titlecrystal structure of the enzyme-product complex of L-azetidine-2-carboxylate hydrolase
ComponentsL-azetidine-2-carboxylate hydrolase
KeywordsHYDROLASE / azetidine-2-carboxylate / alpha/beta hydrolase / dehalogenase-like
Function / homology
Function and homology information


hydrolase activity, acting on acid 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
4-AMINO-2-HYDROXYBUTANOIC ACID / FORMIC ACID / IMIDAZOLE / DI(HYDROXYETHYL)ETHER / L-azetidine-2-carboxylate hydrolase
Similarity search - Component
Biological speciesPseudomonas sp. A2C (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.93 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. / Mizutani, K. / Mikami, B. / Wackett, L.P. / Esaki, N. / Kurihara, T.
History
DepositionMay 19, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-azetidine-2-carboxylate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6798
Polymers27,1471
Non-polymers5337
Water9,836546
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-5 kcal/mol
Surface area10750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.347, 71.353, 72.406
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

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


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

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Non-polymers , 7 types, 553 molecules

#2: Chemical ChemComp-42B / 4-AMINO-2-HYDROXYBUTANOIC ACID


Mass: 119.119 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C4H10O3
#7: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 546 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.25 Å3/Da / Density % sol: 45.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 22.5% PEG3350, 0.1M imidazole-HCl buffer, 85mM magnesium formate, 50mM sodium 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: 0.7 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Oct 6, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7 Å / Relative weight: 1
ReflectionResolution: 0.93→50 Å / Num. obs: 165045 / % possible obs: 100 % / Redundancy: 7 % / CC1/2: 1 / CC star: 1 / Rpim(I) all: 0.019 / Rrim(I) all: 0.05 / Net I/σ(I): 55.2
Reflection shellResolution: 0.93→0.95 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 3.97 / Num. unique obs: 8159 / CC1/2: 0.86 / CC star: 0.962 / Rpim(I) all: 0.311 / Rrim(I) all: 0.821 / % possible all: 100

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Processing

Software
NameClassification
SHELXLrefinement
HKL-2000data scaling
MOLREPphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.93→10 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.1403 8232 -
Rwork0.1161 --
obs-156186 94.89 %
Refinement stepCycle: LAST / Resolution: 0.93→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1915 0 35 546 2496
LS refinement shell
Resolution (Å)Rfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.93-0.960.25314014X-RAY DIFFRACTION94.91
0.96-0.990.21212418X-RAY DIFFRACTION95
0.99-1.040.16817638X-RAY DIFFRACTION94.9
1.04-1.10.13517198X-RAY DIFFRACTION94.91
1.1-1.20.10821545X-RAY DIFFRACTION94.92
1.2-1.30.10115463X-RAY DIFFRACTION94.89
1.3-1.50.09420042X-RAY DIFFRACTION95.25
1.5-1.80.08615770X-RAY DIFFRACTION94.93
1.8-2.40.10412684X-RAY DIFFRACTION95.14
2.4-50.1188416X-RAY DIFFRACTION94.98
5-100.189998X-RAY DIFFRACTION96.05

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