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- PDB-3smv: X-ray Crystal Structure of L-Azetidine-2-Carboxylate Hydrolase -

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Basic information

Entry
Database: PDB / ID: 3smv
TitleX-ray Crystal Structure of L-Azetidine-2-Carboxylate Hydrolase
Components(S)-2-haloacid dehalogenase
KeywordsHYDROLASE / haloacid dehalogenase superfamily / L-Azetidine-2-carboxylate
Function / homology
Function and homology information


Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds / (S)-2-haloacid dehalogenase activity
Similarity search - Function
DNA polymerase; domain 1 - #750 / L-2-Haloacid dehalogenase / : / Haloacid dehalogenase-like hydrolase / HAD hydrolase, subfamily IA / HAD superfamily/HAD-like / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 ...DNA polymerase; domain 1 - #750 / L-2-Haloacid dehalogenase / : / Haloacid dehalogenase-like hydrolase / HAD hydrolase, subfamily IA / HAD superfamily/HAD-like / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
IMIDAZOLE / L-azetidine-2-carboxylate hydrolase
Similarity search - Component
Biological speciesPseudomonas sp. A2C (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.38 Å
AuthorsToyoda, M. / Mikami, B. / Jitsumori, K. / Wackett, L.P. / Esaki, N. / Kurihara, T.
CitationJournal: To be Published
Title: Crystal structure of L-Azetidine-2-carboxylate hydrolase from Pseudomonas sp. strain A2C
Authors: Jitsumori, K. / Toyoda, M. / Mikami, B. / Wackett, L.P. / Kurihara, T. / Esaki, N.
History
DepositionJun 28, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 18, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2May 1, 2024Group: Advisory / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / pdbx_distant_solvent_atoms
Item: _entity.pdbx_description / _entity.pdbx_ec ..._entity.pdbx_description / _entity.pdbx_ec / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type
Revision 1.3Jun 12, 2024Group: Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,04411
Polymers27,1471
Non-polymers89810
Water6,828379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.612, 63.588, 54.665
Angle α, β, γ (deg.)90.00, 105.54, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein (S)-2-haloacid dehalogenase / 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) / Strain: A2C / Production host: Escherichia coli (E. coli) / References: UniProt: B2Z3V8, (S)-2-haloacid dehalogenase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 379 / 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: 2.2 Å3/Da / Density % sol: 44.01 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20% PEG 3350, 0.1M imidazole, 0.1M magnesium acetate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Mar 7, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.38→50 Å / Num. all: 48244 / Num. obs: 47231 / % possible obs: 97.9 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 9.62 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 28.7
Reflection shellResolution: 1.38→1.43 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 2.84 / Num. unique all: 4167 / % possible all: 87.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.autosol)model building
PHENIX(phenix.refine: 1.6.4_486)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.38→20.28 Å / SU ML: 0.14 / σ(F): 1.37 / Phase error: 13.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1577 2385 5.07 %RANDOM
Rwork0.1217 ---
obs0.1235 47036 97.53 %-
Solvent computationShrinkage radii: 0.49 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 65.164 Å2 / ksol: 0.398 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.7505 Å20 Å21.0009 Å2
2---0.1814 Å20 Å2
3---1.9319 Å2
Refine analyzeLuzzati coordinate error obs: 0.14 Å
Refinement stepCycle: LAST / Resolution: 1.38→20.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1865 0 59 379 2303
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052184
X-RAY DIFFRACTIONf_angle_d1.1022970
X-RAY DIFFRACTIONf_dihedral_angle_d12.159869
X-RAY DIFFRACTIONf_chiral_restr0.079313
X-RAY DIFFRACTIONf_plane_restr0.006385
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.3803-1.40850.28631090.2442205677
1.4085-1.43910.23651300.1918248293
1.4391-1.47260.20691390.141263598
1.4726-1.50940.1541380.1144259798
1.5094-1.55020.15611450.1078269999
1.5502-1.59580.1511190.0953262699
1.5958-1.64720.14641390.094268199
1.6472-1.70610.15091480.0877266599
1.7061-1.77440.14021530.0898265799
1.7744-1.85510.15381460.0912265499
1.8551-1.95280.14291390.097267799
1.9528-2.0750.12991520.10622673100
2.075-2.23510.14711540.11192677100
2.2351-2.45960.15681290.11842704100
2.4596-2.81470.17421530.12842709100
2.8147-3.54320.14581270.12682741100
3.5432-20.28240.15961650.1497271899

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