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- PDB-4h7f: Crystal structure of haloalkane dehalogenase LinB V134I mutant fr... -

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Basic information

Entry
Database: PDB / ID: 4h7f
TitleCrystal structure of haloalkane dehalogenase LinB V134I mutant from Sphingobium sp. MI1205
ComponentsHaloalkane dehalogenase
KeywordsHYDROLASE / alpha/beta hydrolase fold
Function / homology
Function and homology information


haloalkane dehalogenase / haloalkane dehalogenase activity / metal ion binding
Similarity search - Function
Haloalkane dehalogenase, subfamily 2 / Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Haloalkane dehalogenase
Similarity search - Component
Biological speciesSphingobium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsOkai, M. / Ohtsuka, J. / Imai, L.F. / Mase, T. / Moriuchi, R. / Tsuda, M. / Nagata, K. / Nagata, Y. / Tanokura, M.
CitationJournal: J.Bacteriol. / Year: 2013
Title: Crystal Structure and Site-Directed Mutagenesis Analyses of Haloalkane Dehalogenase LinB from Sphingobium sp. Strain MI1205.
Authors: Okai, M. / Ohtsuka, J. / Imai, L.F. / Mase, T. / Moriuchi, R. / Tsuda, M. / Nagata, K. / Nagata, Y. / Tanokura, M.
History
DepositionSep 20, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4987
Polymers34,1111
Non-polymers3876
Water4,197233
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.523, 72.272, 73.629
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Haloalkane dehalogenase


Mass: 34110.613 Da / Num. of mol.: 1 / Mutation: V134I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingobium (bacteria) / Strain: MI1205 / Gene: linB, dhaA / Production host: Escherichia coli (E. coli) / References: UniProt: A4PEU6
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 1.97 Å3/Da / Density % sol: 37.58 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / Details: VAPOR DIFFUSION, SITTING DROP, temperature 278K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorDate: Feb 14, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 25649

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4H77

4h77


Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.492 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2002 1307 5.1 %RANDOM
Rwork0.17728 ---
obs0.17846 24252 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.798 Å2
Baniso -1Baniso -2Baniso -3
1--1.05 Å20 Å20 Å2
2---1.18 Å20 Å2
3---2.23 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2333 0 21 233 2587
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192412
X-RAY DIFFRACTIONr_angle_refined_deg1.2531.9593275
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1795293
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.59422.773119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.92215377
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7591525
X-RAY DIFFRACTIONr_chiral_restr0.0880.2345
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211890
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 69 -
Rwork0.222 1577 -
obs--97.86 %

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