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- PDB-4h7h: Crystal structure of haloalkane dehalogenase LinB T135A mutant fr... -

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Basic information

Entry
Database: PDB / ID: 4h7h
TitleCrystal structure of haloalkane dehalogenase LinB T135A 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: 2.1 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _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)34,1423
Polymers34,0671
Non-polymers762
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.353, 71.711, 73.072
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-584-

HOH

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Components

#1: Protein Haloalkane dehalogenase /


Mass: 34066.562 Da / Num. of mol.: 1 / Mutation: T135A
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-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 1.94 Å3/Da / Density % sol: 36.48 %
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: AR-NW12A / Wavelength: 1 Å
DetectorDate: Mar 2, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 16096

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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: 2.1→20 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.91 / SU B: 5.397 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.271 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25014 801 5 %RANDOM
Rwork0.18552 ---
obs0.18864 15182 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.586 Å2
Baniso -1Baniso -2Baniso -3
1--1.43 Å20 Å20 Å2
2---1.45 Å20 Å2
3---2.88 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2330 0 2 139 2471
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192394
X-RAY DIFFRACTIONr_angle_refined_deg1.3711.9543256
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9655293
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.41322.773119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.13415375
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7021525
X-RAY DIFFRACTIONr_chiral_restr0.0930.2341
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211890
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 48 -
Rwork0.233 992 -
obs--99.71 %

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