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- PDB-4h77: Crystal structure of haloalkane dehalogenase LinB from Sphingobiu... -

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Basic information

Entry
Database: PDB / ID: 4h77
TitleCrystal structure of haloalkane dehalogenase LinB 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: 1.6 Å
AuthorsOkai, M. / Ohtsuka, J. / Imai, F.L. / 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)34,4847
Polymers34,0971
Non-polymers3876
Water6,449358
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.404, 72.146, 73.492
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-406-

CL

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Components

#1: Protein Haloalkane dehalogenase


Mass: 34096.586 Da / Num. of mol.: 1
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, haloalkane dehalogenase
#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.: 358 / 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: 1.96 Å3/Da / Density % sol: 37.23 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100mM Tris-HCl (pH 8.0), 20% (w/v) PEG 4000, 200mM CaCl2, 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: Jun 7, 2008
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. obs: 36060

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CV2

1cv2


Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.705 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19101 1797 5 %RANDOM
Rwork0.15863 ---
obs0.16026 34221 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.176 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å20 Å20 Å2
2--0.07 Å20 Å2
3---0.45 Å2
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2332 0 21 358 2711
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222411
X-RAY DIFFRACTIONr_angle_refined_deg1.3711.9593274
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4455293
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.24722.773119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.32815376
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0981525
X-RAY DIFFRACTIONr_chiral_restr0.0920.2342
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021890
X-RAY DIFFRACTIONr_nbd_refined0.2050.21221
X-RAY DIFFRACTIONr_nbtor_refined0.3170.21641
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2294
X-RAY DIFFRACTIONr_metal_ion_refined0.0760.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2130.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2110.236
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0120.21
X-RAY DIFFRACTIONr_mcbond_it0.811.51499
X-RAY DIFFRACTIONr_mcangle_it0.97422354
X-RAY DIFFRACTIONr_scbond_it1.71631038
X-RAY DIFFRACTIONr_scangle_it2.7854.5920
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 126 -
Rwork0.209 2450 -
obs--99.5 %

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