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- PDB-2v9z: Structure of the Rhodococcus haloalkane dehalogenase mutant with ... -

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Basic information

Entry
Database: PDB / ID: 2v9z
TitleStructure of the Rhodococcus haloalkane dehalogenase mutant with enhanced enantioselectivity
ComponentsHALOALKANE DEHALOGENASE
KeywordsHYDROLASE / PLASMID / DETOXIFICATION
Function / homology
Function and homology information


haloalkane dehalogenase / haloalkane dehalogenase activity / response to toxic substance
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 speciesRHODOCOCCUS RHODOCHROUS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsKoudelakova, T. / Prokop, Z. / Sato, Y. / Lapkouski, M. / Chovancova, E. / Monincova, M. / Jesenska, A. / Emmer, J. / Senda, T. / Nagata, Y. ...Koudelakova, T. / Prokop, Z. / Sato, Y. / Lapkouski, M. / Chovancova, E. / Monincova, M. / Jesenska, A. / Emmer, J. / Senda, T. / Nagata, Y. / Kuta Smatanova, I. / Damborsky, J.
CitationJournal: To be Published
Title: Rational Engineering of Rhodococcus Haloalkane Dehalogenase with Enhanced Enantioselectivity
Authors: Koudelakova, T. / Prokop, Z. / Sato, Y. / Lapkouski, M. / Chovancova, E. / Monincova, M. / Jesenska, A. / Emmer, J. / Senda, T. / Nagata, Y. / Kuta Smatanova, I. / Damborsky, J.
History
DepositionAug 28, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / struct_biol / Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HALOALKANE DEHALOGENASE


Theoretical massNumber of molelcules
Total (without water)34,4391
Polymers34,4391
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)52.739, 68.900, 84.695
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HALOALKANE DEHALOGENASE / / HALOALKANE DEHALOGENASE DHAA12


Mass: 34439.059 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RHODOCOCCUS RHODOCHROUS (bacteria) / Strain: NCIMB13064 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A3G2, haloalkane dehalogenase
Compound detailsENGINEERED RESIDUE IN CHAIN A, TRP 141 TO PHE ENGINEERED RESIDUE IN CHAIN A, PRO 142 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, TRP 141 TO PHE ENGINEERED RESIDUE IN CHAIN A, PRO 142 TO ALA ENGINEERED RESIDUE IN CHAIN A, PHE 144 TO ALA ENGINEERED RESIDUE IN CHAIN A, GLY 171 TO ARG ENGINEERED RESIDUE IN CHAIN A, ALA 172 TO VAL ENGINEERED RESIDUE IN CHAIN A, LYS 175 TO GLY ENGINEERED RESIDUE IN CHAIN A, CYS 176 TO GLY ENGINEERED RESIDUE IN CHAIN A, VAL 245 TO ALA

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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: 2.31 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop
Details: 1 UL OF PROTEIN (5 MG/ML IN 25 MM TRIS-HCL PH 7.5, 150 MM AMMONIUM SULPHATE, 1 MM EDTA) WAS MIXED 1:1 WITH THE RESERVOIR (1 ML) CONSISTED OF 20 % PEG 6000, 0.1 M SODIUM ACETATE, 0.2 M ...Details: 1 UL OF PROTEIN (5 MG/ML IN 25 MM TRIS-HCL PH 7.5, 150 MM AMMONIUM SULPHATE, 1 MM EDTA) WAS MIXED 1:1 WITH THE RESERVOIR (1 ML) CONSISTED OF 20 % PEG 6000, 0.1 M SODIUM ACETATE, 0.2 M AMMONIUM SULPHATE, 0.1 M TRIS-HCL PH 8.5-9.0. SITTING-DROP 281K.

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorDetector: IMAGE PLATE / Date: Apr 21, 2007 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→53.45 Å / Num. obs: 6389 / % possible obs: 97.9 % / Observed criterion σ(I): 3.7 / Redundancy: 3.4 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 8.2
Reflection shellResolution: 3→3.08 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.3 / % possible all: 92.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BN6

1bn6


Resolution: 3→53.45 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.796 / SU B: 22.618 / SU ML: 0.422 / Cross valid method: THROUGHOUT / ESU R Free: 0.602 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES MET A 1 AND SER A 2 ARE DISORDERED. GLU A 3 DUE TO DISORDERED SIDE CHAIN IS SUBSTITUTED BY ALA. SIDE CHAINS OF ASP A 167 AND VAL A ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES MET A 1 AND SER A 2 ARE DISORDERED. GLU A 3 DUE TO DISORDERED SIDE CHAIN IS SUBSTITUTED BY ALA. SIDE CHAINS OF ASP A 167 AND VAL A 168 WERE MODELLED STEREOCHEMICALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.267 712 11.2 %RANDOM
Rwork0.195 ---
obs0.203 5648 97.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.46 Å2
Refinement stepCycle: LAST / Resolution: 3→53.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2415 0 0 0 2415
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222497
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6011.9543416
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg22.2085302
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.30823.361122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg25.37215370
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.4711518
X-RAY DIFFRACTIONr_chiral_restr0.2810.2360
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021987
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3040.21330
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.340.21664
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2240.2104
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.226
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2390.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0391.51537
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.83322466
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.78631058
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.3964.5950
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.08 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.379 51
Rwork0.251 384

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