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- PDB-4hzg: Structure of haloalkane dehalogenase DhaA from Rhodococcus rhodochrous -

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Basic information

Entry
Database: PDB / ID: 4hzg
TitleStructure of haloalkane dehalogenase DhaA from Rhodococcus rhodochrous
ComponentsHaloalkane dehalogenase
KeywordsHYDROLASE / Catalytic pentad / alpha/beta Hydrolase Fold / Halide binding / Hydrolytic dehalogenation
Function / homology
Function and homology information


haloalkane dehalogenase / haloalkane dehalogenase activity / response to toxic substance / membrane
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 sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsStsiapanava, A. / Weiss, M.S. / Mesters, J.R. / Kuta Smatanova, I.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Crystallographic analysis of 1,2,3-trichloropropane biodegradation by the haloalkane dehalogenase DhaA31.
Authors: Lahoda, M. / Mesters, J.R. / Stsiapanava, A. / Chaloupkova, R. / Kuty, M. / Damborsky, J. / Kuta Smatanova, I.
History
DepositionNov 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2014Group: Database references
Revision 1.2Mar 5, 2014Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 20, 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)34,1462
Polymers34,1111
Non-polymers351
Water4,071226
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.770, 44.470, 46.510
Angle α, β, γ (deg.)115.27, 97.77, 109.23
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Haloalkane dehalogenase


Mass: 34110.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus sp. (bacteria) / Strain: NCIB 13064 / Gene: dhaA / Plasmid: pAQN / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P0A3G3, haloalkane dehalogenase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 2.1 Å3/Da / Density % sol: 41.31 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.75
Details: 39% PEG 4000, 100 mM sodium acetate, 8% 1,2,3-trichloropropane, pH 7.75, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 1.9 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Oct 14, 2011
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.9 Å / Relative weight: 1
ReflectionResolution: 1.85→22 Å / Num. all: 23843 / Num. obs: 20934 / % possible obs: 87.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 20.45 Å2 / Rmerge(I) obs: 0.158 / Net I/σ(I): 5.3
Reflection shellResolution: 1.85→1.94 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.568 / Mean I/σ(I) obs: 2 / Num. unique all: 3508 / % possible all: 81.5

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Processing

Software
NameVersionClassification
MAR345225 detector softwaredata collection
MOLREPphasing
REFMAC5.7.0029refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FBW

3fbw


Resolution: 1.95→22 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.861 / SU B: 6.487 / SU ML: 0.179 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.285 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27287 923 5.1 %RANDOM
Rwork0.21558 ---
all0.21857 19150 --
obs0.21857 17017 88.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.533 Å2
Baniso -1Baniso -2Baniso -3
1-2.4 Å21.19 Å20.9 Å2
2---0.34 Å2-0.03 Å2
3----1.43 Å2
Refinement stepCycle: LAST / Resolution: 1.95→22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2368 0 1 226 2595
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192503
X-RAY DIFFRACTIONr_bond_other_d0.0010.022346
X-RAY DIFFRACTIONr_angle_refined_deg1.6651.9553434
X-RAY DIFFRACTIONr_angle_other_deg0.9235417
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5235307
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.72523.171123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.80115384
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4641519
X-RAY DIFFRACTIONr_chiral_restr0.0920.2361
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212828
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02591
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 57 -
Rwork0.403 1175 -
obs-1175 84.21 %

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