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- PDB-4fwb: Structure of Rhodococcus rhodochrous haloalkane dehalogenase muta... -

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Basic information

Entry
Database: PDB / ID: 4fwb
TitleStructure of Rhodococcus rhodochrous haloalkane dehalogenase mutant DhaA31 in complex with 1, 2, 3 - trichloropropane
ComponentsHaloalkane dehalogenase
KeywordsHYDROLASE / catalytic pentad / Structural Genomics / Enzyme Function Initiative / 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
1,2,3-trichloropropane / Haloalkane dehalogenase
Similarity search - Component
Biological speciesRhodococcus rhodochrous (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 Å
AuthorsLahoda, M. / Stsiapanava, A. / Mesters, J. / 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
DepositionJun 30, 2012Deposition site: RCSB / Processing site: RCSB
SupersessionSep 5, 2012ID: 3RLT
Revision 1.0Sep 5, 2012Provider: 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 1.4Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.5Sep 13, 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 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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)33,6266
Polymers33,3371
Non-polymers2895
Water6,359353
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.498, 44.395, 46.538
Angle α, β, γ (deg.)115.32, 97.70, 109.58
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Haloalkane dehalogenase


Mass: 33336.996 Da / Num. of mol.: 1 / Mutation: I135F,C176Y,V245F,L246I,Y273F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus rhodochrous (bacteria) / Strain: NCIB 13064 / Gene: dhaA, DhaA31 / Plasmid: pAQN / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P0A3G2, haloalkane dehalogenase
#2: Chemical ChemComp-3KP / 1,2,3-trichloropropane


Mass: 147.431 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5Cl3
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / 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: 2.12 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 100 mM MES sodium salt, 29% (w/v) peg 4000; 1,2,3-trichloropropane was added at room temperature, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 25, 2009
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.26→10 Å / Num. all: 176338 / % possible obs: 92.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 14.6 Å2 / Rmerge(I) obs: 0.033 / Rsym value: 0.033
Reflection shellResolution: 1.26→1.27 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.061 / Mean I/σ(I) obs: 17.6 / Rsym value: 0.061 / % possible all: 82.7

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Processing

Software
NameVersionClassification
MAR345CCD 225 detector softwaredata collection
MOLREPphasing
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3fbw

3fbw


Resolution: 1.26→10 Å
Isotropic thermal model: mixed isotropic and anisotropic thermal model
Cross valid method: FREE R / σ(F): 0 / σ(I): -999 / Stereochemistry target values: ENGH AND HUBER
Details: conjugate gradient least squares refinement in SHELXL 97 with anisotropic adps for all atoms except for water molecules above a certain adp cut off
RfactorNum. reflection% reflectionSelection details
Rfree0.1655 3454 -RANDOM
Rwork0.1359 ---
all0.1359 69189 --
obs0.1359 69189 100 %-
Displacement parametersBiso mean: 11.3 Å2
Refine analyzeLuzzati coordinate error obs: 0.12 Å / Luzzati d res low obs: 5 Å / Num. disordered residues: 26
Refinement stepCycle: LAST / Resolution: 1.26→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2361 0 10 353 2724
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d0.029
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0273
X-RAY DIFFRACTIONs_zero_chiral_vol0.102
LS refinement shellHighest resolution: 1.26 Å

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