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- PDB-4e46: Structure of Rhodococcus rhodochrous haloalkane dehalogenase DhaA... -

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Basic information

Entry
Database: PDB / ID: 4.0E+46
TitleStructure of Rhodococcus rhodochrous haloalkane dehalogenase DhaA in complex with 2-propanol
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
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
ACETATE ION / ISOPROPYL ALCOHOL / Haloalkane dehalogenase
Similarity search - Component
Biological speciesRhodococcus rhodochrous (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 Å
AuthorsStsiapanava, A. / Chaloupkova, R. / Damborsky, J. / Kuta Smatanova, I.
CitationJournal: Chembiochem / Year: 2013
Title: Expansion of access tunnels and active-site cavities influence activity of haloalkane dehalogenases in organic cosolvents.
Authors: Stepankova, V. / Khabiri, M. / Brezovsky, J. / Pavelka, A. / Sykora, J. / Amaro, M. / Minofar, B. / Prokop, Z. / Hof, M. / Ettrich, R. / Chaloupkova, R. / Damborsky, J.
History
DepositionMar 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 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)33,9105
Polymers33,6961
Non-polymers2144
Water9,764542
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.646, 44.480, 46.334
Angle α, β, γ (deg.)115.39, 98.05, 109.40
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Haloalkane dehalogenase /


Mass: 33696.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus rhodochrous (bacteria) / Strain: NCIB 13064 / Gene: dhaA / Plasmid: pAQN / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P0A3G2, haloalkane dehalogenase
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 542 / 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: 41.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 100 mM sodium acetate, 24% PEG4000, 11% 2-propanol, 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: double crystal Si(111), horizontally focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.26→50 Å / Num. all: 69524 / Num. obs: 65492 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 13.3 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 29.9
Reflection shellResolution: 1.26→1.31 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.113 / Mean I/σ(I) obs: 6.8 / % possible all: 90.2

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Processing

Software
NameVersionClassification
MAR345Mosaic CCD 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 / Num. parameters: 24815 / Num. restraintsaints: 30840
Isotropic thermal model: MIXED ISOTROPIC AND ANISOTROPIC THERMAL MODEL
σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: STRUCTURE SOLUTION AND REFINEMENT WERE PERFORMED USING FREE R FOR CROSS-VALIDATION THROUGHOUT: FREE R = 0.150 FROM A RANDOM TEST SET COMPRISING 5% OF REFLECTIONS (3476 TOTAL). FINAL ...Details: STRUCTURE SOLUTION AND REFINEMENT WERE PERFORMED USING FREE R FOR CROSS-VALIDATION THROUGHOUT: FREE R = 0.150 FROM A RANDOM TEST SET COMPRISING 5% OF REFLECTIONS (3476 TOTAL). FINAL REFINEMENT WAS PERFORMED USING ALL REFLECTIONS.
RfactorNum. reflection% reflectionSelection details
Rwork0.1125 ---
all0.1125 69524 --
obs0.1125 65492 94.2 %-
Rfree---RANDOM
Displacement parametersBiso mean: 16 Å2
Refine analyzeNum. disordered residues: 49 / Occupancy sum hydrogen: 2134 / Occupancy sum non hydrogen: 2902.45
Refinement stepCycle: LAST / Resolution: 1.26→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2359 0 13 542 2914
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d0.027
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.027
X-RAY DIFFRACTIONs_zero_chiral_vol0.083
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.076
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.027
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.033
X-RAY DIFFRACTIONs_approx_iso_adps0

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