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- PDB-3sk0: structure of Rhodococcus rhodochrous haloalkane dehalogenase DhaA... -

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Basic information

Entry
Database: PDB / ID: 3sk0
Titlestructure of Rhodococcus rhodochrous haloalkane dehalogenase DhaA mutant DhaA12
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 rhodochrous (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsLahoda, M. / Stsiapanava, A. / Mesters, J. / Koudelakova, T. / Damborsky, J. / Kuta-Smatanova, I.
Citation
Journal: Nat.Chem.Biol. / Year: 2014
Title: Dynamics and hydration explain failed functional transformation in dehalogenase design.
Authors: Sykora, J. / Brezovsky, J. / Koudelakova, T. / Lahoda, M. / Fortova, A. / Chernovets, T. / Chaloupkova, R. / Stepankova, V. / Prokop, Z. / Smatanova, I.K. / Hof, M. / Damborsky, J.
#1: Journal: To Be Published
Title: Crystal structure of haloalkane dehalogenase mutant DhaA12 from Gram-positive bacterium Rhodococcus rhodochrous NCIMB13064
Authors: Lahoda, M. / Koudelakova, T. / Stsiapanava, A. / Mesters, J. / Damborsky, J. / Kuta-Smatanova, I.
History
DepositionJun 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2014Group: Database references
Revision 1.2May 21, 2014Group: Database references
Revision 1.3Jun 4, 2014Group: Database references
Revision 1.4Nov 8, 2017Group: Database references / Refinement description / Category: citation_author / software / Item: _citation_author.name / _software.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 / 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)35,4322
Polymers35,3971
Non-polymers351
Water4,864270
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.583, 68.689, 84.370
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


Mass: 35397.043 Da / Num. of mol.: 1
Mutation: W138F, 139HHTEVAEEQDH149 insertion, P150A, F152A, G179R, A180V, K183G, C184G, V253A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus rhodochrous (bacteria) / Gene: dhaA / Plasmid: pAQN / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P0A3G2, 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.: 270 / 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: 2.11 Å3/Da / Density % sol: 41.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.1
Details: 100 mM MES sodium salt, 20% peg 4000, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 24, 2009
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.78→10 Å / Num. obs: 34658 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 22.7 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 14.4
Reflection shellResolution: 1.78→1.88 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 4.2 / Num. unique all: 4241 / Rsym value: 0.37 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MAR345Mosaic CCD 225 mmdata collection
MOLREPphasing
SHELXL-97refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FBW

3fbw


Resolution: 1.78→10 Å / Num. parameters: 11235 / Num. restraintsaints: 10651 / Isotropic thermal model: isotropic / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER
Details: CONJUGATE GRADIENT LEAST SQUARES REFINEMENT IN SHELXL 97
RfactorNum. reflection% reflectionSelection details
Rfree0.207 1734 -RANDOM
Rwork0.1759 ---
obs0.176 34658 100 %-
Displacement parametersBiso mean: 17.1 Å2
Refine analyzeLuzzati coordinate error obs: 0.188 Å / Luzzati d res low obs: 6.67 Å / Num. disordered residues: 15 / Occupancy sum hydrogen: 2288 / Occupancy sum non hydrogen: 2751
Refinement stepCycle: LAST / Resolution: 1.78→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2480 0 1 270 2751
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.024
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0231
X-RAY DIFFRACTIONs_zero_chiral_vol0.037
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.043
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.01
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.061
X-RAY DIFFRACTIONs_approx_iso_adps0
LS refinement shellResolution: 1.78→1.88 Å
RfactorNum. reflection% reflection
Rfree0.207 1734 -
Rwork0.1759 --
obs-34658 99.9 %

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