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- PDB-3fwh: Structure of haloalkane dehalogenase mutant Dha15 (I135F/C176Y) f... -

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Basic information

Entry
Database: PDB / ID: 3fwh
TitleStructure of haloalkane dehalogenase mutant Dha15 (I135F/C176Y) from Rhodococcus rhodochrous
ComponentsHaloalkane dehalogenase
KeywordsHYDROLASE / alpha/beta hydrolase core / helical cap domain / catalytic triad (Asp106 / His272 / Glu130) / mutant / I135F / C176Y / haloalkanes / Detoxification
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
ACETATE ION / ISOPROPYL ALCOHOL / Haloalkane dehalogenase
Similarity search - Component
Biological speciesRhodococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22 Å
AuthorsGavira, J.A. / Stsiapanava, A. / Kuty, M. / Dohnalek, J. / Lapkouski, M. / Kuta Smatanova, I.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2010
Title: Atomic resolution studies of haloalkane dehalogenases DhaA04, DhaA14 and DhaA15 with engineered access tunnels.
Authors: Stsiapanava, A. / Dohnalek, J. / Gavira, J.A. / Kuty, M. / Koudelakova, T. / Damborsky, J. / Kuta Smatanova, I.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2008
Title: Crystals of DhaA mutants from Rhodococcus rhodochrous NCIMB 13064 diffracted to ultrahigh resolution: crystallization and preliminary diffraction analysis
Authors: Stsiapanava, A. / Koudelakova, T. / Lapkouski, M. / Pavlova, M. / Damborsky, J. / Kuta Smatanova, I.
#2: Journal: To be Published
Title: Pathways and Mechanisms for Product Release in Engineered Haloalkane Dehalogenase DhaA Explored using Classical and Random Acceleration Molecular Dynamics Simulations
Authors: Klvana, M. / Pavlova, M. / Koudelakova, T. / Chaloupkova, R. / Dvorak, P. / Stsiapanava, A. / Kuty, M. / Kuta Smatanova, I. / Dohnalek, J. / Kulhanek, P. / Wade, R.C. / Damborsky, J.
History
DepositionJan 18, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 28, 2012Group: Database references
Revision 1.3Oct 20, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / 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
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)34,3955
Polymers34,2051
Non-polymers1904
Water11,115617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.524, 44.370, 46.541
Angle α, β, γ (deg.)115.48, 98.41, 109.60
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Haloalkane dehalogenase


Mass: 34204.914 Da / Num. of mol.: 1 / Mutation: I135F, C176Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus sp. (bacteria) / Strain: NCIMB 13064 / Gene: dhaA / Plasmid: pAQN / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P0A3G3, haloalkane dehalogenase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 617 / 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: 2.05 Å3/Da / Density % sol: 40.05 %
Crystal growTemperature: 277 K / pH: 7.5
Details: 25 % PEG 4 000, 8 % iso-propanol and 100 mM Na-Acetate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 1.15
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Details: MIRROR: ELLIPTICALLY BENT 12 QUARTZ SEGMENTS
RadiationMonochromator: MONOCHROMATOR: GE(111) TRIANGULAR BENT COMPRESSING 7 FANKUCHEN CUT
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.15 Å / Relative weight: 1
ReflectionResolution: 1.2→20 Å / Num. obs: 77114 / % possible obs: 90.7 % / Observed criterion σ(I): 1 / Redundancy: 3.4 % / Biso Wilson estimate: 11.1 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 29.6
Reflection shellResolution: 1.2→1.24 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.179 / Mean I/σ(I) obs: 6.8 / % possible all: 45

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BN6

1bn6


Resolution: 1.22→20 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.96 / SU B: 0.769 / SU ML: 0.016 / Cross valid method: THROUGHOUT / ESU R: 0.042 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.162 3872 5 %RANDOM
Rwork0.13 ---
obs0.132 77113 94.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.817 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20.34 Å20.12 Å2
2---0.08 Å20.1 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.22→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2393 0 10 617 3020
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222866
X-RAY DIFFRACTIONr_bond_other_d0.0010.021996
X-RAY DIFFRACTIONr_angle_refined_deg1.6051.9573973
X-RAY DIFFRACTIONr_angle_other_deg0.97434872
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8635377
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.90223.462156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.24515463
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9331525
X-RAY DIFFRACTIONr_chiral_restr0.1020.2402
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213353
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02627
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2565
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2040.250
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2420.299
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4331.51684
X-RAY DIFFRACTIONr_mcbond_other2.0251.5645
X-RAY DIFFRACTIONr_mcangle_it2.05822788
X-RAY DIFFRACTIONr_scbond_it2.73131182
X-RAY DIFFRACTIONr_scangle_it3.7894.51159
X-RAY DIFFRACTIONr_rigid_bond_restr1.51732866
X-RAY DIFFRACTIONr_sphericity_free8.3813168
X-RAY DIFFRACTIONr_sphericity_bonded4.29332733
LS refinement shellResolution: 1.22→1.25 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 224 -
Rwork0.267 4551 -
obs--75.57 %

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