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- PDB-3fbw: Structure of Rhodococcus rhodochrous haloalkane dehalogenase DhaA... -

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Basic information

Entry
Database: PDB / ID: 3fbw
TitleStructure of Rhodococcus rhodochrous haloalkane dehalogenase DhaA mutant C176Y
ComponentsHaloalkane dehalogenase
KeywordsHYDROLASE / Detoxification / alpha/beta-Hydrolase / catalytic triad / halide-binding site
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
BENZOIC ACID / Haloalkane dehalogenase
Similarity search - Component
Biological speciesRhodococcus rhodochrous (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.23 Å
AuthorsDohnalek, J. / Stsiapanava, A. / Gavira, J.A. / Kuta Smatanova, I. / Kuty, M.
CitationJournal: 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.
History
DepositionNov 20, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 20, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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)34,55410
Polymers34,1711
Non-polymers3839
Water8,179454
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.678, 76.294, 93.098
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 / E.C.3.8.1.5


Mass: 34170.898 Da / Num. of mol.: 1 / Mutation: C176Y
Source method: isolated from a genetically manipulated source
Details: The active site partially occupied by a small ligand and by a chloride ion
Source: (gene. exp.) Rhodococcus rhodochrous (bacteria) / Strain: NCIMB 13064 / Gene: dhaA / Plasmid: pAQN / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P0A3G2, haloalkane dehalogenase
#2: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O2
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 454 / 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: 2.22 Å3/Da / Density % sol: 44.54 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 0.08M bicine, 8% PEG 8000, 0.08M magnesium chloride, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8158 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 16, 2007
RadiationMonochromator: Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8158 Å / Relative weight: 1
ReflectionResolution: 1.23→100 Å / Num. all: 88814 / Num. obs: 88814 / % possible obs: 100 % / Observed criterion σ(I): -999 / Redundancy: 7.4 % / Biso Wilson estimate: 9.2 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 25.6
Reflection shellResolution: 1.23→1.25 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.581 / Mean I/σ(I) obs: 4.2 / Num. unique all: 4384 / Rsym value: 0.581 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MAR345CCD165 detector softwaredata collection
MOLREPphasing
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BN6

1bn6


Resolution: 1.23→100 Å / Num. parameters: 26510 / Num. restraintsaints: 37060
Isotropic thermal model: MIXED ISOTROPIC AND ANISOTROPIC THERMAL MODEL
Cross valid method: FREE R / σ(F): 0
Stereochemistry target values: ENGH & HUBER, LIGAND TARGET VALUES BASED ON AVERAGED BEST CAMBRIDGE STRUCTURAL DATABASE VALUES
Details: CONJUGATE GRADIENT LEAST SQUARES REFINEMENT IN SHELXL97 WITH ANISOTROPIC ADPS FOR ALL ATOMS EXCEPT FOR WATER MOLECULES ABOVE A CERTAIN ADP CUTTOF
RfactorNum. reflection% reflectionSelection details
Rfree0.167 3425 3.86 %RANDOM
Rwork0.1364 ---
all0.1369 88731 --
obs0.1369 88731 99.9 %-
Solvent computationSolvent model: BABINET, SHELXL97 IMPLEMENTATION, G=1.007, U=4.133
Displacement parametersBiso mean: 13.4 Å2
Refine analyzeLuzzati coordinate error obs: 0.122 Å / Luzzati d res low obs: 5 Å / Num. disordered residues: 61 / Occupancy sum hydrogen: 2267.9 / Occupancy sum non hydrogen: 2738.52
Refinement stepCycle: LAST / Resolution: 1.23→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2355 0 17 454 2826
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.028
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0268
X-RAY DIFFRACTIONs_zero_chiral_vol0.08
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.076
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.024
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.036
X-RAY DIFFRACTIONs_approx_iso_adps0.031

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