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- PDB-1bn6: HALOALKANE DEHALOGENASE FROM A RHODOCOCCUS SPECIES -

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Basic information

Entry
Database: PDB / ID: 1bn6
TitleHALOALKANE DEHALOGENASE FROM A RHODOCOCCUS SPECIES
ComponentsHALOALKANE DEHALOGENASE
KeywordsHYDROLASE / DEHALOGENASE / ALPHA/BETA-HYDROLASE / DHLA
Function / homology
Function and homology information


haloalkane dehalogenase / haloalkane dehalogenase activity
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 sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsNewman, J. / Peat, T.S. / Richard, R. / Kan, L. / Swanson, P.E. / Affholter, J.A. / Holmes, I.H. / Schindler, J.F. / Unkefer, C.J. / Terwilliger, T.C.
CitationJournal: Biochemistry / Year: 1999
Title: Haloalkane dehalogenases: structure of a Rhodococcus enzyme.
Authors: Newman, J. / Peat, T.S. / Richard, R. / Kan, L. / Swanson, P.E. / Affholter, J.A. / Holmes, I.H. / Schindler, J.F. / Unkefer, C.J. / Terwilliger, T.C.
History
DepositionJul 31, 1998Processing site: BNL
Revision 1.0Feb 18, 2000Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HALOALKANE DEHALOGENASE


Theoretical massNumber of molelcules
Total (without water)33,3671
Polymers33,3671
Non-polymers00
Water5,927329
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.520, 79.970, 43.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein HALOALKANE DEHALOGENASE


Mass: 33367.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus sp. (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P59336, haloalkane dehalogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 329 / 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: 2.43 Å3/Da / Density % sol: 38.8 %
Crystal growpH: 7 / Details: pH 7.0
Crystal grow
*PLUS
Temperature: 8 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
210 mMTris-SO41drop
325 %PEG15001reservoir
40.1 MMES1reservoir
50.3 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.8157
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1998
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8157 Å / Relative weight: 1
ReflectionResolution: 1.48→50 Å / Num. obs: 53599 / % possible obs: 97.2 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 11.5 Å2 / Rsym value: 0.065 / Net I/σ(I): 9
Reflection shellResolution: 1.48→1.56 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2.8 / Rsym value: 0.264 / % possible all: 83.6
Reflection
*PLUS
Rmerge(I) obs: 0.065
Reflection shell
*PLUS
% possible obs: 83.6 % / Rmerge(I) obs: 0.264

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Processing

Software
NameVersionClassification
CNS0.3refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNS0.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MODEL AT PH 5.5

Resolution: 1.5→50 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: MLF
RfactorNum. reflection% reflectionSelection details
Rfree0.174 2577 5 %RANDOM
Rwork0.167 ---
obs0.167 51084 96.8 %-
Solvent computationBsol: 28.53 Å2 / ksol: 0.385 e/Å3
Displacement parametersBiso mean: 10.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.413 Å20 Å20 Å2
2---0.224 Å20 Å2
3----0.189 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.14 Å0.14 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.05 Å
Refinement stepCycle: LAST / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2336 0 4 329 2669
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.033
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.17
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.411.5
X-RAY DIFFRACTIONc_mcangle_it0.692
X-RAY DIFFRACTIONc_scbond_it0.52
X-RAY DIFFRACTIONc_scangle_it0.792.5
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.202 437 5.3 %
Rwork0.179 7873 -
obs--96 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.3 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 51094 / Rfactor Rfree: 0.175 / Rfactor Rwork: 0.168
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg2.65
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg2.17

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