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- PDB-4c6h: Haloalkane dehalogenase with 1-hexanol -

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Basic information

Entry
Database: PDB / ID: 4c6h
TitleHaloalkane dehalogenase with 1-hexanol
ComponentsHALOALKANE DEHALOGENASE
KeywordsHYDROLASE
Function / homology
Function and homology information


haloalkane dehalogenase / haloalkane dehalogenase activity
Similarity search - Function
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
HEXAN-1-OL / TRIETHYLENE GLYCOL / Haloalkane dehalogenase
Similarity search - Component
Biological speciesRHODOBACTERACEAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsNovak, H.R. / Sayer, C. / Isupov, M. / Gotz, D. / Spragg, A.M. / Littlechild, J.A.
CitationJournal: FEBS Lett. / Year: 2014
Title: Biochemical and Structural Characterisation of a Haloalkane Dehalogenase from a Marine Rhodobacteraceae.
Authors: Novak, H.R. / Sayer, C. / Isupov, M.N. / Gotz, D. / Spragg, A.M. / Littlechild, J.A.
History
DepositionSep 18, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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)32,9474
Polymers32,6591
Non-polymers2883
Water5,963331
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.450, 71.410, 59.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2012-

HOH

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Components

#1: Protein HALOALKANE DEHALOGENASE


Mass: 32658.732 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: 1-HEXANOL PRODUCT IN ACTIVE SITE / Source: (gene. exp.) RHODOBACTERACEAE (bacteria)
Description: CATALYSES BREAKDOWN OF HALOGENATED ALKANES TO THEIR CORRESPONDING HYDROGEN HALIDES AND ALCOHOL COMPOUNDS
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2
References: UniProt: A0A067XG66*PLUS, haloalkane dehalogenase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-HE2 / HEXAN-1-OL


Mass: 102.175 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsGB KF032932

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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: 41.1 % / Description: NONE

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 19, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.61→47.84 Å / Num. obs: 36192 / % possible obs: 99.9 % / Observed criterion σ(I): 3.5 / Redundancy: 12.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 26
Reflection shellResolution: 1.61→1.66 Å / Redundancy: 12.6 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 3.6 / % possible all: 100

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Processing

SoftwareName: REFMAC / Version: 5.7.0032 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CV2

1cv2


Resolution: 1.61→26.36 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.609 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.18703 1803 5 %RANDOM
Rwork0.15286 ---
obs0.1546 34350 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.604 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å20 Å20 Å2
2---0.79 Å20 Å2
3---1.31 Å2
Refinement stepCycle: LAST / Resolution: 1.61→26.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2302 0 18 331 2651
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192497
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4381.9553410
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5365324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.19123.73126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.46615414
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6381521
X-RAY DIFFRACTIONr_chiral_restr0.0970.2368
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211953
X-RAY DIFFRACTIONr_gen_planes_other
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_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.424.681199
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.137.8611505
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.8945.491296
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.613→1.655 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 131 -
Rwork0.248 2486 -
obs--99.92 %

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