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- PDB-4brz: Haloalkane dehalogenase -

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Basic information

Entry
Database: PDB / ID: 4brz
TitleHaloalkane dehalogenase
ComponentsHALOALKANE DEHALOGENASE
KeywordsHYDROLASE
Function / homology
Function and homology information


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 speciesRHODOBACTERACEAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 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
DepositionJun 6, 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

Downloads & links

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Assembly

Deposited unit
A: HALOALKANE DEHALOGENASE
B: HALOALKANE DEHALOGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1864
Polymers65,1152
Non-polymers712
Water8,395466
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-27.6 kcal/mol
Surface area20520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.970, 75.520, 64.870
Angle α, β, γ (deg.)90.00, 92.94, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HALOALKANE DEHALOGENASE


Mass: 32557.631 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RHODOBACTERACEAE (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2 / References: UniProt: A0A067XG63*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 466 / 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: 2.06 Å3/Da / Density % sol: 40 % / Description: NONE
Crystal growpH: 7 / Details: 0.3 M MGCL2, 0.1 M TRIS-HCL AND 30% PEG-4000, pH 7

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9778
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 1.67→44.4 Å / Num. obs: 61186 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 14.2
Reflection shellResolution: 1.67→1.71 Å / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2 / % possible all: 99.6

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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: 1.67→44.4 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.985 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD4 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.246 3100 5.1 %RANDOM
Rwork0.20486 ---
obs0.207 58063 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.608 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å20 Å2-0.58 Å2
2--0.44 Å20 Å2
3----1.12 Å2
Refinement stepCycle: LAST / Resolution: 1.67→44.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4590 0 2 466 5058
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0194955
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2351.9526796
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.345654
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.45923.976249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.15315835
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7551538
X-RAY DIFFRACTIONr_chiral_restr0.0850.2740
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213902
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_it3.0826.4772396
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.88310.9053011
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.8727.072559
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: 1.67→1.713 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 214 -
Rwork0.307 4269 -
obs--99.62 %

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