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- PDB-1cv2: Hydrolytic haloalkane dehalogenase linb from sphingomonas paucimo... -

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Basic information

Entry
Database: PDB / ID: 1cv2
TitleHydrolytic haloalkane dehalogenase linb from sphingomonas paucimobilis UT26 AT 1.6 A resolution
ComponentsHALOALKANE DEHALOGENASE
KeywordsHYDROLASE / DEHALOGENASE / LINDANE / BIODEGRADATION / ALPHA/BETA-HYDROLASE
Function / homology
Function and homology information


haloalkane dehalogenase / haloalkane dehalogenase activity / response to toxic substance / periplasmic space
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 / Haloalkane dehalogenase
Similarity search - Component
Biological speciesSphingomonas paucimobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsMarek, J. / Vevodova, J. / Damborsky, J. / Smatanova, I. / Svensson, L.A. / Newman, J. / Nagata, Y. / Takagi, M.
Citation
Journal: Biochemistry / Year: 2000
Title: Crystal structure of the haloalkane dehalogenase from Sphingomonas paucimobilis UT26.
Authors: Marek, J. / Vevodova, J. / Smatanova, I.K. / Nagata, Y. / Svensson, L.A. / Newman, J. / Takagi, M. / Damborsky, J.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Crystallization and Preliminary X-Ray Diffraction Analysis of Haloalkane Dehalogenase Linb from Sphingomonas Paucimobilis Ut26
Authors: Smatanova, I. / Nagata, Y. / Svensson, L.A. / Takagi, M. / Marek, J.
History
DepositionAug 22, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Data collection / Refinement description / Category: diffrn_source / software
Item: _diffrn_source.pdbx_synchrotron_site / _software.classification / _software.name
Revision 1.4Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)33,1451
Polymers33,1451
Non-polymers00
Water8,089449
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.264, 71.669, 72.698
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Cell settingorthorhombic
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-1047-

HOH

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Components

#1: Protein HALOALKANE DEHALOGENASE / E.C.3.8.1.5 / LINB / 1 / 3 / 4 / 6-TETRACHLORO-1 / 4-CYCLOHEXADIENE HYDROLASE


Mass: 33144.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas paucimobilis (bacteria) / Strain: UT26 / Plasmid details: TAC PROMOTER SYSTEM / Plasmid: PMYLB1 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101
References: UniProt: P51698, UniProt: D4Z2G1*PLUS, haloalkane dehalogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 449 / 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: 2.07 Å3/Da / Density % sol: 40.2 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 8.9
Details: 19% (W/V) PEG 6000, 100 MM TRIS-HCL, 200MM CA ACETATE, PH=8.9, VAPOR DIFFUSION, HANGING DROP at 278K
Crystal grow
*PLUS
Details: microseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
118-20 %(w/v)PEG60001reservoir
20.2 Mcalcium acetate1reservoir
30.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.942
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 18, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.942 Å / Relative weight: 1
ReflectionResolution: 1.575→23.75 Å / Num. all: 34649 / Num. obs: 34649 / % possible obs: 94.2 % / Redundancy: 4.84 % / Biso Wilson estimate: 11.5 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 18.31
Reflection shellResolution: 1.575→1.6 Å / Redundancy: 2.79 % / Rmerge(I) obs: 0.146 / Mean I/σ(I) obs: 5.98 / % possible all: 81.4
Reflection
*PLUS
Highest resolution: 1.58 Å / Lowest resolution: 20 Å / Num. obs: 34513
Reflection shell
*PLUS
% possible obs: 81.4 %

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Processing

Software
NameClassification
AMoREphasing
SHELXL-97refinement
MAR345data collection
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BN6

1bn6


Resolution: 1.58→20 Å / Rfactor Rfree error: 0.005 / Num. parameters: 1100 / Num. restraintsaints: 958 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2108 1730 5 %RANDOM
all0.1522 34513 --
obs0.1491 34513 94.2 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Displacement parametersBiso mean: 14.7 Å2
Refine analyzeOccupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2749.5
FreeObs
Luzzati coordinate error0.19 Å0.13 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.58→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2301 0 0 449 2750
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.009
X-RAY DIFFRACTIONs_angle_d0.027
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.027
X-RAY DIFFRACTIONs_zero_chiral_vol0.05
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.062
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.014
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.071
X-RAY DIFFRACTIONs_approx_iso_adps
LS refinement shellResolution: 1.58→1.68 Å / Rfactor Rfree error: 0.014
RfactorNum. reflection% reflection
Rfree0.222 263 4.9 %
Rwork0.185 5087 -
obs--89.1 %
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.204 / Rfactor Rwork: 0.145
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg2.3
X-RAY DIFFRACTIONs_improper_angle_d
X-RAY DIFFRACTIONs_improper_angle_deg1.3

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