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- PDB-1d07: Hydrolytic haloalkane dehalogenase linb from sphingomonas paucimo... -

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Basic information

Entry
Database: PDB / ID: 1d07
TitleHydrolytic haloalkane dehalogenase linb from sphingomonas paucimobilis UT26 with 1,3-propanediol, a product of debromidation of dibrompropane, at 2.0A 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
BROMIDE ION / 1,3-PROPANDIOL / Haloalkane dehalogenase / Haloalkane dehalogenase
Similarity search - Component
Biological speciesSphingomonas paucimobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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
DepositionSep 9, 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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)33,3814
Polymers33,1451
Non-polymers2363
Water4,846269
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.227, 71.721, 73.319
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Cell settingorthorhombic
Space group name H-MP21212

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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: PMYLB1 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101
References: UniProt: P51698, UniProt: D4Z2G1*PLUS, haloalkane dehalogenase
#2: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#3: Chemical ChemComp-PDO / 1,3-PROPANDIOL


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / 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. CRYSTAL WAS SOAKED 4 HOURS IN RESERVOIR LIQUOR WITH 25MM 1,3-DIBROMPROPANE AT 278K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: used 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: 0.9
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 4, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 16801 / % possible obs: 86.6 % / Redundancy: 7.67 % / Biso Wilson estimate: 10.9 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 12.37
Reflection shellResolution: 2→2.13 Å / Redundancy: 7.64 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 4.55 / % possible all: 99.8
Reflection
*PLUS
Lowest resolution: 20 Å / Rmerge(I) obs: 0.113
Reflection shell
*PLUS
Highest resolution: 2 Å / % possible obs: 99.8 % / Rmerge(I) obs: 0.289

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Processing

Software
NameClassification
AMoREphasing
SHELXLrefinement
MAR345data collection
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CV2

1cv2


Resolution: 2→20 Å / Rfactor Rfree error: 0.007 / Num. parameters: 1036 / Num. restraintsaints: 971 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2737 1385 8 %RANDOM
all0.1804 16801 --
obs0.1693 -86.6 %-
Solvent computationSolvent model: MOEWS & KRETSINGER: J.MOL.BIOL. 91 (1973) 201-228
Displacement parametersBiso mean: 20.8 Å2
Refine analyzeOccupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2574
FreeObs
Luzzati coordinate error0.29 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2301 0 2 274 2577
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.005
X-RAY DIFFRACTIONs_angle_d0.021
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.024
X-RAY DIFFRACTIONs_zero_chiral_vol0.025
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.035
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.02
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.079
X-RAY DIFFRACTIONs_approx_iso_adps
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.022
RfactorNum. reflection% reflection
Rfree0.342 240 8 %
Rwork0.231 2767 -
obs--99.8 %
Software
*PLUS
Name: SHELXL / Version: 96 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / Rfactor all: 0.18 / Rfactor obs: 0.169 / Rfactor Rfree: 0.258
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg1.8

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