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- PDB-1g42: STRUCTURE OF 1,3,4,6-TETRACHLORO-1,4-CYCLOHEXADIENE HYDROLASE (LI... -

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Basic information

Entry
Database: PDB / ID: 1g42
TitleSTRUCTURE OF 1,3,4,6-TETRACHLORO-1,4-CYCLOHEXADIENE HYDROLASE (LINB) FROM SPHINGOMONAS PAUCIMOBILIS COMPLEXED WITH 1,2-DICHLOROPROPANE
Components1,3,4,6-TETRACHLORO-1,4-CYCLOHEXADIENE HYDROLASE
KeywordsHYDROLASE / LinB dehalogenase alpha/beta-hydrolase halocarbons
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 / ACETATE ION / 1,2-DICHLORO-PROPANE / Haloalkane dehalogenase
Similarity search - Component
Biological speciesSphingomonas paucimobilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsOakley, A.J. / Prokop, Z. / Bohac, M. / Kmunicek, J. / Jedlicka, T. / Monincova, M. / Kuta-Smatanova, I. / Nagata, Y. / Damborsky, J. / Wilce, M.C.J.
Citation
Journal: Biochemistry / Year: 2002
Title: Exploring the structure and activity of haloalkane dehalogenase from Sphingomonas paucimobilis UT26: evidence for product- and water-mediated inhibition.
Authors: Oakley, A.J. / Prokop, Z. / Bohac, M. / Kmunicek, J. / Jedlicka, T. / Monincova, M. / Kuta-Smatanova, I. / Nagata, Y. / Damborsky, J. / Wilce, M.C.
#1: 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.
History
DepositionOct 26, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 1,3,4,6-TETRACHLORO-1,4-CYCLOHEXADIENE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7259
Polymers33,1721
Non-polymers5548
Water7,332407
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.800, 72.000, 73.300
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-601-

CA

DetailsThe asymmetric unit contains the functional monomer

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Components

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Protein , 1 types, 1 molecules A

#1: Protein 1,3,4,6-TETRACHLORO-1,4-CYCLOHEXADIENE HYDROLASE / 1 / 4-TCDN CHLOROHYDROLASE


Mass: 33171.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas paucimobilis (bacteria) / Gene: LINB / Plasmid: PMLBH6 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101
References: UniProt: P51698, UniProt: D4Z2G1*PLUS, Hydrolases; Acting on halide bonds; In carbon-halide compounds

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Non-polymers , 5 types, 415 molecules

#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-CP2 / 1,2-DICHLORO-PROPANE


Mass: 112.986 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H6Cl2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 407 / 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: 2.03 Å3/Da / Density % sol: 39.09 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 8.9
Details: 0.1 M Tris-HCl pH 8.9, 18-20%(w/v) PEG 6000, 0.2 M calcium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
118 %PEG60001reservoir
20.2 Mcalcium acetate1reservoir
30.1 MTris1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 13, 2000 / Details: Ni Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 25682 / Num. obs: 55091 / % possible obs: 97 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 2.21 % / Biso Wilson estimate: 11.4 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 12.75
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2.06 % / Rmerge(I) obs: 0.241 / Mean I/σ(I) obs: 2.97 / Num. unique all: 2402 / % possible all: 95.7
Reflection
*PLUS
Num. obs: 24918 / Num. measured all: 55091
Reflection shell
*PLUS
% possible obs: 95.7 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CV2
Resolution: 1.8→18.78 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1468372.72 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.193 1265 5.1 %RANDOM
Rwork0.167 ---
all0.167 25682 --
obs0.167 24803 97.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.67 Å2 / ksol: 0.369 e/Å3
Displacement parametersBiso mean: 13.2 Å2
Baniso -1Baniso -2Baniso -3
1--1.32 Å20 Å20 Å2
2---0.25 Å20 Å2
3---1.57 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.8→18.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2356 0 23 407 2786
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d0.86
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.244 194 4.8 %
Rwork0.233 3831 -
obs-3831 96 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CP.PARAMCP.TOP
X-RAY DIFFRACTION3ION.PARAMACY.TOP
X-RAY DIFFRACTION4WATER_REP.PARAM
X-RAY DIFFRACTION5ACY.PARAM
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 13.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.86
LS refinement shell
*PLUS
Rfactor Rfree: 0.244 / Rfactor Rwork: 0.233

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