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- PDB-5kvb: The crystal structure of hexachlorocyclohexane dehydrochlorinase ... -

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Basic information

Entry
Database: PDB / ID: 5kvb
TitleThe crystal structure of hexachlorocyclohexane dehydrochlorinase LinA-type3 from Novosphingobium barchaimii LL02
ComponentsGamma-hexachlorocyclohexane dehydrochlorinase
KeywordsLYASE / dehydrochlorinase
Function / homologySnoaL-like domain / SnoaL-like domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / Gamma-hexachlorocyclohexane dehydrochlorinase
Function and homology information
Biological speciesNovosphingobium barchaimii LL02 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsDellas, N. / Oakeshott, J. / Pearce, S.L. / Pandey, G. / Pushiri, H.
CitationJournal: to be published
Title: The crystal structure of hexachlorocyclohexane dehydrochlorinase LinA-type3 from Novosphingobium barchaimii LL02
Authors: Dellas, N. / Oakeshott, J. / Pearce, S.L. / Pandey, G. / Pushiri, H.
History
DepositionJul 14, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / 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: Gamma-hexachlorocyclohexane dehydrochlorinase


Theoretical massNumber of molelcules
Total (without water)17,7211
Polymers17,7211
Non-polymers00
Water2,396133
1
A: Gamma-hexachlorocyclohexane dehydrochlorinase

A: Gamma-hexachlorocyclohexane dehydrochlorinase

A: Gamma-hexachlorocyclohexane dehydrochlorinase


Theoretical massNumber of molelcules
Total (without water)53,1633
Polymers53,1633
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area6240 Å2
ΔGint-36 kcal/mol
Surface area18350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.169, 50.169, 147.968
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-319-

HOH

21A-330-

HOH

31A-333-

HOH

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Components

#1: Protein Gamma-hexachlorocyclohexane dehydrochlorinase


Mass: 17720.896 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: DSMZ 25411
Source: (gene. exp.) Novosphingobium barchaimii LL02 (bacteria)
Gene: V474_07160 / Plasmid: pDEST14 / Details (production host): gateway / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0J7XEF9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2.14 Å3/Da / Density % sol: 42.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.05
Details: 20.5% PEG 1000, 10% propionate-cacodylate-bis tris propane

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 7, 2013
RadiationMonochromator: Silicon Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.45→41.688 Å / Num. all: 24639 / Num. obs: 24639 / % possible obs: 100 % / Redundancy: 5.7 % / Biso Wilson estimate: 10.68 Å2 / Rpim(I) all: 0.024 / Rrim(I) all: 0.057 / Rsym value: 0.052 / Net I/av σ(I): 9.804 / Net I/σ(I): 19.6 / Num. measured all: 140021
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.45-1.535.60.3352.32013636000.1560.3355100
1.53-1.625.60.2273.41925534250.1050.2277.1100
1.62-1.735.70.15451814732040.0710.1549.9100
1.73-1.875.70.1017.61668529380.0460.10114.1100
1.87-2.055.70.06311.71571227570.0290.06320.7100
2.05-2.295.70.05213.11421624890.0240.05227.3100
2.29-2.655.70.05411.71242621660.0250.05430.8100
2.65-3.245.70.03517.41045518380.0160.03537.8100
3.24-4.595.80.02423.5839514420.0110.02447.5100
4.59-41.6885.90.02913.545947800.0130.02947.199.9

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PHENIX1.9-1962refinement
PDB_EXTRACT3.15data extraction
MOLREPphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3A76

3a76


Resolution: 1.45→37.465 Å / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2004 1228 4.98 %0
Rwork0.1639 23409 --
obs0.1657 24637 100 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 52.36 Å2 / Biso mean: 13.211 Å2 / Biso min: 3.33 Å2
Refinement stepCycle: final / Resolution: 1.45→37.465 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1163 0 0 133 1296
Biso mean---19.76 -
Num. residues----146
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071241
X-RAY DIFFRACTIONf_angle_d1.0531695
X-RAY DIFFRACTIONf_chiral_restr0.045180
X-RAY DIFFRACTIONf_plane_restr0.005221
X-RAY DIFFRACTIONf_dihedral_angle_d12.298443
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.50810.24811370.19992603X-RAY DIFFRACTION100
1.5081-1.57670.20571360.17922607X-RAY DIFFRACTION100
1.5767-1.65980.20641370.17312572X-RAY DIFFRACTION100
1.6598-1.76380.19191510.16952583X-RAY DIFFRACTION100
1.7638-1.90.21531400.16962621X-RAY DIFFRACTION100
1.9-2.09120.19991370.16332579X-RAY DIFFRACTION100
2.0912-2.39380.21161370.17112627X-RAY DIFFRACTION100
2.3938-3.01570.19811270.17612609X-RAY DIFFRACTION100
3.0157-3.747750.18231260.14062608X-RAY DIFFRACTION100

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