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- PDB-3s5c: Crystal Structure of a Hexachlorocyclohexane dehydrochlorinase (L... -

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Basic information

Entry
Database: PDB / ID: 3s5c
TitleCrystal Structure of a Hexachlorocyclohexane dehydrochlorinase (LinA) Type2
ComponentsLinA
KeywordsTRANSFERASE / hexachlorocyclohexane 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 / LinA
Function and homology information
Biological speciesuncultured organism (environmental samples)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsKukshal, V. / Macwan, A.S. / Kumar, A. / Ramachandran, R.
CitationJournal: Plos One / Year: 2012
Title: Crystal structure of the hexachlorocyclohexane dehydrochlorinase (LinA-type2): mutational analysis, thermostability and enantioselectivity
Authors: Macwan, A.S. / Kukshal, V. / Srivastava, N. / Javed, S. / Kumar, A. / Ramachandran, R.
History
DepositionMay 23, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2013Group: Database references
Revision 1.2Nov 1, 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
B: LinA
A: LinA
C: LinA
D: LinA
E: LinA
F: LinA
G: LinA


Theoretical massNumber of molelcules
Total (without water)121,3487
Polymers121,3487
Non-polymers00
Water00
1
B: LinA

B: LinA

B: LinA


Theoretical massNumber of molelcules
Total (without water)52,0063
Polymers52,0063
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area6420 Å2
ΔGint-35 kcal/mol
Surface area17870 Å2
MethodPISA
2
A: LinA
C: LinA
E: LinA


Theoretical massNumber of molelcules
Total (without water)52,0063
Polymers52,0063
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6710 Å2
ΔGint-40 kcal/mol
Surface area18980 Å2
MethodPISA
3
D: LinA
F: LinA
G: LinA


Theoretical massNumber of molelcules
Total (without water)52,0063
Polymers52,0063
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6530 Å2
ΔGint-39 kcal/mol
Surface area18820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.529, 162.529, 186.282
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein
LinA / Hexachlorocyclohexane dehydrochlorinase


Mass: 17335.467 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Details: The sequence was isolated from bacteria from a soil sample, metagenome source. It shows very high identity with the LinA from Sphingobium japonicum UT26 whose sequence is in PDB id: 3A76.
Source: (gene. exp.) uncultured organism (environmental samples)
Plasmid: pET-26b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B5ANU3, Lyases; Carbon-halide lyases

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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: 2.93 Å3/Da / Density % sol: 57.97 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 2% PEG 8000,0.1 M trisodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 24, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.5→30.72 Å / Num. all: 18690 / Num. obs: 18690 / % possible obs: 99.1 % / Observed criterion σ(F): 8.7 / Observed criterion σ(I): 8.7 / Rmerge(I) obs: 0.239
Reflection shellResolution: 3.5→3.69 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.663 / Mean I/σ(I) obs: 2.7 / Num. unique all: 2656 / % possible all: 98.5

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3A76

3a76


Resolution: 3.5→30.72 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.839 / Occupancy max: 1 / Occupancy min: 1 / SU B: 31.762 / SU ML: 0.486 / Cross valid method: THROUGHOUT / ESU R Free: 0.662 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2708 969 5.2 %RANDOM
Rwork0.1788 ---
all0.1834 18669 --
obs0.1834 18669 98.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 105.35 Å2 / Biso mean: 50.1874 Å2 / Biso min: 18.29 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 3.5→30.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8266 0 0 0 8266
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0228472
X-RAY DIFFRACTIONr_angle_refined_deg1.3761.93811526
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.69651042
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.15324.296419
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.256151326
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2751549
X-RAY DIFFRACTIONr_chiral_restr0.090.21231
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216593
X-RAY DIFFRACTIONr_mcbond_it0.491.55171
X-RAY DIFFRACTIONr_mcangle_it0.93728254
X-RAY DIFFRACTIONr_scbond_it0.97233301
X-RAY DIFFRACTIONr_scangle_it1.7444.53272
LS refinement shellResolution: 3.5→3.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 78 -
Rwork0.23 1245 -
all-1323 -
obs--97.71 %

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