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- PDB-3a76: The crystal structure of LinA -

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Basic information

Entry
Database: PDB / ID: 3a76
TitleThe crystal structure of LinA
ComponentsGamma-hexachlorocyclohexane dehydrochlorinase
KeywordsLYASE / barrel fold / Detoxification
Function / homology
Function and homology information


Lyases; Carbon-halide lyases / response to toxic substance / periplasmic space / lyase activity
Similarity search - Function
SnoaL-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
Similarity search - Domain/homology
SPERMIDINE / Gamma-hexachlorocyclohexane dehydrochlorinase
Similarity search - Component
Biological speciesSphingomonas paucimobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.25 Å
AuthorsOkai, M. / Kubota, K. / Fukuda, M. / Nagata, Y. / Nagata, K. / Tanokura, M.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Crystal structure of g-hexachlorocyclohexane dehydrochlorinase LinA from Sphingobium japonicum UT26
Authors: Okai, M. / Kubota, K. / Fukuda, M. / Nagata, Y. / Nagata, K. / Tanokura, M.
History
DepositionSep 15, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Gamma-hexachlorocyclohexane dehydrochlorinase
B: Gamma-hexachlorocyclohexane dehydrochlorinase
C: Gamma-hexachlorocyclohexane dehydrochlorinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3059
Polymers58,5933
Non-polymers7126
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8060 Å2
ΔGint-36 kcal/mol
Surface area18800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.921, 68.921, 101.892
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Gamma-hexachlorocyclohexane dehydrochlorinase / Gamma-HCH dehydrochlorinase


Mass: 19530.924 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas paucimobilis (bacteria) / Strain: UT26 / Gene: linA / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: P51697, Lyases; Carbon-halide lyases
#2: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


Mass: 145.246 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H19N3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 40.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 3, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→20 Å / Num. obs: 22188 / % possible obs: 98 %
Reflection shellResolution: 2.25→2.33 Å / % possible all: 89

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.25→20 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.92 / SU B: 16.872 / SU ML: 0.215 / Cross valid method: THROUGHOUT / ESU R: 0.39 / ESU R Free: 0.262 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26964 1138 5.1 %RANDOM
Rwork0.21649 ---
obs0.21924 20981 97.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.051 Å2
Baniso -1Baniso -2Baniso -3
1-1.66 Å20 Å20 Å2
2--1.66 Å20 Å2
3----3.32 Å2
Refinement stepCycle: LAST / Resolution: 2.25→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3578 0 48 93 3719
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223709
X-RAY DIFFRACTIONr_angle_refined_deg1.3291.9465022
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1955449
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.66623.978181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.02315584
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9011524
X-RAY DIFFRACTIONr_chiral_restr0.0910.2536
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022840
X-RAY DIFFRACTIONr_nbd_refined0.220.21556
X-RAY DIFFRACTIONr_nbtor_refined0.3080.22406
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2180
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2190.2101
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2050.211
X-RAY DIFFRACTIONr_mcbond_it0.771.52297
X-RAY DIFFRACTIONr_mcangle_it0.88623571
X-RAY DIFFRACTIONr_scbond_it1.49531649
X-RAY DIFFRACTIONr_scangle_it2.1334.51451
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.404 76 -
Rwork0.279 1397 -
obs--88.52 %

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