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- PDB-1k63: Complex of hydrolytic haloalkane dehalogenase linb from sphingomo... -

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Basic information

Entry
Database: PDB / ID: 1k63
TitleComplex of hydrolytic haloalkane dehalogenase linb from sphingomonas paucimobilis with UT26 2-BROMO-2-PROPENE-1-OL at 1.8A resolution
Components1,3,4,6-tetrachloro-1,4-cyclohexadiene hydrolase
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 / 2-BROMO-2-PROPENE-1-OL / Haloalkane dehalogenase / Haloalkane dehalogenase
Similarity search - Component
Biological speciesSphingomonas paucimobilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsStreltsov, V.A. / Damborsky, J. / Wilce, M.C.J.
CitationJournal: Biochemistry / Year: 2003
Title: Haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26: X-ray crystallographic studies of dehalogenation of brominated substrates
Authors: Streltsov, V.A. / Prokop, Z. / Damborsky, J. / Nagata, Y. / Oakley, A. / Wilce, M.C.J.
History
DepositionOct 15, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 26, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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 / pdbx_struct_conn_angle / software / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _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: 1,3,4,6-tetrachloro-1,4-cyclohexadiene hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,59110
Polymers33,0131
Non-polymers5789
Water8,323462
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.180, 68.951, 80.681
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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 / Haloalkane Dehalogenase Linb


Mass: 33013.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas paucimobilis (bacteria) / Plasmid: PMYLB1 / Production host: Escherichia coli (E. coli)
References: UniProt: P51698, UniProt: D4Z2G1*PLUS, haloalkane dehalogenase

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Non-polymers , 5 types, 471 molecules

#2: Chemical ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-BRP / 2-BROMO-2-PROPENE-1-OL


Mass: 136.975 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5BrO
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 462 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsBR(1001) AND CL(1003) ARE IN ALTERNATE CONFORMATIONS OF EACH OTHER. CL(1004) AND BR(1002) ARE IN ...BR(1001) AND CL(1003) ARE IN ALTERNATE CONFORMATIONS OF EACH OTHER. CL(1004) AND BR(1002) ARE IN ALTERNATE CONFORMATIONS OF EACH OTHER. BRP(2001) AND BRP(2002) ARE IN ALTERNATE CONFORMATIONS OF EACH OTHER.

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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: 1.63 Å3/Da / Density % sol: 24.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: PEG 4000, magnesium chloride, TRIS , pH 8.20, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54179
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 2001 / Details: MONOCHROMATOR AND MIRRORS
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 1.8→27.8 Å / Num. all: 23055 / Num. obs: 23055 / % possible obs: 93.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 7.2 Å2 / Rmerge(I) obs: 0.117 / Net I/σ(I): 11.859
Reflection shellResolution: 1.8→1.98 Å / Redundancy: 4 % / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 4.7 / Num. unique all: 4506 / % possible all: 83.5

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Processing

Software
NameClassification
MAR345data collection
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1K5P

1k5p


Resolution: 1.8→27.8 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 365901.69 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Details: The structure was refined also with XTALVIEW.
RfactorNum. reflection% reflectionSelection details
Rfree0.2003 2278 9.9 %RANDOM
Rwork0.1413 ---
all0.1413 23055 --
obs0.1413 23055 93.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 77.76 Å2 / ksol: 0.374018 e/Å3
Displacement parametersBiso mean: 12 Å2
Baniso -1Baniso -2Baniso -3
1-1.78 Å20 Å20 Å2
2---1.31 Å20 Å2
3----0.47 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.14 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.8→27.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2328 0 17 462 2807
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_improper_angle_d1.1
LS refinement shellResolution: 1.8→1.98 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 4
RfactorNum. reflection% reflection
Rfree0.271 527 10.5 %
Rwork0.202 4506 -
obs-4506 83.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5BRP.PARAMBRP.TOP

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