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- PDB-1k6e: COMPLEX OF HYDROLYTIC HALOALKANE DEHALOGENASE LINB FROM SPHINGOMO... -

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Basic information

Entry
Database: PDB / ID: 1k6e
TitleCOMPLEX OF HYDROLYTIC HALOALKANE DEHALOGENASE LINB FROM SPHINGOMONAS PAUCIMOBILIS UT26 WITH 1,2-PROPANEDIOL (PRODUCT OF DEHALOGENATION OF 1,2-DIBROMOPROPANE) AT 1.85A
ComponentsHALOALKANE DEHALOGENASE
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
1-BROMOPROPANE-2-OL / BROMIDE ION / S-1,2-PROPANEDIOL / Haloalkane dehalogenase / Haloalkane dehalogenase
Similarity search - Component
Biological speciesSphingomonas paucimobilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsStreltsov, V.A. / Prokop, Z. / Damborsky, J. / Nagata, Y. / Oakley, A. / 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 16, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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
Remark 600HETEROGEN BR(1001) AND CL(1003) ARE IN ALTERNATE CONFORMATIONS OF EACH OTHER. CL(1004) AND BR(1002) ...HETEROGEN BR(1001) AND CL(1003) ARE IN ALTERNATE CONFORMATIONS OF EACH OTHER. CL(1004) AND BR(1002) ARE IN ALTERNATE CONFORMATIONS OF EACH OTHER. PGO(2001) AND 1BP(2002) AND 1BP(2003) ARE IN ALTERNATE CONFORMATIONS OF EACH OTHER.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HALOALKANE DEHALOGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,67111
Polymers33,0131
Non-polymers65810
Water8,431468
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.410, 68.330, 80.980
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 HALOALKANE DEHALOGENASE / LINB / 1 / 3 / 4 / 6-TETRACHLORO-1 / 4-CYCLOHEXADIENE HYDROLASE


Mass: 33013.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas paucimobilis (bacteria) / Strain: UT26 / Plasmid: PMYLB1 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101
References: UniProt: P51698, UniProt: D4Z2G1*PLUS, haloalkane dehalogenase

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Non-polymers , 6 types, 478 molecules

#2: Chemical ChemComp-BR / BROMIDE ION


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


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-PGO / S-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#6: Chemical ChemComp-1BP / 1-BROMOPROPANE-2-OL


Mass: 138.991 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7BrO
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 468 / 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: 1.94 Å3/Da / Density % sol: 36.71 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: PEG 4000,magnesium chloride, TRIS, pH 8.20, VAPOR DIFFUSION, SITTING DROP, temperature 289.0K

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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: 1.85→34.69 Å / Num. obs: 21714 / % possible obs: 95.6 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 10.4 Å2 / Rmerge(I) obs: 0.117 / Net I/σ(I): 11.859
Reflection shellResolution: 1.85→1.98 Å / Redundancy: 4 % / Mean I/σ(I) obs: 4 / % possible all: 65

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Processing

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

1k5p


Resolution: 1.85→34.69 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: THE STRUCTURE WAS REFINED ALSO WITH XTALVIEW.
RfactorNum. reflection% reflectionSelection details
Rfree0.201 2155 9.9 %RANDOM
Rwork0.142 ---
obs0.142 21714 95.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 75.86 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 15.8 Å2
Baniso -1Baniso -2Baniso -3
1-3.66 Å20 Å20 Å2
2---3.02 Å20 Å2
3----0.64 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.85→34.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2327 0 22 468 2817
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.08
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.85→1.98 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 4
RfactorNum. reflection% reflection
Rfree0.227 389 10 %
Rwork0.191 3513 -
obs--65 %
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 DIFFRACTION5PGO_DRG.PARPGO_DRG.TOP

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