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- PDB-2bfn: The crystal structure of the complex of the haloalkane dehalogena... -

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Basic information

Entry
Database: PDB / ID: 2bfn
TitleThe crystal structure of the complex of the haloalkane dehalogenase LinB with the product of dehalogenation reaction 1,2-dichloropropane.
ComponentsHALOGENALKANE DEHALOGENASE
KeywordsHYDROLASE / HALOALKANE DEHALOGENASE LINB / 1\ / 2\ / 3-TRICHLOROPROPANE / 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
(2S)-2,3-DICHLOROPROPAN-1-OL / Haloalkane dehalogenase / Haloalkane dehalogenase
Similarity search - Component
Biological speciesSPHINGOMONAS PAUCIMOBILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsBanas, P. / Otyepka, M. / Jerabek, P. / Vevodova, J. / Bohac, M. / Damborsky, J.
Citation
Journal: Appl.Environ.Microbiol. / Year: 2007
Title: Weak Activity of Haloalkane Dehalogenase Linb with 1,2,3-Trichloropropane Revealed by X-Ray Crystallography and Microcalorimetry
Authors: Minincova, M. / Prokop, Z. / Vevodova, J. / Nagata, Y. / Damborsky, J.
#1: Journal: Biochemistry / Year: 2000
Title: Crystal Structure of the Haloalkane Dehalogenase from Sphingomonas Paucimobilis Ut26
Authors: Marek, J. / Vevodova, J. / Kuta Smatanova, I. / Nagata, Y. / Svensson, L.A. / Newman, J. / Takagi, M. / Damborsky, J.
History
DepositionDec 9, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HALOGENALKANE DEHALOGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4296
Polymers33,1451
Non-polymers2855
Water6,071337
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)50.571, 72.142, 73.311
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HALOGENALKANE DEHALOGENASE / 1 / 3 / 4 / 6-TETRACHLORO-1 / 4-CYCLOHEXADIENE HYDROLASE / 1 / 4-TCDN CHLOROHYDROLASE


Mass: 33144.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SPHINGOMONAS PAUCIMOBILIS (bacteria) / Strain: UT26
References: UniProt: P51698, UniProt: D4Z2G1*PLUS, haloalkane dehalogenase
#2: Chemical ChemComp-D2P / (2S)-2,3-DICHLOROPROPAN-1-OL


Mass: 128.985 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6Cl2O
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.93
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 3, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 36132 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 9 % / Rmerge(I) obs: 0.05
Reflection shellResolution: 1.6→1.66 Å / Rmerge(I) obs: 0.17 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CV2

1cv2


Resolution: 1.6→72.55 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.211 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.171 1796 5.08 %RANDOM
Rwork0.149 ---
obs0.15 34207 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 8.16 Å2
Baniso -1Baniso -2Baniso -3
1--0.047 Å20 Å20 Å2
2---0.273 Å20 Å2
3---0.319 Å2
Refinement stepCycle: LAST / Resolution: 1.6→72.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2322 0 10 337 2669
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222457
X-RAY DIFFRACTIONr_bond_other_d0.0020.022217
X-RAY DIFFRACTIONr_angle_refined_deg1.4781.9573339
X-RAY DIFFRACTIONr_angle_other_deg0.92235132
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr
X-RAY DIFFRACTIONr_gen_planes_refined
X-RAY DIFFRACTIONr_gen_planes_other0.0120.02533
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other0.2540.22689
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0830.21418
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2720.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.195 121
Rwork0.153 2464

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