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- PDB-6s06: Crystal structure of haloalkane dehalogenase LinB D147C+L177C mut... -

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Basic information

Entry
Database: PDB / ID: 6s06
TitleCrystal structure of haloalkane dehalogenase LinB D147C+L177C mutant (LinB73) from Sphingobium japonicum UT26
ComponentsHaloalkane dehalogenase
KeywordsHYDROLASE / haloalkane dehalogenase / protein engineering / mutant
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
Haloalkane dehalogenase
Similarity search - Component
Biological speciesSphingobium japonicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsIermak, I. / Mesters, J.R. / Degtjarik, O. / Chaloupkova, R. / Kuta Smatanova, I.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Czech Science FoundationGACR (17-24321S) Czech Republic
CitationJournal: Catalysts / Year: 2021
Title: Description of Transport Tunnel in Haloalkane Dehalogenase Variant LinB D147C+L177C from Sphingobium japonicum
Authors: Iermak, I. / Degtjarik, O. / Havlickova, P. / Kuty, M. / Chaloupkova, R. / Damborsky, J. / Prudnikova, T. / Kuta Smatanova, I.
History
DepositionJun 14, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.2Jan 24, 2024Group: 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
A: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0605
Polymers33,9521
Non-polymers1084
Water4,197233
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area310 Å2
ΔGint-20 kcal/mol
Surface area11000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.724, 68.709, 80.614
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Haloalkane dehalogenase / / 1 / 3 / 4 / 6-tetrachloro-1 / 4-cyclohexadiene halidohydrolase / 4-TCDN halidohydrolase


Mass: 33951.520 Da / Num. of mol.: 1 / Mutation: D147C, L177C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingobium japonicum (strain DSM 16413 / CCM 7287 / MTCC 6362 / UT26 / NBRC 101211 / UT26S) (bacteria)
Strain: DSM 16413 / CCM 7287 / MTCC 6362 / UT26 / NBRC 101211 / UT26S
Gene: linB, SJA_C1-19590 / Production host: Escherichia coli (E. coli) / References: UniProt: D4Z2G1, haloalkane dehalogenase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.83 Å3/Da / Density % sol: 32.7 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.2 M magnesium chloride, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.15→50 Å / Num. obs: 88614 / % possible obs: 99.6 % / Redundancy: 6.21 % / Rrim(I) all: 0.069 / Net I/σ(I): 14.93
Reflection shellResolution: 1.15→1.22 Å / Num. unique obs: 13949 / Rrim(I) all: 0.67 / % possible all: 98.4

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Processing

Software
NameVersionClassification
SHELXLVersion 2014/7refinement
MxCuBEdata collection
XDSJanuary 10, 2014data reduction
XDSJanuary 10, 2014data scaling
MOLREP11.2.08phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CV2

1cv2


Resolution: 1.15→10 Å / Cross valid method: FREE R-VALUE / σ(F): 0
Details: LEAST SQUARES ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF)
RfactorNum. reflection% reflectionSelection details
Rfree0.2302 --RANDOM
Rwork0.1759 ---
obs-84016 99.9 %-
Displacement parametersBiso max: 63.82 Å2 / Biso mean: 15.7159 Å2 / Biso min: 7.23 Å2
Refinement stepCycle: final / Resolution: 1.15→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2272 0 4 233 2509
Biso mean--18.21 25.27 -
Num. residues----294
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d205
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.004
X-RAY DIFFRACTIONs_zero_chiral_vol84
X-RAY DIFFRACTIONs_non_zero_chiral_vol2
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.026
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.046
X-RAY DIFFRACTIONs_approx_iso_adps0

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