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- PDB-4wdq: Crystal structure of haloalkane dehalogenase LinB32 mutant (L177W... -

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Basic information

Entry
Database: PDB / ID: 4wdq
TitleCrystal structure of haloalkane dehalogenase LinB32 mutant (L177W) from Sphingobium japonicum UT26
ComponentsHaloalkane dehalogenase
KeywordsHYDROLASE / Protein Engineering
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 / Haloalkane dehalogenase
Similarity search - Component
Biological speciesSphingobium japonicum UT26S (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.58 Å
AuthorsDegtjarik, O. / Rezacova, P. / Chaloupkova, R. / Damborsky, J. / Kuta-Smatanova, I.
Funding support Czech Republic, 4items
OrganizationGrant numberCountry
Czech Academy of SciencesRVO 61388963 Czech Republic
Czech Academy of SciencesRVO 68378050 Czech Republic
Czech Science FoundationP207/12/0775 Czech Republic
Ministry of Education of Czech RepublicLO1214 Czech Republic
CitationJournal: Acs Catalysis / Year: 2016
Title: Crystal structure of haloalkane dehalogenase LinB mutant (L177W) from Sphingobium japonicum UT26
Authors: Degtjarik, O. / Rezacova, P. / Chaloupkova, R. / Damborsky, J. / Kuta-Smatanova, I.
History
DepositionSep 9, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2016Group: Database references
Revision 2.0Sep 6, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Derived calculations / Refinement description
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_distant_solvent_atoms / pdbx_struct_conn_angle / pdbx_validate_close_contact / software / struct_conn / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.occupancy / _pdbx_audit_support.funding_organization / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_site_gen.auth_seq_id
Revision 2.1Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.2Jan 10, 2024Group: 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 / struct_conn
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.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

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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)33,5076
Polymers33,3631
Non-polymers1445
Water12,863714
1


  • Idetical with deposited unit
  • defined by software
  • MONOMERIC
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area520 Å2
ΔGint-34 kcal/mol
Surface area11650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.729, 68.490, 81.055
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 hydrolase / 4-TCDN chlorohydrolase


Mass: 33362.750 Da / Num. of mol.: 1 / Mutation: L177W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingobium japonicum UT26S (bacteria) / Gene: linB / Production host: Escherichia coli (E. coli)
References: UniProt: P51698, UniProt: D4Z2G1*PLUS, haloalkane dehalogenase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 714 / 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: 36.72 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: 0.1M MES; 0.2M MgCl2; 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8123 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 19, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8123 Å / Relative weight: 1
ReflectionResolution: 1.57→50 Å / Num. all: 37131 / Num. obs: 36500 / % possible obs: 98.3 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.094 / Χ2: 0.908 / Net I/av σ(I): 20.75 / Net I/σ(I): 6.5 / Num. measured all: 251483
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.57-1.635.40.28531110.69585.2
1.63-1.696.80.25736370.482100
1.69-1.777.10.21536690.515100
1.77-1.867.10.17736620.544100
1.86-1.987.10.1736701.02100
1.98-2.137.10.10736900.724100
2.13-2.357.10.12136901.351100
2.35-2.687.10.07637330.839100
2.68-3.3870.05937621.033100
3.38-506.70.06338761.7998.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.75 Å40.53 Å
Translation1.75 Å40.53 Å

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Processing

Software
NameVersionClassification
HKL-3000data reduction
MOLREP6phasing
REFMAC5.3.0037refinement
PDB_EXTRACT3.14data extraction
Cootmodel building
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CV2

1cv2


Resolution: 1.58→40.49 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.937 / SU B: 1.78 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2057 1802 5 %RANDOM
Rwork0.1596 34335 --
obs0.1619 36137 98.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 78.67 Å2 / Biso mean: 12.777 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 1.58→40.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2353 0 5 714 3072
Biso mean--9.99 27.29 -
Num. residues----297
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222483
X-RAY DIFFRACTIONr_angle_refined_deg1.3991.9493389
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9935314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.323.023129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.89915394
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6921526
X-RAY DIFFRACTIONr_chiral_restr0.0970.2349
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021987
X-RAY DIFFRACTIONr_nbd_refined0.2030.21196
X-RAY DIFFRACTIONr_nbtor_refined0.3140.21658
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2586
X-RAY DIFFRACTIONr_metal_ion_refined0.0160.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1840.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1780.2142
X-RAY DIFFRACTIONr_mcbond_it0.7161.51550
X-RAY DIFFRACTIONr_mcangle_it1.00522424
X-RAY DIFFRACTIONr_scbond_it1.76231076
X-RAY DIFFRACTIONr_scangle_it2.6864.5956
LS refinement shellResolution: 1.576→1.617 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 125 -
Rwork0.189 2404 -
all-2529 -
obs--94.23 %

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