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- PDB-3wib: Crystal structure of Y109W Mutant Haloalkane Dehalogenase DatA fr... -

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Basic information

Entry
Database: PDB / ID: 3wib
TitleCrystal structure of Y109W Mutant Haloalkane Dehalogenase DatA from Agrobacterium tumefaciens C58
ComponentsHaloalkane dehalogenase
KeywordsHYDROLASE / haloalkane dehalogenase / hydrolase fold family
Function / homology
Function and homology information


haloalkane dehalogenase / haloalkane dehalogenase activity
Similarity search - Function
Haloalkane dehalogenase, subfamily 2 / 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 speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsGuan, L.J. / Yabuki, H. / Okai, M. / Ohtsuka, J. / Tanokura, M.
CitationJournal: Appl.Microbiol.Biotechnol. / Year: 2014
Title: Crystal structure of the novel haloalkane dehalogenase DatA from Agrobacterium tumefaciens C58 reveals a special halide-stabilizing pair and enantioselectivity mechanism.
Authors: Guan, L. / Yabuki, H. / Okai, M. / Ohtsuka, J. / Tanokura, M.
History
DepositionSep 9, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Haloalkane dehalogenase
B: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,5305
Polymers68,9082
Non-polymers6223
Water3,225179
1
A: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8693
Polymers34,4541
Non-polymers4152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6612
Polymers34,4541
Non-polymers2071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)123.620, 123.620, 88.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number89
Space group name H-MP422

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Components

#1: Protein Haloalkane dehalogenase


Mass: 34453.949 Da / Num. of mol.: 2 / Mutation: Y115W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Strain: C58 / ATCC 33970 / Gene: dhaA, dha, Atu6064, AGR_pTi_130 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: Q8U671, haloalkane dehalogenase
#2: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.44 Å3/Da / Density % sol: 49.63 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 8.5
Details: 0.1M N-cyclohexyl-2-aminoethanesulfonic acid (CHES), 1.0M potassium sodium tartrate, 0.2M lithium sulfate, 0.1M manganese chloride, 1mM DTT, pH 8.5, EVAPORATION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 6, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→20 Å / Num. obs: 50218

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Processing

SoftwareName: REFMAC / Version: 5.7.0032 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→19.8 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.926 / SU B: 3.511 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23531 2552 5.1 %RANDOM
Rwork0.19371 ---
obs0.19578 47662 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.881 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å2-0 Å2-0 Å2
2--0.2 Å2-0 Å2
3----0.4 Å2
Refinement stepCycle: LAST / Resolution: 1.95→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4655 0 39 179 4873
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0194848
X-RAY DIFFRACTIONr_bond_other_d0.0010.024569
X-RAY DIFFRACTIONr_angle_refined_deg1.7861.9516618
X-RAY DIFFRACTIONr_angle_other_deg0.876310467
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3055580
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.01423.112241
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.9615731
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7391541
X-RAY DIFFRACTIONr_chiral_restr0.1110.2716
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215516
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021213
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
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_other
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_it2.3862.4712323
X-RAY DIFFRACTIONr_mcbond_other2.3852.472322
X-RAY DIFFRACTIONr_mcangle_it3.1493.692902
X-RAY DIFFRACTIONr_mcangle_other3.1493.6912903
X-RAY DIFFRACTIONr_scbond_it2.8242.692525
X-RAY DIFFRACTIONr_scbond_other2.8232.692526
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2113.9523717
X-RAY DIFFRACTIONr_long_range_B_refined5.33719.9355588
X-RAY DIFFRACTIONr_long_range_B_other5.32119.8995529
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 204 -
Rwork0.242 3449 -
obs--100 %

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