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- PDB-7wan: Crystal structure of HaloTag complexed with UL2 -

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Basic information

Entry
Database: PDB / ID: 7wan
TitleCrystal structure of HaloTag complexed with UL2
ComponentsHaloalkane dehalogenase
KeywordsHYDROLASE / halotag / haloalkane dehalogenase
Function / homology
Function and homology information


haloalkane dehalogenase / haloalkane dehalogenase activity / response to toxic substance / membrane
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
Chem-8MS / Haloalkane dehalogenase
Similarity search - Component
Biological speciesRhodococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.284 Å
AuthorsPratyush, M. / Kang, M. / Lee, H. / Lee, C. / Rhee, H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Chem Sci / Year: 2022
Title: A chemical tool for blue light-inducible proximity photo-crosslinking in live cells.
Authors: Mishra, P.K. / Kang, M.G. / Lee, H. / Kim, S. / Choi, S. / Sharma, N. / Park, C.M. / Ko, J. / Lee, C. / Seo, J.K. / Rhee, H.W.
History
DepositionDec 14, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)34,1363
Polymers33,7161
Non-polymers4202
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-12 kcal/mol
Surface area11050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.906, 72.764, 44.432
Angle α, β, γ (deg.)90.000, 109.300, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Haloalkane dehalogenase


Mass: 33716.398 Da / Num. of mol.: 1
Mutation: S2A, L47V, S58T, D78G, Y87F, L88M, C128F, A155T, E160K, A167V, A172T, K175C, C176G, K195N, A224E, N227D, E257K, T264A, H272N, Y273L, P291S, A292T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus sp. (bacteria) / Gene: dhaA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A3G3, haloalkane dehalogenase
#2: Chemical ChemComp-8MS / (R)-[4-(2-azanylhydrazinyl)phenyl]-[2-[2-(2-hexoxyethoxy)ethoxy]ethylamino]methanol


Mass: 384.514 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H36N4O4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 1.99 Å3/Da / Density % sol: 38.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 25% PEG 8K, 0.1 M MES pH 6.5, 0.2 M Na-acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.28→50 Å / Num. obs: 11723 / % possible obs: 97.9 % / Redundancy: 3 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 12.8
Reflection shellResolution: 2.3→2.34 Å / Rmerge(I) obs: 0.289 / Num. unique obs: 551

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Y2X

5y2x


Resolution: 2.284→32.284 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 22.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2283 587 5.01 %
Rwork0.1778 11126 -
obs0.1803 11713 97.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 67.98 Å2 / Biso mean: 21.4749 Å2 / Biso min: 10.62 Å2
Refinement stepCycle: final / Resolution: 2.284→32.284 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2326 0 28 96 2450
Biso mean--23.44 23.42 -
Num. residues----290
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.284-2.51370.28011410.2169260392
2.5137-2.87720.24311430.2101280698
2.8772-3.62420.23041500.1785282699
3.6242-32.2840.20181530.14922891100

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