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- PDB-7wam: Crystal structure of HaloTag complexed with VL1 -

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Basic information

Entry
Database: PDB / ID: 7wam
TitleCrystal structure of HaloTag complexed with VL1
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-8MH / Haloalkane dehalogenase
Similarity search - Component
Biological speciesRhodococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 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)34,2373
Polymers33,7161
Non-polymers5212
Water6,395355
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-13 kcal/mol
Surface area11420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.078, 63.078, 164.112
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-703-

HOH

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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-8MH / 3-[6-(2-azanylhydrazinyl)-1,3-bis(oxidanylidene)benzo[de]isoquinolin-2-yl]-N-[2-(2-hexoxyethoxy)ethyl]propanamide


Mass: 485.576 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H35N5O5
#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.: 355 / 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: 2.42 Å3/Da / Density % sol: 49.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1.2 M Ammonium sulfate, 0.1 M citric acid pH 5.3, and 1% MPD

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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: 0.9796 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: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.49→50 Å / Num. obs: 54493 / % possible obs: 98.7 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 29.1
Reflection shellResolution: 1.49→1.52 Å / Rmerge(I) obs: 0.799 / Num. unique obs: 2634

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Y2X

5y2x


Resolution: 1.49→27.802 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1883 2000 3.67 %
Rwork0.1486 52433 -
obs0.1501 54433 98.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.11 Å2 / Biso mean: 21.5987 Å2 / Biso min: 8.32 Å2
Refinement stepCycle: final / Resolution: 1.49→27.802 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2353 0 36 355 2744
Biso mean--49.12 33.77 -
Num. residues----294
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132470
X-RAY DIFFRACTIONf_angle_d1.4933374
X-RAY DIFFRACTIONf_chiral_restr0.062354
X-RAY DIFFRACTIONf_plane_restr0.008439
X-RAY DIFFRACTIONf_dihedral_angle_d13.192901
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.49-1.52720.28181380.2037360297
1.5272-1.56850.25761400.1798368798
1.5685-1.61470.20931390.1553364498
1.6147-1.66680.20071390.1498365398
1.6668-1.72630.19531410.1417368099
1.7263-1.79540.19841420.1414372099
1.7954-1.87710.16811400.1403369399
1.8771-1.97610.18491440.1379374499
1.9761-2.09980.17191420.1372373599
2.0998-2.26190.20781440.1417376799
2.2619-2.48940.21440.14653789100
2.4894-2.84930.1931450.1573382099
2.8493-3.58860.17141480.15293876100
3.5886-27.8020.17241540.1453402398

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