+Open data
-Basic information
Entry | Database: PDB / ID: 7wan | ||||||
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Title | Crystal structure of HaloTag complexed with UL2 | ||||||
Components | Haloalkane dehalogenase | ||||||
Keywords | HYDROLASE / halotag / haloalkane dehalogenase | ||||||
Function / homology | Function and homology information haloalkane dehalogenase / haloalkane dehalogenase activity / response to toxic substance Similarity search - Function | ||||||
Biological species | Rhodococcus sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.284 Å | ||||||
Authors | Pratyush, M. / Kang, M. / Lee, H. / Lee, C. / Rhee, H. | ||||||
Funding support | 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wan.cif.gz | 76.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wan.ent.gz | 53.8 KB | Display | PDB format |
PDBx/mmJSON format | 7wan.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7wan_validation.pdf.gz | 604.4 KB | Display | wwPDB validaton report |
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Full document | 7wan_full_validation.pdf.gz | 605.7 KB | Display | |
Data in XML | 7wan_validation.xml.gz | 13.4 KB | Display | |
Data in CIF | 7wan_validation.cif.gz | 18.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wa/7wan ftp://data.pdbj.org/pub/pdb/validation_reports/wa/7wan | HTTPS FTP |
-Related structure data
Related structure data | 7wamC 5y2xS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 |
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#2: Chemical | ChemComp-8MS / ( |
#3: Chemical | ChemComp-CL / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.09 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 25% PEG 8K, 0.1 M MES pH 6.5, 0.2 M Na-acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 2, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97933 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 2.3→2.34 Å / Rmerge(I) obs: 0.289 / Num. unique obs: 551 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 67.98 Å2 / Biso mean: 21.4749 Å2 / Biso min: 10.62 Å2 | ||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.284→32.284 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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