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Yorodumi- PDB-8b5k: Structure of haloalkane dehalogenase DmmarA from Mycobacterium ma... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8b5k | ||||||
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Title | Structure of haloalkane dehalogenase DmmarA from Mycobacterium marinum at pH 6.5 | ||||||
Components | Haloalkane dehalogenase DhaA | ||||||
Keywords | HYDROLASE / haloalkane dehalogenase / enzyme | ||||||
Function / homology | Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / hydrolase activity / FORMIC ACID / Haloalkane dehalogenase DhaA Function and homology information | ||||||
Biological species | Mycobacterium marinum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.849 Å | ||||||
Authors | Snajdarova, K. / Marek, M. | ||||||
Funding support | Czech Republic, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2023 Title: Atypical homodimerization revealed by the structure of the (S)-enantioselective haloalkane dehalogenase DmmarA from Mycobacterium marinum. Authors: Snajdarova, K. / Marques, S.M. / Damborsky, J. / Bednar, D. / Marek, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8b5k.cif.gz | 469.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8b5k.ent.gz | 387.3 KB | Display | PDB format |
PDBx/mmJSON format | 8b5k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8b5k_validation.pdf.gz | 4.6 MB | Display | wwPDB validaton report |
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Full document | 8b5k_full_validation.pdf.gz | 4.6 MB | Display | |
Data in XML | 8b5k_validation.xml.gz | 46.5 KB | Display | |
Data in CIF | 8b5k_validation.cif.gz | 66.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b5/8b5k ftp://data.pdbj.org/pub/pdb/validation_reports/b5/8b5k | HTTPS FTP |
-Related structure data
Related structure data | 8b5oC 1mj5S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 33226.438 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium marinum (bacteria) / Gene: dhaA, MMAR_4113 / Production host: Escherichia coli (E. coli) / References: UniProt: B2HR89 |
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-Non-polymers , 5 types, 597 molecules
#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-FMT / #4: Chemical | ChemComp-TRS / | #5: Chemical | ChemComp-B3P / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.36 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: potassium phosphate, Bis-Tris propane, PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 13, 2019 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.849→48.37 Å / Num. obs: 97565 / % possible obs: 99.8 % / Redundancy: 6.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.063 / Rrim(I) all: 0.163 / Net I/σ(I): 10 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Resolution: 1.85→1.88 Å
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1MJ5 Resolution: 1.849→44.073 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.92 / 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: 90.71 Å2 / Biso mean: 28.1315 Å2 / Biso min: 12.94 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.849→44.073 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 36.2516 Å / Origin y: -6.9044 Å / Origin z: 26.7575 Å
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Refinement TLS group |
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