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Yorodumi- PDB-6lvw: Polyextremophilic Beta-galactosidase from the Antarctic haloarcha... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6lvw | ||||||
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Title | Polyextremophilic Beta-galactosidase from the Antarctic haloarchaeon Halorubrum lacusprofundi | ||||||
Components | Beta-galactosidase Bga | ||||||
Keywords | HYDROLASE / polyextremophilic enzyme / halophile / psychrophile / extremozyme / extremophile / SUGAR BINDING PROTEIN | ||||||
Function / homology | Function and homology information beta-galactosidase complex / beta-galactosidase / beta-galactosidase activity / carbohydrate metabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | Halorubrum lacusprofundi | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.493 Å | ||||||
Authors | Muhammad, R. / Arold, S.T. | ||||||
Citation | Journal: Microorganisms / Year: 2020 Title: Understanding High-Salt and Cold Adaptation of a Polyextremophilic Enzyme. Authors: Karan, R. / Mathew, S. / Muhammad, R. / Bautista, D.B. / Vogler, M. / Eppinger, J. / Oliva, R. / Cavallo, L. / Arold, S.T. / Rueping, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lvw.cif.gz | 281.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lvw.ent.gz | 228.6 KB | Display | PDB format |
PDBx/mmJSON format | 6lvw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6lvw_validation.pdf.gz | 442.1 KB | Display | wwPDB validaton report |
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Full document | 6lvw_full_validation.pdf.gz | 467.2 KB | Display | |
Data in XML | 6lvw_validation.xml.gz | 27.3 KB | Display | |
Data in CIF | 6lvw_validation.cif.gz | 36.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lv/6lvw ftp://data.pdbj.org/pub/pdb/validation_reports/lv/6lvw | HTTPS FTP |
-Related structure data
Related structure data | 1kwgS S: Starting model for refinement |
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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: 78136.375 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Halorubrum lacusprofundi (strain ATCC 49239 / DSM 5036 / JCM 8891 / ACAM 34) (archaea) Strain: ATCC 49239 / DSM 5036 / JCM 8891 / ACAM 34 / Gene: Hlac_2868 / Production host: Haloferax volcanii (archaea) / References: UniProt: B9LW38, beta-galactosidase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-MG / |
#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: 2.55 Å3/Da / Density % sol: 51.68 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 85 mM Tris-HCl (pH 8.5), 142 mM MgCl2, 2.78 M 1,6-hexanediol, 450 mM NDSB-195 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 8, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.49→50.07 Å / Num. obs: 27127 / % possible obs: 99.3 % / Redundancy: 19.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.034 / Rrim(I) all: 0.153 / Net I/σ(I): 15 / Num. measured all: 539186 / Scaling rejects: 7 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1KWG Resolution: 2.493→34.357 Å / SU ML: 0.59 / Cross valid method: THROUGHOUT / σ(F): 0.01 / Phase error: 44.65
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 251.44 Å2 / Biso mean: 100.9852 Å2 / Biso min: 39.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.493→34.357 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: 18.2566 Å / Origin y: 37.2514 Å / Origin z: 2.3014 Å
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Refinement TLS group | Selection details: all |