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Yorodumi- PDB-2fvg: Crystal structure of Endoglucanase (tm1049) from THERMOTOGA MARIT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2fvg | ||||||
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Title | Crystal structure of Endoglucanase (tm1049) from THERMOTOGA MARITIMA at 2.01 A resolution | ||||||
Components | endoglucanaseCellulase | ||||||
Keywords | HYDROLASE / tm1049 / Endoglucanase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.01 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of Endoglucanase (tm1049) from THERMOTOGA MARITIMA at 2.01 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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Remark 999 | SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fvg.cif.gz | 73.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fvg.ent.gz | 56.4 KB | Display | PDB format |
PDBx/mmJSON format | 2fvg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fv/2fvg ftp://data.pdbj.org/pub/pdb/validation_reports/fv/2fvg | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 37669.066 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: tm1049 / Plasmid: MH4TEVa / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q9X0D9 | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.46 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 10.5 Details: 0.2M NaCl, 20.0% PEG-8000, 0.1M CAPS pH 10.5 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.01→29.5 Å / Num. obs: 22815 / % possible obs: 85.9 % / Redundancy: 3.49 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 11.06 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.01→29.5 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.945 / SU B: 10.396 / SU ML: 0.138 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.195 / ESU R Free: 0.173 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. THE PEPTIDE BOND BETWEEN ASP 166 AND ASP 167 NEAR THE PUTATIV ACTIVE SITE WAS MODELED IN THE CIS CONFORMATION 3.ELECTRON DENSITIES ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. THE PEPTIDE BOND BETWEEN ASP 166 AND ASP 167 NEAR THE PUTATIV ACTIVE SITE WAS MODELED IN THE CIS CONFORMATION 3.ELECTRON DENSITIES BETWEEN RESIDUE RANGES 109-119,198-202, AND 279-291 WERE DISORDERED; THEREFORE, THESE REGIONS WERE NOT MODELED. 4. THE ELECTRON DENSITY MAP SHOWS SUBSTANTIAL DIFFERENCE DENSITY THE VICINITY OF LYS 249.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.477 Å2
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Refinement step | Cycle: LAST / Resolution: 2.01→29.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.01→2.059 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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