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Yorodumi- PDB-2b8m: Crystal structure of a rmlc-like cupin family protein with a doub... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2b8m | ||||||
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Title | Crystal structure of a rmlc-like cupin family protein with a double-stranded beta-helix fold (mj0764) from methanocaldococcus jannaschii at 1.70 A resolution | ||||||
Components | Hypothetical protein MJ0764Hypothesis | ||||||
Keywords | UNKNOWN FUNCTION / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 | ||||||
Function / homology | Cupin 1 / Cupin / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta / Uncharacterized protein MJ0764 Function and homology information | ||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of (1499583) from METHANOCOCCUS JANNASCHII at 1.70 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 GLY-0 followed by residues 1-116 of the 1499583 gene target. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2b8m.cif.gz | 37.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2b8m.ent.gz | 28 KB | Display | PDB format |
PDBx/mmJSON format | 2b8m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b8/2b8m ftp://data.pdbj.org/pub/pdb/validation_reports/b8/2b8m | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 13833.426 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Gene: 1499583 / Plasmid: HK100::SpeedET / Production host: Escherichia coli (E. coli) / References: UniProt: Q58174 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-CL / | #4: Chemical | #5: 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: 1.91 Å3/Da / Density % sol: 39.7 % |
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Crystal grow | Temperature: 277 K / pH: 6 Details: 0.2M (NH4)2SO4, 20.0% PEG-3350, No Buffer, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K, pH 6 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9796, 0.9797, 1.0000 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 9, 2005 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.7→29.08 Å / Num. all: 12925 / Num. obs: 12267 / % possible obs: 99.3 % / Redundancy: 3.48 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 7.84 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Rmerge(I) obs: 0.527 / Diffraction-ID: 1
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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: 1.7→29.08 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.918 / SU ML: 0.067 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.104 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ELECTRON DENSITY IS DISORDERED AT THE C-TERMINUS, THEREFORE, THE STRUCTURE WAS NOT MODELED IN THIS REGION 4. ELECTRON DENSITY BETWEEN THE SIDECHAINS OF HIS 25 AND HIS 49 ON SYMMETRY-RELATED SUBUNITS WAS MODELED AS A CHLORIDE ANION
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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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.146 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→29.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.745 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 24.974 Å / Origin y: 6.734 Å / Origin z: 32.456 Å
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Refinement TLS group | Selection: all |