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Yorodumi- PDB-3gn6: Crystal structure of CT0912, ORFan protein from Chlorobium tepidu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gn6 | ||||||
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Title | Crystal structure of CT0912, ORFan protein from Chlorobium tepidum with a ferredoxin-like domain repeat (NP_661805.1) from CHLOROBIUM TEPIDUM TLS at 1.80 A resolution | ||||||
Components | CT0912, ORFan protein with a ferredoxin-like domain repeat | ||||||
Keywords | structural genomics / unknown function / NP_661805.1 / CT0912 / ORFan protein from Chlorobium tepidum with a ferredoxin-like domain repeat / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 | ||||||
Function / homology | metal ion binding / DI(HYDROXYETHYL)ETHER / Uncharacterized protein Function and homology information | ||||||
Biological species | Chlorobium tepidum TLS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of CT0912, ORFan protein from Chlorobium tepidum with a ferredoxin-like domain repeat (NP_661805.1) from CHLOROBIUM TEPIDUM TLS at 1.80 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gn6.cif.gz | 270.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gn6.ent.gz | 221.8 KB | Display | PDB format |
PDBx/mmJSON format | 3gn6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gn/3gn6 ftp://data.pdbj.org/pub/pdb/validation_reports/gn/3gn6 | 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 35520.859 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlorobium tepidum TLS (bacteria) / Gene: CT0912, NP_661805.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8KDY2 |
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-Non-polymers , 5 types, 1063 molecules
#2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-PEG / | #5: Chemical | ChemComp-2PE / | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATI |
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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: 2.6 Å3/Da / Density % sol: 52.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2430M magnesium acetate, 13.6000% polyethylene glycol 3350, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97949 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 17, 2009 / Details: Flat collimating mirror, toroid focusing mirror | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→46.829 Å / Num. obs: 137561 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 23.421 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 9.63 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: SAD |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.8→46.829 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 5.354 / SU ML: 0.073 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.104 / ESU R Free: 0.1 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 0.85 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 4. GLYCEROLS, PEG FRAGMENTS (PEG AND 2PE) ARE PRESENT IN CYRO/CRYSTALLIZATION CONDITIONS. THE ASSIGNMENTS OF PEG FRAGMENTS AND GLYCEROLS ARE TENTATIVE DUE TO NOT WELL DEFINED DENSITY. 5. DISORDERED REGIONS: A33-34, A149-152,B149-152 AND D149-152. 6. MAGNESIUM IONS ARE ASSIGNED BASED COORDINATION, CRYSTALLIZATION CONDITIONS AND FLUORESCENCE SCAN WHICH INDICATES ABSENCE OF HEAVY METALS.
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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 max: 73.46 Å2 / Biso mean: 21.407 Å2 / Biso min: 4.04 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→46.829 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Ens-ID: 1 / Number: 3660 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.8→1.847 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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