+Open data
-Basic information
Entry | Database: PDB / ID: 2yjm | ||||||
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Title | Structure of TtrD from Archaeoglobus fulgidus | ||||||
Components | TTRD | ||||||
Keywords | CHAPERONE | ||||||
Function / homology | TorD-like / TorD-like / DMSO/Nitrate reductase chaperone / TorD-like superfamily / Nitrate reductase delta subunit / Orthogonal Bundle / Mainly Alpha / cytoplasm / Tat proofreading chaperone TtrD Function and homology information | ||||||
Biological species | ARCHAEOGLOBUS FULGIDUS (archaea) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.84 Å | ||||||
Authors | Dawson, A. / Coulthurst, S.J. / Hunter, W.N. / Sargent, F. | ||||||
Citation | Journal: Biochemistry / Year: 2012 Title: Conserved Signal Peptide Recognition Systems Across the Prokaryotic Domains. Authors: Coulthurst, S.J. / Dawson, A. / Hunter, W.N. / Sargent, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yjm.cif.gz | 82.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yjm.ent.gz | 62 KB | Display | PDB format |
PDBx/mmJSON format | 2yjm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2yjm_validation.pdf.gz | 435.5 KB | Display | wwPDB validaton report |
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Full document | 2yjm_full_validation.pdf.gz | 435.9 KB | Display | |
Data in XML | 2yjm_validation.xml.gz | 9.4 KB | Display | |
Data in CIF | 2yjm_validation.cif.gz | 12.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yj/2yjm ftp://data.pdbj.org/pub/pdb/validation_reports/yj/2yjm | HTTPS FTP |
-Related structure data
Related structure data | 2xolC 2y6yC 2idgS C: citing same article (ref.) 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: 20396.436 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ARCHAEOGLOBUS FULGIDUS (archaea) / Plasmid: PET15BTEV_TTRD / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O30077 |
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#2: Chemical | ChemComp-NHE / |
#3: Water | ChemComp-HOH / |
Sequence details | ADDITIONAL |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.8 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: PROTEIN BUFFER: 50 MM TRIS, 250 MM NACL, 5 MM GMP-PNP; RESERVOIR: 0.1 M CHES PH 9.5, 20% W/V PEG 8K. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 |
Detector | Type: RIGAKU CCD / Detector: CCD / Date: Aug 28, 2009 / Details: MIRRORS |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→35.01 Å / Num. obs: 13256 / % possible obs: 90.6 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 24.4 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 1.84→1.94 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 4.3 / % possible all: 84.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2IDG Resolution: 1.84→48.99 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.921 / SU B: 6.655 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.193 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.209 Å2
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Refinement step | Cycle: LAST / Resolution: 1.84→48.99 Å
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