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Yorodumi- PDB-2c7i: Structure of protein Ta0514, putative lipoate protein ligase from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2c7i | ||||||
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Title | Structure of protein Ta0514, putative lipoate protein ligase from T. acidophilum. | ||||||
Components | PUTATIVE LIPOATE PROTEIN LIGASELipoic acid | ||||||
Keywords | LIGASE / LIPOYLATION | ||||||
Function / homology | Function and homology information lipoate-protein ligase activity / lipoate-protein ligase / lipoic acid binding / protein lipoylation / protein-containing complex / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | THERMOPLASMA ACIDOPHILUM (acidophilic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Mcmanus, E. / Perham, R.N. / Luisi, B.F. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: Structure of a Putative Lipoate Protein Ligase from Thermoplasma Acidophilum and the Mechanism of Target Selection for Post-Translational Modification. Authors: Mcmanus, E. / Luisi, B.F. / Perham, R.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2c7i.cif.gz | 193.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2c7i.ent.gz | 161.4 KB | Display | PDB format |
PDBx/mmJSON format | 2c7i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c7/2c7i ftp://data.pdbj.org/pub/pdb/validation_reports/c7/2c7i | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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3 |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 29915.252 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) THERMOPLASMA ACIDOPHILUM (acidophilic) / Strain: DSM 1728 / Plasmid: PET 3A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HKT1 #2: Water | ChemComp-HOH / | |
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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: 3.11 Å3/Da / Density % sol: 60.13 % Description: A STRUCTURE OF RELATIVELY POOR QUALITY DERIVED FROM A SELENOMETHIONE CONTAINING PROTEIN CRYSTAL WAS USED AS MODEL IN CONJUNCTION WITH A GOOD QUALITY NATIVE DATA SET TO GIVE THE STRUCTURE FILES DEPOSITED. |
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Crystal grow | pH: 6.7 / Details: pH 6.70 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.54 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→19.87 Å / Num. obs: 68335 / % possible obs: 95.3 % / Observed criterion σ(I): 2 / Redundancy: 10 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 22 |
Reflection shell | Resolution: 2.08→2.17 Å / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 6 / % possible all: 72.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: SEE REMARK Resolution: 2.1→19.87 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.933 / SU B: 9.866 / SU ML: 0.129 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THIS ENTRY CONTAINS ATOMS WITH ZERO OCCUPANCY FOR WHICH B-FACTORS HAVE BEEN REFINED.
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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: 42.12 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→19.87 Å
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Refine LS restraints |
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