+Open data
-Basic information
Entry | Database: PDB / ID: 3a7l | ||||||
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Title | Crystal structure of E. coli apoH-protein | ||||||
Components | Glycine cleavage system H protein | ||||||
Keywords | TRANSPORT PROTEIN / glycine cleavage system / lipoic acid / Lipoyl | ||||||
Function / homology | Function and homology information glycine cleavage complex / glycine decarboxylation via glycine cleavage system / one-carbon metabolic process / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.3 Å | ||||||
Authors | Fujiwara, K. / Maita, N. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Global conformational change associated with the two-step reaction catalyzed by Escherichia coli lipoate-protein ligase A. Authors: Fujiwara, K. / Maita, N. / Hosaka, H. / Okamura-Ikeda, K. / Nakagawa, A. / Taniguchi, H. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR DETERMINED |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3a7l.cif.gz | 37.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3a7l.ent.gz | 25.3 KB | Display | PDB format |
PDBx/mmJSON format | 3a7l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3a7l_validation.pdf.gz | 416.3 KB | Display | wwPDB validaton report |
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Full document | 3a7l_full_validation.pdf.gz | 416.4 KB | Display | |
Data in XML | 3a7l_validation.xml.gz | 7.4 KB | Display | |
Data in CIF | 3a7l_validation.cif.gz | 9.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a7/3a7l ftp://data.pdbj.org/pub/pdb/validation_reports/a7/3a7l | HTTPS FTP |
-Related structure data
Related structure data | 3a7aC 3a7rC 3a7uC 1htpS 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: 13688.902 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: gcvH / Plasmid: pET-3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P0A6T9 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.89 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.9 Details: 2.3M ammonium sulfate, 0.1M sodium citrate, 3%(v/v) 2-methyl-2,4-pentanediol, pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: Bruker DIP-6040 / Detector: CCD / Date: Oct 16, 2008 / Details: mirrors |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→30 Å / Num. all: 27372 / Num. obs: 26800 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 3.4 % / Biso Wilson estimate: 11.83 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 32.5 |
Reflection shell | Resolution: 1.3→1.35 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 3.1 / Num. unique all: 2585 / Rsym value: 0.473 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Starting model: PDB ENTRY 1HTP Resolution: 1.3→15 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / SU B: 0.749 / SU ML: 0.032 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 3 / ESU R: 0.052 / ESU R Free: 0.055 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.797 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.301→1.335 Å / Total num. of bins used: 20
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