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Yorodumi- PDB-3kh5: Crystal Structure of Protein MJ1225 from Methanocaldococcus janna... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kh5 | ||||||
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Title | Crystal Structure of Protein MJ1225 from Methanocaldococcus jannaschii, a putative archaeal homolog of g-AMPK. | ||||||
Components | protein MJ1225 | ||||||
Keywords | UNKNOWN FUNCTION / MJ1225 / AMPK / AMP / ADP / ATP / CBS domain / archaea / Methanocaldococcus jannaschii. | ||||||
Function / homology | Function and homology information CBS-domain / CBS-domain / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain / CBS domain profile. / Roll / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Gomez Garcia, I. / Oyenarte, I. / Martinez-Cruz, L.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: The crystal structure of protein MJ1225 from Methanocaldococcus jannaschii shows strong conservation of key structural features seen in the eukaryal gamma-AMPK. Authors: Gomez-Garcia, I. / Oyenarte, I. / Martinez-Cruz, L.A. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2009 Title: Purification, crystallization and preliminary crystallographic analysis of protein MJ1225 from Methanocaldococcus jannaschii, a putative archaeal homologue of gamma-AMPK. Authors: Gomez Garcia, I. / Kortazar, D. / Oyenarte, I. / Mato, J.M. / Martinez-Chantar, M.L. / Martinez-Cruz, L.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kh5.cif.gz | 75.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kh5.ent.gz | 56.6 KB | Display | PDB format |
PDBx/mmJSON format | 3kh5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3kh5_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 3kh5_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 3kh5_validation.xml.gz | 15.5 KB | Display | |
Data in CIF | 3kh5_validation.cif.gz | 21.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kh/3kh5 ftp://data.pdbj.org/pub/pdb/validation_reports/kh/3kh5 | HTTPS FTP |
-Related 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: 31761.885 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Gene: MJ1225 / Plasmid: pET101-D / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta References: UniProt: Q58622, hydroxymethylglutaryl-CoA reductase (NADPH) | ||||||
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#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-SO4 / | #5: 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: 2.56 Å3/Da / Density % sol: 52.02 % |
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Crystal grow | Temperature: 291 K / pH: 7.5 Details: 2.4 M Ammonium sulfate, 2.8 % PEG 400, 100 mM Hepes, 114 mM FOS-choline 8 or 11 mM FOS-choline 10, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 |
Detector | Date: Sep 19, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 19237 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 24.7 % / Biso Wilson estimate: 39.5 Å2 / Rsym value: 0.086 / Net I/σ(I): 45.2 |
Reflection shell | Highest resolution: 2.1 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PROTEIN MJ0100 Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.898 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.267 / ESU R Free: 0.232 / 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: 45.31 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.15 Å / Total num. of bins used: 20
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