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Yorodumi- PDB-3lfz: Crystal Structure of Protein MJ1225 from Methanocaldococcus janna... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3lfz | ||||||
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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 / 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: 2.2 Å | ||||||
Authors | Gomez-Garcia, I. / Oyenarte, I. / Kortazar, D. / 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 | 3lfz.cif.gz | 71.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lfz.ent.gz | 53.3 KB | Display | PDB format |
PDBx/mmJSON format | 3lfz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lf/3lfz ftp://data.pdbj.org/pub/pdb/validation_reports/lf/3lfz | HTTPS FTP |
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-Related structure data
Related structure data | 3kh5C 3kpdS 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: 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) / References: UniProt: Q58622 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-ADP / | #4: Chemical | ChemComp-AMP / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.14 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Ligand soaks, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 12, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9395 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→78.81 Å / Num. obs: 15961 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3KPD Resolution: 2.2→78.81 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.909 / SU B: 7.68 / SU ML: 0.2 / Cross valid method: THROUGHOUT / ESU R: 0.338 / ESU R Free: 0.245 / 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: 47.786 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→78.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.199→2.256 Å / Total num. of bins used: 20
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