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Yorodumi- PDB-3q4r: Crystal Structure of a deletion mutant(11-185) of hypothetical pr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3q4r | ||||||
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Title | Crystal Structure of a deletion mutant(11-185) of hypothetical protein MJ0754 with Zn2+ | ||||||
Components | Uncharacterized protein MJ0754 | ||||||
Keywords | UNKNOWN FUNCTION / ferritin-like protein / four-helix bundle / metal binding / dinuclear center | ||||||
Function / homology | Domain of unknown function DUF2202 / Uncharacterized protein domain (DUF2202) / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha / Uncharacterized protein MJ0754 Function and homology information | ||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Hwang, K.Y. / Lee, E.H. | ||||||
Citation | Journal: Proteins / Year: 2011 Title: Structural insights into the metal binding properties of hypothetical protein MJ0754 from Methanococcus jannaschii. Authors: Lee, E.H. / Kim, H.S. / Kim, H.Y. / Jeon, Y.H. / Hwang, K.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3q4r.cif.gz | 55.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3q4r.ent.gz | 37.5 KB | Display | PDB format |
PDBx/mmJSON format | 3q4r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3q4r_validation.pdf.gz | 691 KB | Display | wwPDB validaton report |
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Full document | 3q4r_full_validation.pdf.gz | 694 KB | Display | |
Data in XML | 3q4r_validation.xml.gz | 11.2 KB | Display | |
Data in CIF | 3q4r_validation.cif.gz | 15.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q4/3q4r ftp://data.pdbj.org/pub/pdb/validation_reports/q4/3q4r | HTTPS FTP |
-Related structure data
Related structure data | 3q4nSC 3q4oC 3q4qC S: Starting model for refinement C: citing same article (ref.) |
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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: 22933.805 Da / Num. of mol.: 1 / Fragment: residues 11-185(deletion 1-10) / Mutation: deletion 1-10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Strain: DSM 2661 / Gene: MJ0754 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q58164 | ||||
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#2: Chemical | #3: Chemical | ChemComp-B3P / | #4: 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: 2.17 Å3/Da / Density % sol: 43.2 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M Bis-tris propane, 22% PEG3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 20, 2009 | |||||||||||||||||||||||||||||||||
Radiation | Monochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.6→50 Å / Num. obs: 24608 / % possible obs: 90.4 % | |||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3Q4N Resolution: 1.6→32.13 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.943 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 1.923 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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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 max: 394.28 Å2 / Biso mean: 25.2956 Å2 / Biso min: 9.69 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→32.13 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.601→1.643 Å / Total num. of bins used: 20
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