+Open data
-Basic information
Entry | Database: PDB / ID: 2i15 | ||||||
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Title | Crystal structure of MPN423 from Mycoplasma pneumoniae | ||||||
Components | Hypothetical protein MG296 homologHypothesis | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / MPN423 / Hypothetical protein / all alpha structure / PSI / Protein Structure Initiative / Berkeley Structural Genomics Center / BSGC | ||||||
Function / homology | Function and homology information mg296 homolog like / Mg296 protein / Mg296-like, C-terminal / MG296-like superfamily / Mg296 protein / mpn423 like domain / cAMP-dependent Protein Kinase, Chain A / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha Similarity search - Domain/homology | ||||||
Biological species | Mycoplasma pneumoniae (Filterable agent of primary atypical pneumonia) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å | ||||||
Authors | Shin, D.H. / Yokota, H. / Kim, R. / Kim, S.-H. / Berkeley Structural Genomics Center (BSGC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of MPN423 from Mycoplasma pneumoniae Authors: Shin, D.H. / Yokota, H. / Kim, R. / Kim, S.-H. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2i15.cif.gz | 85.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2i15.ent.gz | 65.5 KB | Display | PDB format |
PDBx/mmJSON format | 2i15.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i1/2i15 ftp://data.pdbj.org/pub/pdb/validation_reports/i1/2i15 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 15296.377 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycoplasma pneumoniae (Filterable agent of primary atypical pneumonia) Gene: MPN423, MP418 / Plasmid: pB3 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3), pSJS1240 / References: UniProt: P75364 #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: 2.34 Å3/Da / Density % sol: 47.39 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1M Bis-Tris pH 5.5, 25% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 7, 2004 |
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→99 Å / Num. all: 16221 / Num. obs: 16221 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 21 Å2 |
Reflection shell | Resolution: 2.3→2.34 Å / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.4→19.98 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 98916.87 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.3696 Å2 / ksol: 0.326294 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→19.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
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Xplor file |
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