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Yorodumi- PDB-3i86: Crystal structure of the P60 Domain from M. avium subspecies para... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3i86 | ||||||
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Title | Crystal structure of the P60 Domain from M. avium subspecies paratuberculosis antigen MAP1204 | ||||||
Components | Putative uncharacterized protein | ||||||
Keywords | HYDROLASE / ALPHA AND BETA PROTEIN / HYPOTHETICAL CYSTEINE PROTEASE | ||||||
Function / homology | Endopeptidase, NLPC/P60 domain / NlpC/P60 family / endopeptidase domain like (from Nostoc punctiforme) / endopeptidase fold (from Nostoc punctiforme) / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta / ISOPROPYL ALCOHOL / NLPC_P60 domain-containing protein Function and homology information | ||||||
Biological species | Mycobacterium avium subsp. paratuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Ramyar, K.X. / Lingle, C.K. / McWhorter, W.J. / Bouyain, S. / Bannantine, J.P. / Geisbrecht, B.V. | ||||||
Citation | Journal: To be Published Title: Atypical structural features of two P60 family members from Mycobacterium avium subspecies paratuberculosis Authors: Ramyar, K.X. / Lingle, C.K. / McWhorter, W.J. / Bouyain, S. / Bannantine, J.P. / Geisbrecht, B.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3i86.cif.gz | 63.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3i86.ent.gz | 46.4 KB | Display | PDB format |
PDBx/mmJSON format | 3i86.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3i86_validation.pdf.gz | 448.3 KB | Display | wwPDB validaton report |
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Full document | 3i86_full_validation.pdf.gz | 450.9 KB | Display | |
Data in XML | 3i86_validation.xml.gz | 12.3 KB | Display | |
Data in CIF | 3i86_validation.cif.gz | 16.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i8/3i86 ftp://data.pdbj.org/pub/pdb/validation_reports/i8/3i86 | HTTPS FTP |
-Related structure data
Related structure data | 3gt2S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 14872.784 Da / Num. of mol.: 2 / Fragment: P60 DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium avium subsp. paratuberculosis (bacteria) Strain: K-10 / Gene: MAP1204, MAP_1204 / Plasmid: pT7HMT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q740Y8, gamma-D-glutamyl-meso-diaminopimelate peptidase #2: Chemical | ChemComp-IPA / | #3: 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: 2.57 Å3/Da / Density % sol: 52.05 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 22% PEG 3350, 18% 2-propanol, 0.1M NaHEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 12, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→43.43 Å / Num. obs: 12254 / % possible obs: 99.6 % / Observed criterion σ(F): 2.8 / Observed criterion σ(I): 5.6 / Redundancy: 13 % / Biso Wilson estimate: 39.333 Å2 / Rmerge(I) obs: 0.169 / Rsym value: 0.199 / Net I/σ(I): 14.09 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.856 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1213 / Rsym value: 0.856 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3GT2 Resolution: 2.4→43.428 Å / SU ML: 1.11 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHT / σ(F): 1.34 / σ(I): 3.9 / Stereochemistry target values: ML / Details: USED PHENIX.REFINE
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.938 Å2 / ksol: 0.297 e/Å3 | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.21 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→43.428 Å
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Refine LS restraints |
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LS refinement shell |
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