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Yorodumi- PDB-3gt2: Crystal Structure of the P60 Domain from M. avium paratuberculosi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gt2 | ||||||
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Title | Crystal Structure of the P60 Domain from M. avium paratuberculosis Antigen MAP1272c | ||||||
Components | Putative uncharacterized protein | ||||||
Keywords | UNKNOWN FUNCTION / P60 Domain / Antigen | ||||||
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 / membrane => GO:0016020 / Alpha-Beta Complex / Alpha Beta / NLPC_P60 domain-containing protein Function and homology information | ||||||
Biological species | Mycobacterium avium subsp. paratuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 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: Crystal Structures of Two P60-Family Antigens from Mycobacterium Avium 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 | 3gt2.cif.gz | 62.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gt2.ent.gz | 49.3 KB | Display | PDB format |
PDBx/mmJSON format | 3gt2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gt/3gt2 ftp://data.pdbj.org/pub/pdb/validation_reports/gt/3gt2 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 15128.056 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium avium subsp. paratuberculosis (bacteria) Strain: K-10 / Gene: MAP1272c, MAP_1272c / Plasmid: pT7HMT / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q740S0 | ||||
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#2: Chemical | #3: Chemical | #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: 2.28 Å3/Da / Density % sol: 46.06 % |
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Crystal grow | Temperature: 273 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: 0.1 M BisTris-HCl, 1.6 M Ammonium Sulfate, 4% (v/v) PEG 400, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 273K |
-Data collection
Diffraction | Mean temperature: 97 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9724 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9724 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 3.6 % / Av σ(I) over netI: 9.45 / Number: 47147 / Rmerge(I) obs: 0.072 / Χ2: 1.04 / D res high: 1.75 Å / D res low: 500 Å / Num. obs: 13278 / % possible obs: 96.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.75→500 Å / Num. obs: 13278 / % possible obs: 96.1 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 9.446 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.216 / % possible all: 78.1 |
-Phasing
Phasing | Method: SAD | |||||||||||||||||||||||||||||||||||||||||||||||||
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Phasing MAD | D res high: 0 Å / D res low: 0 Å / FOM : 0 / Reflection: 0 | |||||||||||||||||||||||||||||||||||||||||||||||||
Phasing dm | FOM : 0.64 / FOM acentric: 0.65 / FOM centric: 0.6 / Reflection: 13001 / Reflection acentric: 12391 / Reflection centric: 610 | |||||||||||||||||||||||||||||||||||||||||||||||||
Phasing dm shell |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.75→22.675 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.76 / σ(F): 0.03 / Phase error: 20.11 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 74.643 Å2 / ksol: 0.383 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.627 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→22.675 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -7.3847 Å / Origin y: 30.8294 Å / Origin z: 34.5798 Å
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Refinement TLS group | Selection details: all |