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Yorodumi- PDB-1lmi: 1.5 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF A SECRETED PROTEIN F... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lmi | ||||||
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Title | 1.5 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF A SECRETED PROTEIN FROM MYCOBACTERIUM TUBERCULOSIS-MPT63 | ||||||
Components | Immunogenic protein MPT63/MPB63 | ||||||
Keywords | IMMUNE SYSTEM / beta-sandwich / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC | ||||||
Function / homology | Function and homology information cell wall / nucleotidyltransferase activity / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.5 Å | ||||||
Authors | Goulding, C.W. / Parseghian, A. / Sawaya, M.R. / Cascio, D. / Apostol, M. / Gennaro, M.L. / Eisenberg, D. / TB Structural Genomics Consortium (TBSGC) | ||||||
Citation | Journal: Protein Sci. / Year: 2002 Title: Crystal structure of a major secreted protein of Mycobacterium tuberculosis-MPT63 at 1.5-A resolution Authors: Goulding, C.W. / Parseghian, A. / Sawaya, M.R. / Cascio, D. / Apostol, M. / Gennaro, M.L. / Eisenberg, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lmi.cif.gz | 40.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lmi.ent.gz | 28 KB | Display | PDB format |
PDBx/mmJSON format | 1lmi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lm/1lmi ftp://data.pdbj.org/pub/pdb/validation_reports/lm/1lmi | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 13749.392 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Tissue: H37Rv / Gene: Rv1926c, MPT63 / Plasmid: pQE30 / Species (production host): Escherichia coli / Production host: Escherichia coli K12 (bacteria) / Strain (production host): K12 / References: UniProt: P97155, UniProt: P9WIP1*PLUS |
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#2: 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: 1.65 Å3/Da / Density % sol: 25.6 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 26.5% PEG4000, 0.1M Tris/HCl, 15% glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 190 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 10, 2000 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→37.35 Å / Num. all: 20397 / Num. obs: 20397 / % possible obs: 82.4 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -3 / Redundancy: 18 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 29.9 |
Reflection shell | Resolution: 1.49→1.58 Å / Redundancy: 14 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 6.18 / Num. unique all: 3282 / % possible all: 92.9 |
Reflection | *PLUS Highest resolution: 1.5 Å / Lowest resolution: 100 Å / Num. obs: 2537 / % possible obs: 97.3 % / Num. measured all: 20972 |
Reflection shell | *PLUS % possible obs: 92.7 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 14.28 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO / Resolution: 1.5→10 Å / Num. parameters: 4555 / Num. restraintsaints: 4024 / Cross valid method: FREE R / σ(F): 0 / σ(I): -3 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1141 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→10 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.5 Å / Lowest resolution: 20 Å / Num. reflection Rfree: 986 / % reflection Rfree: 5 % / Rfactor Rfree: 0.246 / Rfactor Rwork: 0.192 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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