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Yorodumi- PDB-2v7s: Crystal structure of the putative lipoprotein LppA from Mycobacte... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2v7s | ||||||
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Title | Crystal structure of the putative lipoprotein LppA from Mycobacterium tuberculosis | ||||||
Components | PROBABLE CONSERVED LIPOPROTEIN LPPA | ||||||
Keywords | UNKNOWN FUNCTION / LIPOPROTEIN / PUTATIVE LIPOPROTEIN | ||||||
Function / homology | TBP-like - #20 / Putative lipoprotein, pathogenic bacteria / Lipoprotein confined to pathogenic Mycobacterium / TBP-like / 2-Layer Sandwich / plasma membrane / Alpha Beta / Putative lipoprotein LppA / Putative lipoprotein LppA Function and homology information | ||||||
Biological species | MYCOBACTERIUM TUBERCULOSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.96 Å | ||||||
Authors | Grana, M. / Miras, I. / Haouz, A. / Winter, N. / Buschiazzo, A. / Bellinzoni, M. / Alzari, P.M. | ||||||
Citation | Journal: Proteins / Year: 2010 Title: Crystal Structure of Mycobacterium Tuberculosis Lppa, a Lipoprotein Confined to Pathogenic Mycobacteria. Authors: Grana, M. / Bellinzoni, M. / Bellalou, J. / Haouz, A. / Miras, I. / Buschiazzo, A. / Winter, N. / Alzari, P.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2v7s.cif.gz | 44.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v7s.ent.gz | 34.1 KB | Display | PDB format |
PDBx/mmJSON format | 2v7s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2v7s_validation.pdf.gz | 432.9 KB | Display | wwPDB validaton report |
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Full document | 2v7s_full_validation.pdf.gz | 434.2 KB | Display | |
Data in XML | 2v7s_validation.xml.gz | 9.4 KB | Display | |
Data in CIF | 2v7s_validation.cif.gz | 12.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v7/2v7s ftp://data.pdbj.org/pub/pdb/validation_reports/v7/2v7s | HTTPS FTP |
-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: 24337.549 Da / Num. of mol.: 1 / Fragment: RESIDUES 34-219 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P95010, UniProt: P9WK81*PLUS | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | THE RECOMBINANT PROTEIN INCLUDES A N-TERMINAL TAG ( SEQUENCE MSYYHHHHHHLESTSLYKKAGSENLYFQG) FUSED ...THE RECOMBINAN | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56 % / Description: NONE |
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Crystal grow | pH: 9 / Details: 20% PEG-3350, BICINE 0.1 M, PH 9, 50 MM MGCL2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 21, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→45 Å / Num. obs: 15229 / % possible obs: 97.8 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 1.96→2.07 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.7 / % possible all: 85.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 1.96→6 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.912 / SU B: 5.91 / SU ML: 0.086 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.93 Å2
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Refinement step | Cycle: LAST / Resolution: 1.96→6 Å
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Refine LS restraints |
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