+Open data
-Basic information
Entry | Database: PDB / ID: 2v9u | ||||||
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Title | Rim domain of main porin from Mycobacteria smegmatis | ||||||
Components | MSPA | ||||||
Keywords | TRANSPORT PROTEIN / PORI / PORIN / MYCOBACTERIA | ||||||
Function / homology | Function and homology information porin activity / pore complex / cell outer membrane / iron ion transport / extracellular region Similarity search - Function | ||||||
Biological species | MYCOBACTERIUM SMEGMATIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å | ||||||
Authors | Grueninger, D. / Ziegler, M.O.P. / Koetter, J.W.A. / Treiber, N. / Schulze, M.-S. / Schulz, G.E. | ||||||
Citation | Journal: Science / Year: 2008 Title: Designed Protein-Protein Association. Authors: Grueninger, D. / Treiber, N. / Ziegler, M.O.P. / Koetter, J.W.A. / Schulze, M.-S. / Schulz, G.E. #1: Journal: Science / Year: 2004 Title: The Structure of a Mycobacterial Outer-Membrane Channel Authors: Faller, M. / Niederweis, M. / Schulz, G.E. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2v9u.cif.gz | 197.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v9u.ent.gz | 162 KB | Display | PDB format |
PDBx/mmJSON format | 2v9u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v9/2v9u ftp://data.pdbj.org/pub/pdb/validation_reports/v9/2v9u | HTTPS FTP |
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-Related structure data
Related structure data | 2uyuC 2uyvC 2v7gC 2v9eC 2v9fC 2v9gC 2v9iC 2v9lC 2v9mC 2v9nC 2v9oC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 13995.358 Da / Num. of mol.: 8 / Fragment: RIM DOMAIN, RESIDUES 28-96,149-211 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM SMEGMATIS (bacteria) / Strain: MC2 155 / Plasmid: PMN501 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9RLP7, UniProt: A0QR29*PLUS #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: 3.2 Å3/Da / Density % sol: 61.57 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.95373 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95373 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→65.79 Å / Num. obs: 36299 / % possible obs: 82.6 % / Observed criterion σ(I): 4.1 / Redundancy: 2.17 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.18 |
Reflection shell | Resolution: 2.59→2.69 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 4.1 / % possible all: 87.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.59→65.79 Å / Cor.coef. Fo:Fc: 0.857 / Cor.coef. Fo:Fc free: 0.839 / SU B: 30.093 / SU ML: 0.299 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.086 / ESU R Free: 0.371 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.43 Å2
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Refinement step | Cycle: LAST / Resolution: 2.59→65.79 Å
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Refine LS restraints |
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