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Yorodumi- PDB-1r1m: Structure of the OmpA-like domain of RmpM from Neisseria meningitidis -
+Open data
-Basic information
Entry | Database: PDB / ID: 1r1m | ||||||
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Title | Structure of the OmpA-like domain of RmpM from Neisseria meningitidis | ||||||
Components | Outer membrane protein class 4 | ||||||
Keywords | MEMBRANE PROTEIN | ||||||
Function / homology | Function and homology information porin activity / pore complex / monoatomic ion transport / cell outer membrane Similarity search - Function | ||||||
Biological species | Neisseria meningitidis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SAD / Resolution: 1.9 Å | ||||||
Authors | Grizot, S. / Buchanan, S.K. | ||||||
Citation | Journal: Mol.Microbiol. / Year: 2004 Title: Structure of the OmpA-like domain of RmpM from Neisseria meningitidis Authors: Grizot, S. / Buchanan, S.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1r1m.cif.gz | 38.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1r1m.ent.gz | 29.5 KB | Display | PDB format |
PDBx/mmJSON format | 1r1m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r1/1r1m ftp://data.pdbj.org/pub/pdb/validation_reports/r1/1r1m | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 18333.705 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria meningitidis (bacteria) / Gene: RMPM / Plasmid: pET-20b / Production host: Escherichia coli (E. coli) / Strain (production host): Origami(DE3) / References: UniProt: P38367, UniProt: P0A0V3*PLUS |
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#2: Chemical | ChemComp-TRS / |
#3: 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: 2.3 Å3/Da / Density % sol: 46.64 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 1000, Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 12, 2002 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 13605 / Num. obs: 13591 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 20.2 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 25 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.254 / Mean I/σ(I) obs: 6 / Num. unique all: 1361 / Rsym value: 0.254 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.9→20 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 25.3 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.024
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