+Open data
-Basic information
Entry | Database: PDB / ID: 1nmo | ||||||
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Title | Structural genomics, protein ybgI, unknown function | ||||||
Components | Hypothetical protein ybgI | ||||||
Keywords | structural genomics / unknown function / ybgI / hypothetical protein / toroidal structure / Structure 2 Function Project / S2F | ||||||
Function / homology | Function and homology information cell pole / protein hexamerization / response to ionizing radiation / DNA repair / identical protein binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) Escherichia coli O157:H7 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å | ||||||
Authors | Ladner, J.E. / Obmolova, G. / Teplyakov, A. / Khil, P.P. / Camerini-Otero, R.D. / Gilliland, G.L. / Structure 2 Function Project (S2F) | ||||||
Citation | Journal: BMC Struct.Biol. / Year: 2003 Title: Crystal Structure of Escherichia coli Protein ybgI, a toroidal structure with a dinuclear metal site Authors: Ladner, J.E. / Obmolova, G. / Teplyakov, A. / Howard, A.J. / Khil, P.P. / Camerini-Otero, R.D. / Gilliland, G.L. | ||||||
History |
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Remark 600 | HETEROGEN THE IDENTIFICATION OF THE METAL ION IN THE ACTIVE SITE IS NOT KNOWN. HERE IT IS MODELED AS FE. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nmo.cif.gz | 293.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nmo.ent.gz | 249.7 KB | Display | PDB format |
PDBx/mmJSON format | 1nmo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nmo_validation.pdf.gz | 469.6 KB | Display | wwPDB validaton report |
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Full document | 1nmo_full_validation.pdf.gz | 494.3 KB | Display | |
Data in XML | 1nmo_validation.xml.gz | 59.5 KB | Display | |
Data in CIF | 1nmo_validation.cif.gz | 83.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nm/1nmo ftp://data.pdbj.org/pub/pdb/validation_reports/nm/1nmo | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Details | The biological assembly is a hexamer generated by the application of the symmetry operations: -y, x-y, Z and y-x, -x, z. If applied to the entire asymmetric unit, these operations will generate 3 toroids (3 biological assemblies). If applied to any of the dimers, AB, CD or EF, these operations will produce one biological assembly. |
-Components
#1: Protein | Mass: 27106.980 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli, Escherichia coli O157:H7 Genus: Escherichia, Escherichia / Species: , Escherichia coli / Strain: , O157:H7 / Gene: YBGI OR B0710 OR Z0861 OR ECS0735 / Plasmid: pDEST14 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star (DE3) / References: UniProt: P75743, UniProt: P0AFP6*PLUS #2: Chemical | ChemComp-FE / #3: 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: 2.36 Å3/Da / Density % sol: 47.43 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1M imidazole, 0.2M calcium acetate, 15% (w/v) polyethylene glycol 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9895,0.9793,0.9780 | ||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 1, 2002 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.2→20 Å / Num. obs: 77584 / Redundancy: 2 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 25.6 | ||||||||||||
Reflection | *PLUS Num. obs: 77981 / % possible obs: 97.6 % / Num. measured all: 298987 / Rmerge(I) obs: 0.06 | ||||||||||||
Reflection shell | *PLUS % possible obs: 86.3 % / Rmerge(I) obs: 0.216 / Mean I/σ(I) obs: 3.5 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.2→19.6 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 185523.27 / Data cutoff high rms absF: 185523.27 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 22.511 Å2 / ksol: 0.33392 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.9 Å2
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Refine analyze | Luzzati coordinate error free: 0.34 Å / Luzzati sigma a free: 0.31 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→19.6 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6 /
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.26 / Rfactor Rwork: 0.213 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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