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Yorodumi- PDB-1ids: X-RAY STRUCTURE ANALYSIS OF THE IRON-DEPENDENT SUPEROXIDE DISMUTA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ids | ||||||
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Title | X-RAY STRUCTURE ANALYSIS OF THE IRON-DEPENDENT SUPEROXIDE DISMUTASE FROM MYCOBACTERIUM TUBERCULOSIS AT 2.0 ANGSTROMS RESOLUTIONS REVEALS NOVEL DIMER-DIMER INTERACTIONS | ||||||
Components | IRON SUPEROXIDE DISMUTASE | ||||||
Keywords | SUPEROXIDE DISMUTASE | ||||||
Function / homology | Function and homology information detoxification / Tolerance of reactive oxygen produced by macrophages / superoxide dismutase / superoxide dismutase activity / manganese ion binding / response to oxidative stress / periplasmic space / iron ion binding / extracellular region / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | ||||||
Authors | Cooper, J.B. / Mcintyre, K. / Wood, S.P. / Zhang, Y. / Young, D. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1995 Title: X-ray structure analysis of the iron-dependent superoxide dismutase from Mycobacterium tuberculosis at 2.0 Angstroms resolution reveals novel dimer-dimer interactions. Authors: Cooper, J.B. / McIntyre, K. / Badasso, M.O. / Wood, S.P. / Zhang, Y. / Garbe, T.R. / Young, D. #1: Journal: J.Mol.Biol. / Year: 1994 Title: Crystallisation and Preliminary X-Ray Analysis of the Iron-Dependent Superoxide Dismutase from Mycobacterium Tuberculosis Authors: Cooper, J.B. / Driessen, H.P.C. / Wood, S.P. / Zhang, Y. / Young, D. | ||||||
History |
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Remark 700 | SHEET SHEET SHEET_ID: EA, SHEET IN A SUBUNIT. N-CENTERED OVERHAND TOPOLOGY. SHEET_ID: EB, SHEET IN ...SHEET SHEET SHEET_ID: EA, SHEET IN A SUBUNIT. N-CENTERED OVERHAND TOPOLOGY. SHEET_ID: EB, SHEET IN B SUBUNIT. N-CENTERED OVERHAND TOPOLOGY. SHEET_ID: EC, SHEET IN C SUBUNIT. N-CENTERED OVERHAND TOPOLOGY. SHEET_ID: ED, SHEET IN D SUBUNIT. N-CENTERED OVERHAND TOPOLOGY. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ids.cif.gz | 168.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ids.ent.gz | 131.6 KB | Display | PDB format |
PDBx/mmJSON format | 1ids.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/id/1ids ftp://data.pdbj.org/pub/pdb/validation_reports/id/1ids | 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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Atom site foot note | 1: CIS PROLINE - PRO A 18 / 2: CIS PROLINE - PRO B 18 / 3: CIS PROLINE - PRO C 18 / 4: CIS PROLINE - PRO D 18 |
-Components
#1: Protein | Mass: 23060.861 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) References: UniProt: P17670, UniProt: P9WGE7*PLUS, superoxide dismutase #2: Chemical | ChemComp-FE / #3: Water | ChemComp-HOH / | Nonpolymer details | HETATMS 1001-1004 ARE PUTATIVE OH(-) IONS. | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 41 % | ||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion, hanging dropDetails: drop consists of equal volume of protein and reservoir solutions | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | Num. obs: 40396 / % possible obs: 80.4 % |
Reflection | *PLUS Highest resolution: 2 Å |
-Processing
Software | Name: RESTRAIN / Classification: refinement | ||||||||||||||||||||
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Refinement | Highest resolution: 2 Å / σ(F): 0 /
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Displacement parameters | Biso mean: 20.61 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2 Å
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Refine LS restraints |
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Software | *PLUS Name: RESTRAIN / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / Num. reflection all: 40396 / Rfactor all: 0.167 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |