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Yorodumi- PDB-1mng: STRUCTURE-FUNCTION IN E. COLI IRON SUPEROXIDE DISMUTASE: COMPARIS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mng | ||||||
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Title | STRUCTURE-FUNCTION IN E. COLI IRON SUPEROXIDE DISMUTASE: COMPARISONS WITH THE MANGANESE ENZYME FROM T. THERMOPHILUS | ||||||
Components | MANGANESE SUPEROXIDE DISMUTASESuperoxide dismutase | ||||||
Keywords | OXIDOREDUCTASE(SUPEROXIDE ACCEPTOR) | ||||||
Function / homology | Function and homology information superoxide dismutase / superoxide dismutase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.8 Å | ||||||
Authors | Lah, M.S. / Dixon, M. / Pattridge, K.A. / Stallings, W.C. / Fee, J.A. / Ludwig, M.L. | ||||||
Citation | Journal: Biochemistry / Year: 1995 Title: Structure-function in Escherichia coli iron superoxide dismutase: comparisons with the manganese enzyme from Thermus thermophilus. Authors: Lah, M.S. / Dixon, M.M. / Pattridge, K.A. / Stallings, W.C. / Fee, J.A. / Ludwig, M.L. #1: Journal: J.Mol.Biol. / Year: 1991 Title: Manganese Superoxide Dismutase from Thermus Thermophilus. A Structural Model Refined at 1.8 Angstroms Resolution Authors: Ludwig, M.L. / Metzger, A.L. / Pattridge, K.A. / Stallings, W.C. #2: Journal: Molecular Biology of Free Radical Scavenging Systems Year: 1992 Title: Iron and Manganese Superoxide Dismutases: Catalytic Inferences from the Structures Authors: Stallings, W.C. / Bull, C. / Fee, J.A. / Lah, M.S. / Ludwig, M.L. #3: Journal: Free Radical Res.Commun. / Year: 1991 Title: Structure-Function Relationships in Fe-and Mn-Superoxide Dismutases Authors: Stallings, W.C. / Metzger, A.L. / Pattridge, K.A. / Fee, J.A. / Ludwig, M.L. #4: Journal: J.Biol.Chem. / Year: 1985 Title: The Structure of Manganese Superoxide Dismutase from Thermus Thermophilus at 2.4 Angstroms Resolution Authors: Stallings, W.C. / Pattridge, K.A. / Strong, R.K. / Ludwig, M.L. #5: Journal: J.Biol.Chem. / Year: 1984 Title: Manganese and Iron Superoxide Dismutases are Structural Homologs Authors: Stallings, W.C. / Pattridge, K.A. / Strong, R.K. / Ludwig, M.L. | ||||||
History |
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Remark 650 | HELIX ASSIGNMENTS OF SECONDARY STRUCTURE ARE BASED ON THE ALGORITHM OF KABSCH AND SANDER, WITH THE ...HELIX ASSIGNMENTS OF SECONDARY STRUCTURE ARE BASED ON THE ALGORITHM OF KABSCH AND SANDER, WITH THE FOLLOWING EXCEPTIONS: HELICES START WITH THE FIRST RESIDUE HAVING A HELICAL HYDROGEN BOND; SUCCESSIVE 3/10 TURNS ARE GIVEN PRIORITY OVER SHORT 3/10 HELICES. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mng.cif.gz | 99 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mng.ent.gz | 77.3 KB | Display | PDB format |
PDBx/mmJSON format | 1mng.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mn/1mng ftp://data.pdbj.org/pub/pdb/validation_reports/mn/1mng | HTTPS FTP |
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-Related structure data
-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 3 / 2: CIS PROLINE - PRO A 18 / 3: CIS PROLINE - PRO B 3 / 4: CIS PROLINE - PRO B 18 | ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.0569, -0.94416, 0.32454), Vector: Details | THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *A*. | |
-Components
#1: Protein | Mass: 23129.295 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / References: UniProt: P61503, superoxide dismutase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.24 Å3/Da / Density % sol: 61.99 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
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 | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 20 Å / Num. obs: 52673 / Redundancy: 6.5 % / Rmerge(I) obs: 0.077 |
-Processing
Software |
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Refinement | Resolution: 1.8→20 Å / σ(F): 0 Details: FOR ATOMS THAT ARE PRESENTED IN ALTERNATE CONFORMATIONS, THE ALTERNATE LOCATION INDICATOR *L* REPRESENTS THOSE ATOMS IN THE CONFORMATION WITH AZIDE LIGANDED AND *U* REPRESENTS THOSE ATOMS IN ...Details: FOR ATOMS THAT ARE PRESENTED IN ALTERNATE CONFORMATIONS, THE ALTERNATE LOCATION INDICATOR *L* REPRESENTS THOSE ATOMS IN THE CONFORMATION WITH AZIDE LIGANDED AND *U* REPRESENTS THOSE ATOMS IN THE CONFORMATION WITHOUT AZIDE LIGANDED.
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |