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Yorodumi- PDB-1m2d: Crystal structure at 1.05 Angstroms resolution of the Cys59Ser va... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1m2d | ||||||
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Title | Crystal structure at 1.05 Angstroms resolution of the Cys59Ser variant of the thioredoxin-like [2Fe-2S] ferredoxin from Aquifex aeolicus | ||||||
Components | [2Fe-2S] ferredoxin | ||||||
Keywords | ELECTRON TRANSPORT / ferredoxin / thioredoxin-like fold / [2Fe-2S] cluster / Cys59Ser variant | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Aquifex aeolicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.05 Å | ||||||
Authors | Yeh, A.P. / Ambroggio, X.I. / Andrade, S.L.A. / Einsle, O. / Chatelet, C. / Meyer, J. / Rees, D.C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: High-resolution crystal structures of the wild type and Cys-55-->Ser and Cys-59-->Ser variants of the thioredoxin-like [2Fe-2S] ferredoxin from Aquifex aeolicus Authors: Yeh, A.P. / Ambroggio, X.I. / Andrade, S.L.A. / Einsle, O. / Chatelet, C. / Meyer, J. / Rees, D.C. #1: Journal: J.Mol.Biol. / Year: 2000 Title: Structure of a thioredoxin-like [2Fe-2S] ferredoxin from Aquifex aeolicus Authors: Yeh, A.P. / Chatelet, C. / Soltis, S.M. / Kuhn, P. / Meyer, J. / Rees, D.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1m2d.cif.gz | 100.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1m2d.ent.gz | 77.1 KB | Display | PDB format |
PDBx/mmJSON format | 1m2d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1m2d_validation.pdf.gz | 385.8 KB | Display | wwPDB validaton report |
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Full document | 1m2d_full_validation.pdf.gz | 390.2 KB | Display | |
Data in XML | 1m2d_validation.xml.gz | 6.1 KB | Display | |
Data in CIF | 1m2d_validation.cif.gz | 9.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m2/1m2d ftp://data.pdbj.org/pub/pdb/validation_reports/m2/1m2d | HTTPS FTP |
-Related structure data
Related structure data | 1m2aC 1m2bSC C: citing same article (ref.) S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 12190.091 Da / Num. of mol.: 2 / Mutation: C59S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: Fdx4 / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): K38 / References: UniProt: O66511 #2: Chemical | #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: 1.82 Å3/Da / Density % sol: 32.46 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 1,6 hexanediol, cobalt chloride, sodium acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 | |||||||||||||||||||||||||||||||||||||||||||||||||
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: SSRL / Beamline: BL9-2 / Wavelength: 0.958 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 18, 2001 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.958 Å / Relative weight: 1 |
Reflection | Resolution: 1.05→31.2 Å / Num. all: 77950 / Num. obs: 77950 / % possible obs: 95.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Rmerge(I) obs: 0.035 / Rsym value: 0.035 / Net I/σ(I): 38.2 |
Reflection shell | Resolution: 1.05→1.07 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.216 / Mean I/σ(I) obs: 6.4 / Num. unique all: 3725 / Rsym value: 0.216 / % possible all: 92 |
Reflection | *PLUS Num. measured all: 358550 / Rmerge(I) obs: 0.035 |
Reflection shell | *PLUS % possible obs: 92 % / Rmerge(I) obs: 0.216 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1M2B, Cys55Ser Aquifex aeolicus [2Fe-2S] ferredoxin structure Resolution: 1.05→31.2 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze | Luzzati coordinate error obs: 0.19 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.05→31.2 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 3 % / Rfactor obs: 0.138 / Rfactor Rfree: 0.162 / Rfactor Rwork: 0.138 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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