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Yorodumi- PDB-1lm3: A Multi-generation Analysis of Cytochrome b562 Redox Variants: Ev... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lm3 | ||||||
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Title | A Multi-generation Analysis of Cytochrome b562 Redox Variants: Evolutionary Strategies for Modulating Redox Potential Revealed Using a Library Approach | ||||||
Components | SOLUBLE CYTOCHROME B562 | ||||||
Keywords | ELECTRON TRANSPORT / four helix bundle / cytochrome / heme-binding | ||||||
Function / homology | Function and homology information electron transport chain / periplasmic space / electron transfer activity / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Springs, S.L. / Bass, S.E. / Bowman, G. / Nodelman, I. / Schutt, C.E. / McLendon, G.L. | ||||||
Citation | Journal: Biochemistry / Year: 2002 Title: A multigeneration analysis of cytochrome b(562) redox variants: evolutionary strategies for modulating redox potential revealed using a library approach. Authors: Springs, S.L. / Bass, S.E. / Bowman, G. / Nodelman, I. / Schutt, C.E. / McLendon, G.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lm3.cif.gz | 55.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lm3.ent.gz | 41.2 KB | Display | PDB format |
PDBx/mmJSON format | 1lm3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lm3_validation.pdf.gz | 975.9 KB | Display | wwPDB validaton report |
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Full document | 1lm3_full_validation.pdf.gz | 982.6 KB | Display | |
Data in XML | 1lm3_validation.xml.gz | 11.7 KB | Display | |
Data in CIF | 1lm3_validation.cif.gz | 15 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lm/1lm3 ftp://data.pdbj.org/pub/pdb/validation_reports/lm/1lm3 | HTTPS FTP |
-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
#1: Protein | Mass: 11737.188 Da / Num. of mol.: 2 / Mutation: F61I, F65Y, R106L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cycB / Plasmid: pRW1 / Production host: Escherichia coli (E. coli) / Strain (production host): MV1190 / References: UniProt: P0ABE7 #2: Chemical | #3: Chemical | #4: 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: 2.51 Å3/Da / Density % sol: 51.04 % |
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Crystal grow | Temperature: 302 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 30% polyethylene glycol 4000, 0.1M MgCl2, 0.1M Tris HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 302K |
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Feb 26, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 6896 / % possible obs: 98.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.085 |
Reflection shell | Resolution: 2.7→2.8 Å / Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 8.2 / Num. unique all: 672 / % possible all: 98.4 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. obs: 49249 / Rmerge(I) obs: 0.085 |
Reflection shell | *PLUS % possible obs: 98.4 % / Rmerge(I) obs: 0.287 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→50 Å / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2.7→50 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 50 Å / Rfactor obs: 0.232 / Rfactor Rfree: 0.333 / Rfactor Rwork: 0.232 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |