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Yorodumi- PDB-1mqv: Crystal Structure of the Q1A/F32W/W72F mutant of Rhodopseudomonas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mqv | |||||||||
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Title | Crystal Structure of the Q1A/F32W/W72F mutant of Rhodopseudomonas palustris cytochrome c' (prime) expressed in E. coli | |||||||||
Components | CYTOCHROME C' | |||||||||
Keywords | ELECTRON TRANSPORT / Four-Helix Bundle | |||||||||
Function / homology | Function and homology information electron transport chain / periplasmic space / electron transfer activity / iron ion binding / heme binding Similarity search - Function | |||||||||
Biological species | Rhodopseudomonas palustris (phototrophic) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.78 Å | |||||||||
Authors | Lee, J.C. / Engman, K.C. / Tezcan, F.A. / Gray, H.B. / Winkler, J.R. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2002 Title: Structural Features of Cytochrome c' Folding Intermediates Revealed by Fluorescence Energy-Transfer Kinetics Authors: Lee, J.C. / Engman, K.C. / Tezcan, F.A. / Gray, H.B. / Winkler, J.R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mqv.cif.gz | 62.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mqv.ent.gz | 49.6 KB | Display | PDB format |
PDBx/mmJSON format | 1mqv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mqv_validation.pdf.gz | 533.3 KB | Display | wwPDB validaton report |
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Full document | 1mqv_full_validation.pdf.gz | 539.9 KB | Display | |
Data in XML | 1mqv_validation.xml.gz | 7.2 KB | Display | |
Data in CIF | 1mqv_validation.cif.gz | 11.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mq/1mqv ftp://data.pdbj.org/pub/pdb/validation_reports/mq/1mqv | HTTPS FTP |
-Related structure data
Related structure data | 1a7vS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 13095.089 Da / Num. of mol.: 2 / Mutation: Q1A, F32W, W72F Source method: isolated from a genetically manipulated source Details: The protein is in the OXIDIZED (FE(III)) STATE. Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic) Plasmid: BL21(DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: P00149 #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: 2.27 Å3/Da / Density % sol: 45.91 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 Details: PEG6000, sodium chloride, MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Mar 24, 2002 |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→50 Å / Num. all: 23685 / Num. obs: 23607 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.062 / Net I/σ(I): 24.8 |
Reflection shell | Resolution: 1.78→1.81 Å / Mean I/σ(I) obs: 1.9 / Rsym value: 0.487 / % possible all: 99 |
Reflection | *PLUS Lowest resolution: 50 Å / % possible obs: 99.7 % / Rmerge(I) obs: 0.062 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1A7V Resolution: 1.78→42 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.78→42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.78→1.84 Å / Rfactor Rfree error: 0.043
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Refinement | *PLUS Lowest resolution: 42 Å / Rfactor Rwork: 0.211 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |