+Open data
-Basic information
Entry | Database: PDB / ID: 1e2v | ||||||
---|---|---|---|---|---|---|---|
Title | N153Q mutant of cytochrome f from Chlamydomonas reinhardtii | ||||||
Components | CYTOCHROME F | ||||||
Keywords | ELECTRON TRANSPORT / INTERNAL WATER CHAIN / PHOTOSYNTHETIC FUNCTION IMPAIRED | ||||||
Function / homology | Function and homology information chloroplast thylakoid membrane / photosynthesis / electron transfer activity / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | CHLAMYDOMONAS REINHARDTII (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Sainz, G. / Carrell, C.J. / Ponamarev, M.V. / Soriano, G.M. / Cramer, W.A. / Smith, J.L. | ||||||
Citation | Journal: Biochemistry / Year: 2000 Title: Interruption of the Internal Water Chain of Cytochrome F Impairs Photosynthetic Function Authors: Sainz, G. / Carrell, C.J. / Ponamarev, M.V. / Soriano, G.M. / Cramer, W.A. / Smith, J.L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1e2v.cif.gz | 186.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1e2v.ent.gz | 147.4 KB | Display | PDB format |
PDBx/mmJSON format | 1e2v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1e2v_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1e2v_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 1e2v_validation.xml.gz | 43.3 KB | Display | |
Data in CIF | 1e2v_validation.cif.gz | 65.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e2/1e2v ftp://data.pdbj.org/pub/pdb/validation_reports/e2/1e2v | HTTPS FTP |
-Related structure data
Related structure data | 1e2wC 1e2zC 1ewhSC C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 27195.988 Da / Num. of mol.: 3 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) CHLAMYDOMONAS REINHARDTII (plant) / Gene: PETA / Plasmid: PUCPF2 / Gene (production host): CCMABCDEFGH / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): MV1190 / References: UniProt: P23577 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Compound details | CHAIN A, B, C ENGINEERED MUTATION ASN153GLN. ONLY THE SOLUBLE DOMAIN OF THE MATURE MEMBRANE PROTEIN ...CHAIN A, B, C ENGINEERED | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.43 % | ||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 6.5 Details: THE PROTEIN WAS BUFFERED IN 10 MM NA2HPO4/NAH2PO4, 1 MM DTT, PH 6.5 AND THE RESERVOIR CONTAINED 100 MM MES, PH 6.5, 25 MM CALCIUM ACETATE, 1 MM DTT AND 17-19% PEG 8000. | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 12 ℃ / pH: 7.5 / Method: vapor diffusion / Details: temperature was changed to 20 degress after 4 days | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 15, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→43.85 Å / Num. obs: 73484 / % possible obs: 97.9 % / Redundancy: 4.5 % / Biso Wilson estimate: 12.5 Å2 / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 26.1 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.305 / Mean I/σ(I) obs: 3.73 / Rsym value: 0.305 / % possible all: 90.2 |
Reflection | *PLUS Num. measured all: 329989 |
Reflection shell | *PLUS % possible obs: 90.2 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EWH Resolution: 1.85→42.33 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2405744.61 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.308 Å2 / ksol: 0.340713 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.4 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→42.33 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.85→1.97 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|