+Open data
-Basic information
Entry | Database: PDB / ID: 1e2w | ||||||
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Title | N168F mutant of cytochrome f from Chlamydomonas reinhardtii | ||||||
Components | CYTOCHROME F | ||||||
Keywords | ELECTRON TRANSPORT PROTEINS / 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: 1.6 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1e2w.cif.gz | 128.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e2w.ent.gz | 99.1 KB | Display | PDB format |
PDBx/mmJSON format | 1e2w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e2/1e2w ftp://data.pdbj.org/pub/pdb/validation_reports/e2/1e2w | HTTPS FTP |
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-Related structure data
Related structure data | 1e2vSC 1e2zC 1ewhC S: Starting model for refinement C: citing same article (ref.) |
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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: 27215.033 Da / Num. of mol.: 2 / 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: Water | ChemComp-HOH / | Compound details | CHAIN A, B, C ENGINEERED MUTATION ASN168PHE. ONLY THE SOLUBLE DOMAIN OF THE MATURE MEMBRANE PROTEIN ...CHAIN A, B, C ENGINEERED | |
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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: 2.62 Å3/Da / Density % sol: 52.6 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.7 Details: THE PROTEIN WAS BUFFERED IN 10 MM NA2HPO4/NAH2PO4, PH 7.5, 1 MM DTT, THE RESERVOIR CONTAINED 100 MM MES, PH 6.7, 200 MM AMMONIUM FORMATE, 14% GLYCEROL, 17% PEG-3350. | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion | |||||||||||||||||||||||||||||||||||
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: APS / Beamline: 19-ID / Wavelength: 0.6526 |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Apr 15, 1999 / Details: MIRROR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.6526 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→27.84 Å / Num. obs: 73580 / % possible obs: 99.6 % / Redundancy: 3.8 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 28.6 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.378 / Mean I/σ(I) obs: 3.54 / Rsym value: 0.378 / % possible all: 100 |
Reflection | *PLUS Num. measured all: 277890 |
Reflection shell | *PLUS % possible obs: 100 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1E2V Resolution: 1.6→27.41 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1175031.81 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: THE LOOP 186-190 IS BADLY DEFINED IN THE ELECTRON DENSITY. ONLY THE MAIN CHAIN OF THE ARG 251 WAS SEEN IN THE ELCTRON DENSITY MAP FOR THE B CHAIN , SO AN ALA 251 WAS USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 54.4172 Å2 / ksol: 0.359825 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→27.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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