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Yorodumi- PDB-1rzh: PHOTOSYNTHETIC REACTION CENTER DOUBLE MUTANT FROM RHODOBACTER SPH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rzh | ||||||
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Title | PHOTOSYNTHETIC REACTION CENTER DOUBLE MUTANT FROM RHODOBACTER SPHAEROIDES WITH ASP L213 REPLACED WITH ASN AND ARG M233 REPLACED WITH CYS IN THE CHARGE-NEUTRAL DQAQB STATE (TRIGONAL FORM) | ||||||
Components | (Reaction center protein ...) x 3 | ||||||
Keywords | PHOTOSYNTHESIS / BACTERIAL PHOTOSYNTHESIS / RHODOBACTER SPHAEROIDES / PROTON TRANSFER PATHWAY / REVERTANT / INTEGRAL MEMBRANE PROTEIN | ||||||
Function / homology | Function and homology information : / plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthetic electron transport in photosystem II / membrane => GO:0016020 / metal ion binding Similarity search - Function | ||||||
Biological species | Rhodobacter sphaeroides (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Xu, Q. / Axelrod, H.L. / Abresch, E.C. / Paddock, M.L. / Okamura, M.Y. / Feher, G. | ||||||
Citation | Journal: STRUCTURE / Year: 2004 Title: X-Ray Structure Determination of Three Mutants of the Bacterial Photosynthetic Reaction Centers from Rb. sphaeroides; Altered Proton Transfer Pathways. Authors: Xu, Q. / Axelrod, H.L. / Abresch, E.C. / Paddock, M.L. / Okamura, M.Y. / Feher, G. #1: Journal: Photosynth.Res. / Year: 1998 Title: Characterization of Second Site Mutations Show that Fast Proton Transfer to Qb- is Restored in Bacterial Reaction Centers of Rhodobacter Sphaeroides Containing the Asp-L213->Asn Lesion Authors: Paddock, M.L. / Senft, M.E. / Graige, M.S. / Rongey, S.H. / Turanchik, T. / Feher, G. / Okamura, M.Y. #2: Journal: Proc.Natl.Acad.Sci.USA / Year: 2000 Title: Determination of the Binding Sites of the Proton Transfer Inhibitors Cd2+ and Zn2+ in Bacterial Reaction Centers Authors: Axelrod, H.L. / Abresch, E.C. / Paddock, M.L. / Okamura, M.Y. / Feher, G. #3: Journal: Photosynth.Res. / Year: 1998 Title: Identification of Proton Transfer Pathways in the X-Ray Crystal Structure of the Bacterial Reaction Center from Rhodobacter Sphaeroides Authors: Abresch, E.C. / Paddock, M.L. / Stowell, M.H.B. / McPhillips, T.M. / Axelrod, H.L. / Soltis, S.M. / Rees, D.C. / Okamura, M.Y. / Feher, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rzh.cif.gz | 212 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rzh.ent.gz | 161.4 KB | Display | PDB format |
PDBx/mmJSON format | 1rzh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1rzh_validation.pdf.gz | 3.1 MB | Display | wwPDB validaton report |
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Full document | 1rzh_full_validation.pdf.gz | 3.2 MB | Display | |
Data in XML | 1rzh_validation.xml.gz | 46.4 KB | Display | |
Data in CIF | 1rzh_validation.cif.gz | 61.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rz/1rzh ftp://data.pdbj.org/pub/pdb/validation_reports/rz/1rzh | HTTPS FTP |
-Related structure data
Related structure data | 1rvjC 1ry5C 1rzzC 1s00C 1qovS 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
-Reaction center protein ... , 3 types, 3 molecules LMH
#1: Protein | Mass: 31345.404 Da / Num. of mol.: 1 / Mutation: D213N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: PUFL / Production host: Rhodobacter sphaeroides (bacteria) / References: UniProt: P02954, UniProt: P0C0Y8*PLUS |
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#2: Protein | Mass: 34344.488 Da / Num. of mol.: 1 / Mutation: R233C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: PUFM / Production host: Rhodobacter sphaeroides (bacteria) / References: UniProt: P02953, UniProt: P0C0Y9*PLUS |
#3: Protein | Mass: 28066.322 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: PUHA / Production host: Rhodobacter sphaeroides (bacteria) / References: UniProt: P11846, UniProt: P0C0Y7*PLUS |
-Non-polymers , 11 types, 489 molecules
#4: Chemical | ChemComp-BCL / #5: Chemical | #6: Chemical | #7: Chemical | #8: Chemical | ChemComp-FE2 / | #9: Chemical | ChemComp-PO4 / | #10: Chemical | ChemComp-SPO / | #11: Chemical | #12: Chemical | ChemComp-CDL / | #13: Chemical | ChemComp-GOL / | #14: 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: 5.2 Å3/Da / Density % sol: 76 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: potassium phosphate, sodium chloride, LDAO, haptanetriol, haxanetriol, dioxane, pH 8.50, VAPOR DIFFUSION, SITTING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.95 / Wavelength: 0.95 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 24, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→39.31 Å / Num. all: 188308 / Num. obs: 188308 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 19.3 Å2 / Rsym value: 0.098 / Net I/σ(I): 5.4 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2 / Rsym value: 0.344 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QOV Resolution: 1.8→39.31 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 2694188.38 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 52.6307 Å2 / ksol: 0.355853 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→39.31 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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