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Yorodumi- PDB-3c4s: Crystal structure of the Ssl0352 protein from Synechocystis sp. N... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3c4s | ||||||
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Title | Crystal structure of the Ssl0352 protein from Synechocystis sp. Northeast Structural Genomics Consortium target SgR42 | ||||||
Components | Ssl0352 protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / P74795_SYNY3 / Ssl0352 / NESG / SgR42 / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium | ||||||
Function / homology | NADH dehydrogenase-like complex, subunit S / NAD(P)H dehydrogenase subunit S / photosynthetic electron transport chain / SH3 type barrels. - #140 / SH3 type barrels. / Roll / Mainly Beta / Ssl0352 protein Function and homology information | ||||||
Biological species | Synechocystis sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Vorobiev, S.M. / Chen, Y. / Seetharaman, J. / Wang, D. / Maglaqui, M. / Janjua, H. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. ...Vorobiev, S.M. / Chen, Y. / Seetharaman, J. / Wang, D. / Maglaqui, M. / Janjua, H. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of the Ssl0352 protein from Synechocystis sp. Authors: Vorobiev, S.M. / Chen, Y. / Seetharaman, J. / Wang, D. / Maglaqui, M. / Janjua, H. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3c4s.cif.gz | 38.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3c4s.ent.gz | 25.5 KB | Display | PDB format |
PDBx/mmJSON format | 3c4s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c4/3c4s ftp://data.pdbj.org/pub/pdb/validation_reports/c4/3c4s | HTTPS FTP |
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-Related structure data
Related structure data | 2jz2S S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | AUTHORS STATE THAT THE BIOLOGICAL UNIT IS A MONOMER ACCORDING TO AGGREGATION SCREENING. |
-Components
#1: Protein | Mass: 7655.642 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Gene: ssl0352 / Plasmid: pET21-23C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: P74795 #2: 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: 2.44 Å3/Da / Density % sol: 49.63 % Description: The structure factor file contains Friedel pairs |
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Crystal grow | Temperature: 291 K / Method: microbatch under oil / pH: 6.5 Details: 30% Jeffamine M-600, 0.05M Cesium chloride, 0.1M MES pH 6.5, MICROBATCH UNDER OIL, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 25, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. all: 31765 / Num. obs: 31765 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 14.1 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 17.36 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.145 / Mean I/σ(I) obs: 6 / Num. unique all: 3200 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2JZ2, chain A Resolution: 1.7→24.89 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1019206.95 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: The Friedel pairs were used in phasing
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 69.6645 Å2 / ksol: 0.421479 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→24.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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