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Yorodumi- PDB-3gl3: Crystal structure of a putative Thiol:disulfide interchange prote... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gl3 | ||||||
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Title | Crystal structure of a putative Thiol:disulfide interchange protein DsbE from Chlorobium tepidum | ||||||
Components | Putative Thiol:disulfide interchange protein DsbE | ||||||
Keywords | OXIDOREDUCTASE / PSI-II / 11210h / Thiol:disulfide interchange protein DsbE / putative / Chlorobium tepidum / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC / New York Structural GenomiX Research Consortium | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Chlorobium tepidum TLS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.09 Å | ||||||
Authors | Damodharan, L. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of a putative Thiol:disulfide interchange protein DsbE from Chlorobium tepidum Authors: Damodharan, L. / Burley, S.K. / Swaminathan, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gl3.cif.gz | 116.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gl3.ent.gz | 97.1 KB | Display | PDB format |
PDBx/mmJSON format | 3gl3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gl/3gl3 ftp://data.pdbj.org/pub/pdb/validation_reports/gl/3gl3 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 16980.709 Da / Num. of mol.: 4 / Fragment: UNP residues 30-170 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlorobium tepidum TLS (bacteria) / Strain: TLS / DSM 12025 / Gene: CT1072 / Plasmid: pSGX3(BC) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8KDH8 #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: 1.99 Å3/Da / Density % sol: 38.15 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 2.4M Sodium malonate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 27, 2009 / Details: mirrors |
Radiation | Monochromator: Si(111) CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.09→39.07 Å / Num. all: 29179 / Num. obs: 29179 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 32.2 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 2.09→2.22 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 2 / Num. unique all: 5321 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.09→39.07 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 115348.82 / 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: 50.072 Å2 / ksol: 0.389351 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.09→39.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.09→2.22 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Xplor file |
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