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Yorodumi- PDB-3i3v: Crystal Structure of probable secreted solute-binding lipoprotein... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3i3v | ||||||
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Title | Crystal Structure of probable secreted solute-binding lipoprotein from Streptomyces coelicolor | ||||||
Components | Probable secreted solute-binding lipoprotein | ||||||
Keywords | TRANSPORT PROTEIN / Transporter / PSI-II / 11318G / solute-binding lipoprotein / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC / Lipoprotein | ||||||
Function / homology | Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta / Probable secreted solute-binding lipoprotein Function and homology information | ||||||
Biological species | Streptomyces coelicolor (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 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 probable secreted solute-binding lipoprotein from Streptomyces coelicolor Authors: Damodhran, 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 | 3i3v.cif.gz | 298.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3i3v.ent.gz | 252.8 KB | Display | PDB format |
PDBx/mmJSON format | 3i3v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i3/3i3v ftp://data.pdbj.org/pub/pdb/validation_reports/i3/3i3v | 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: 44230.680 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Gene: SCO0453, SCF51A.31 / Plasmid: PSGX3(BC) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RL34 #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: 2.52 Å3/Da / Density % sol: 51.13 % |
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Crystal grow | Temperature: 298 K / pH: 7 Details: 2.1M DL-Malic Acid, 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: X29A / Wavelength: 0.979 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 8, 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: 2.3→41 Å / Num. obs: 79106 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 9.1 % / Biso Wilson estimate: 51.6 Å2 / Rmerge(I) obs: 0.127 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2 / % possible all: 91.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.3→36.7 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 55597.95 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 33.9 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→36.7 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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