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- PDB-3gnl: Structure of uncharacterized protein (LMOf2365_1472) from Listeri... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3gnl | ||||||
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Title | Structure of uncharacterized protein (LMOf2365_1472) from Listeria monocytogenes serotype 4b | ||||||
![]() | uncharacterized protein, DUF633, LMOf2365_1472 | ||||||
![]() | structural genomics / unknown function / uncharacterized protein / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Helix Hairpins - #1890 / Vaccinia Virus protein VP39 / Helix Hairpins / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta / : ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Ramagopal, U.A. / Toro, R. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
![]() | ![]() Title: Structure of uncharacterized protein (LMOf2365_1472) from Listeria monocytogenes serotype 4b Authors: Ramagopal, U.A. / Toro, R. / Burley, S.K. / Almo, S.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 110.2 KB | Display | ![]() |
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PDB format | ![]() | 89.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 430.6 KB | Display | ![]() |
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Full document | ![]() | 432 KB | Display | |
Data in XML | ![]() | 23 KB | Display | |
Data in CIF | ![]() | 34.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Details | Unknown |
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Components
#1: Protein | Mass: 27614.949 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: LMOf2365_1472 / Plasmid: BC-pSGX4(BC) / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.15 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M Sodium Cacodylate pH 6.5, 30% PEG 6K , 0.2M Sodium Acetate, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 5, 2008 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.5→40 Å / Num. obs: 81636 / % possible obs: 99.9 % / Redundancy: 11.3 % / Rmerge(I) obs: 0.08 / Χ2: 1.413 / Net I/σ(I): 34.284 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Resolution: 1.5→40 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.952 / WRfactor Rfree: 0.241 / WRfactor Rwork: 0.209 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.845 / SU B: 1.396 / SU ML: 0.053 / SU R Cruickshank DPI: 0.079 / SU Rfree: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 59.72 Å2 / Biso mean: 24.724 Å2 / Biso min: 10.27 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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