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Open data
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Basic information
Entry | Database: PDB / ID: 2wyk | ||||||||||||
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Title | SiaP in complex with Neu5Gc | ||||||||||||
![]() | SIALIC ACID-BINDING PERIPLASMIC PROTEIN SIAP | ||||||||||||
![]() | TRANSPORT PROTEIN / SUGAR TRANSPORT / TRAP TRANSPORTER | ||||||||||||
Function / homology | ![]() | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Fischer, M. / Hubbard, R.E. | ||||||||||||
![]() | ![]() Title: Water networks can determine the affinity of ligand binding to proteins. Authors: Darby, J.F. / Hopkins, A.P. / Shimizu, S. / Roberts, S.M. / Brannigan, J.A. / Turkenburg, J.P. / Thomas, G.H. / Hubbard, R.E. / Fischer, M. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 158.4 KB | Display | ![]() |
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PDB format | ![]() | 124.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 828.5 KB | Display | ![]() |
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Full document | ![]() | 829.6 KB | Display | |
Data in XML | ![]() | 18.2 KB | Display | |
Data in CIF | ![]() | 28.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2v4cSC ![]() 2wx9C ![]() 2wypC ![]() 2xa5C ![]() 6h75C ![]() 6h76C C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 34480.035 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Sugar | ChemComp-NGE / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 45 % / Description: NONE |
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Crystal grow | Temperature: 277 K / pH: 7 Details: 30 MG/ML SIAP (IN 20 MM HEPES, 10 MM NACL, PH 8.0) AND EQUAL VOLUME OF RESERVOIR SOLUTION (100MM MES PH 6.0, 28.5% PEG 6K, 3% W/V 1,5-DIAMINOPENTANE DIHYDROCHLORIDE), TEMPERATURE 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 20, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→40 Å / Num. obs: 49622 / % possible obs: 98.4 % / Observed criterion σ(I): 2 / Redundancy: 8 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 19.4 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.3 / % possible all: 96.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2V4C Resolution: 1.5→40.04 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.521 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. UNIDENTIFIED DENSITY IN PROXIMITY TO N150.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.936 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→40.04 Å
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Refine LS restraints |
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