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- PDB-4akd: High resolution structure of Mannose Binding lectin from Champeda... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4akd | ||||||
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Title | High resolution structure of Mannose Binding lectin from Champedak (CMB) | ||||||
![]() | MANNOSE-SPECIFIC LECTIN KM+ | ||||||
![]() | SUGAR BINDING PROTEIN | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gabrielsen, M. / Abdul-Rahman, P.S. / Othman, S. / Hashim, O.H. / Cogdell, R.J. | ||||||
![]() | ![]() Title: Structures and Binding Specificity of Galactose- and Mannose-Binding Lectins from Champedak: Differences from Jackfruit Lectins Authors: Gabrielsen, M. / Abdul-Rahman, P.S. / Othman, S. / Hashim, O.H. / Cogdell, R.J. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2010 Title: Crystallization and Initial X-Ray Diffraction Analysis of a Mannose-Binding Lectin from Champedak. Authors: Gabrielsen, M. / Abdul-Rahman, P.S. / Isaacs, N.W. / Hashim, O.H. / Cogdell, R.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 248.3 KB | Display | ![]() |
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PDB format | ![]() | 200 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 458 KB | Display | ![]() |
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Full document | ![]() | 465 KB | Display | |
Data in XML | ![]() | 26 KB | Display | |
Data in CIF | ![]() | 37.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ak4C ![]() 4akbC ![]() 4akcC ![]() 1j4uS 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: 16175.169 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Chemical | ChemComp-CD / #3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | Sequence details | CROSS-REFERENCE IS TO NEAREST UNIPROT BUT SEQUENCE IS VARIANT WITH GENBANK REFERENCE GB FR728241. | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.51 % / Description: NONE |
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Crystal grow | pH: 7.6 Details: 0.1 M CADMIUM CHLORIDE, 0.1 M SODIUM ACETATE PH 4.6, 30% POLYETHYLENE GLYCOL 400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 14, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→49.17 Å / Num. obs: 37852 / % possible obs: 99.8 % / Observed criterion σ(I): 22.4 / Redundancy: 14.5 % / Biso Wilson estimate: 36.1 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 22.4 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 14.6 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 4.9 / % possible all: 99.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1J4U Resolution: 2.1→47.69 Å / Cor.coef. Fo:Fc: 0.9451 / Cor.coef. Fo:Fc free: 0.9231 / SU R Cruickshank DPI: 0.208 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.214 / SU Rfree Blow DPI: 0.178 / SU Rfree Cruickshank DPI: 0.177 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=CD CL. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=4814. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=CD CL. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=4814. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=15.
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Displacement parameters | Biso mean: 48.87 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→47.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.16 Å / Total num. of bins used: 19
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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