+Open data
-Basic information
Entry | Database: PDB / ID: 1h9w | ||||||
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Title | Native Dioclea Guianensis seed lectin | ||||||
Components | SEED LECTIN | ||||||
Keywords | LECTIN / LEGUME LECTIN OLIGOMERISATION | ||||||
Function / homology | Function and homology information D-mannose binding / toxin activity / carbohydrate binding / metal ion binding Similarity search - Function | ||||||
Biological species | DIOCLEA GUIANENSIS (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Romero, A. / Wah, D.A. / Sol, F.G.D. / Cavada, B.S. / Ramos, M.V. / Grangeiro, T.B. / Sampaio, A.H. / Calvete, J.J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: Crystal Structure of Native and Cd/Cd-Substituted Dioclea Guianensis Seed Lectin. A Novel Manganese-Binding Site and Structural Basis of Dimer-Tetramer Association Authors: Wah, D.A. / Romero, A. / Gallego, F. / Cavada, B.S. / Ramos, M.V. / Grangeiro, T.B. / Sampaio, A.H. / Calvete, J.J. #1: Journal: Biochim.Biophys.Acta / Year: 1999 Title: Molecular Characterization and Crystallization of Diocleinae Lectins Authors: Calvete, J.J. / Thole, H.H. / Raida, M. / Urbanke, C. / Romero, A. / Grangeiro, T.B. / Ramos, M.V. / Almeida, I.M. / Guimaraes, F.N. / Cavada, B.S. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1h9w.cif.gz | 108 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h9w.ent.gz | 82.1 KB | Display | PDB format |
PDBx/mmJSON format | 1h9w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h9/1h9w ftp://data.pdbj.org/pub/pdb/validation_reports/h9/1h9w | HTTPS FTP |
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-Related structure data
Related structure data | 1h9pC 1cvnS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.00523, 0.99742, -0.07156), Vector: Details | BIOLOGICAL_UNIT: HE BIOLOGICALLY ACTIVE UNIT IS ACANONICAL DIMERIC (BELOW PH 6) OR TETRAMER. | |
-Components
#1: Protein | Mass: 25421.053 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) DIOCLEA GUIANENSIS (plant) / Variant: LASIOPHYLLA / Tissue: SEED / References: UniProt: P81637 #2: Chemical | ChemComp-MN / #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | THE SEQUENCE IS DESCRIBED IN CALVETE ET AL. (1999) BIOCHIM. BIOPHYS. ACTA., 1430, P.367. RESIDUES ...THE SEQUENCE IS DESCRIBED IN CALVETE ET AL. (1999) BIOCHIM. BIOPHYS. ACTA., 1430, P.367. RESIDUES 144 AND 190 (GLY AND SER) ARE NOT SET CORRECTLY IN THE SW DATA BASE. | |
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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: 2.11 Å3/Da / Density % sol: 41.3 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 4.6 Details: CRYSTALS WERE GROWN BY THE HANGING DROP VAPOUR DIFFUSION METHOD USING 30% PEG 400, 0.1M ACO, PH 4.6, 10MM CACL2 AND MNCL2 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 2000 |
Radiation | Monochromator: TOROIDAL MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→22 Å / Num. obs: 26619 / % possible obs: 88.7 % / Redundancy: 5.7 % / Biso Wilson estimate: 10.1 Å2 / Rmerge(I) obs: 0.037 / Rsym value: 0.037 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.089 / Mean I/σ(I) obs: 8 / Rsym value: 0.089 / % possible all: 92.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1CVN Resolution: 2→22.54 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2397478.65 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: SIDE-CHAINS COULD NOT BE ADDED FOR RESIDUES A131, A162, A204, B82, B99 AND B116, AND RESIDUES WERE NOT BUILT FOR B117 AND B237 BECAUSE OF THE LACK OF DENSITY THE RESIDUES 118-122 WERE LEFT ...Details: SIDE-CHAINS COULD NOT BE ADDED FOR RESIDUES A131, A162, A204, B82, B99 AND B116, AND RESIDUES WERE NOT BUILT FOR B117 AND B237 BECAUSE OF THE LACK OF DENSITY THE RESIDUES 118-122 WERE LEFT OUT FOR BOTH MONOMERS BECAUSE OF POOR DENSITY. THE C-TERMINAL RESIDUE ASN237 WAS NOT SEEN IN THE DENSITY MAPS
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 78.4159 Å2 / ksol: 0.436914 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→22.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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