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Yorodumi- PDB-1gzc: High-Resolution crystal structure of Erythrina cristagalli lectin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gzc | |||||||||
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Title | High-Resolution crystal structure of Erythrina cristagalli lectin in complex with lactose | |||||||||
Components | ERYTHRINA CRISTA-GALLI LECTIN | |||||||||
Keywords | SUGAR BINDING PROTEIN / LECTIN / CARBOHYDRATE / SACCHARIDE / PROTEIN-CARBOHYDRATE INTERACTIONS / LACTOSE / GLYCOPROTEIN | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | ERYTHRINA CRISTA-GALLI (ceibo) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å | |||||||||
Authors | Svensson, C. / Krengel, U. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: High-Resolution Crystal Structures of Erythrina Cristagalli Lectin in Complex with Lactose and 2'-Alpha-L-Fucosyllactose and Correlation with Thermodynamic Binding Data Authors: Svensson, C. / Teneberg, S. / Nilsson, C. / Kjellberg, A. / Schwarz, F. / Sharon, N. / Krengel, U. | |||||||||
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 | 1gzc.cif.gz | 70.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gzc.ent.gz | 50.3 KB | Display | PDB format |
PDBx/mmJSON format | 1gzc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gz/1gzc ftp://data.pdbj.org/pub/pdb/validation_reports/gz/1gzc | HTTPS FTP |
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-Related structure data
Related structure data | 1gz9C 1ax1S 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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-Components
#1: Protein | Mass: 26249.189 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ERYTHRINA CRISTA-GALLI (ceibo) / References: UniProt: P83410*PLUS |
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#2: Polysaccharide | beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / beta-lactose |
#3: Chemical | ChemComp-MN / |
#4: Chemical | ChemComp-CA / |
#5: Water | ChemComp-HOH / |
Sequence details | THE SEQUENCE OF THE CRYSTALLIZED PROTEIN WAS CONFIRMED BY MASS SPECTROMETRY, BUT THERE ARE ...THE SEQUENCE OF THE CRYSTALLIZ |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4 Å3/Da / Density % sol: 69 % Description: THE DATA SET INCLUDED REFLECTIONS TO 1.45 A RESOLUTION, BUT THE DATA WERE CUT TO 1.58 A RESOLUTION IN THE FINAL REFINEMENT CYCLE DUE TO CONSIDERABLE INCREASE IN R-FACTORS BEYOND THAT RESOLUTION. | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 Details: 2M AMMONIUM SULFATE, 0.1M TRIS PH 7.5, 10% GLYCEROL | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 / Method: vapor diffusion, hanging drop / Details: used macroseeding | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.03 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 15, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→49.8 Å / Num. obs: 58614 / % possible obs: 99.5 % / Redundancy: 9.4 % / Biso Wilson estimate: 22.6 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 20.9 |
Reflection shell | Resolution: 1.58→1.64 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.608 / Mean I/σ(I) obs: 2.3 / % possible all: 99.4 |
Reflection | *PLUS Highest resolution: 1.6 Å / Num. measured all: 551905 |
Reflection shell | *PLUS % possible obs: 99.4 % / Num. unique obs: 6065 / Num. measured obs: 38515 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1AX1 Resolution: 1.58→49.9 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: ALTERNATIVE CONFORMATIONS REFINED FOR RESIDUES 9, 10, 12, 95, 159, 173, 180, 234 LACTOSE ARE DEPOSITED: LAT_XPLOR_TOP.TXT LAT_XPLOR_PAR.TXT. INITIAL STAGES OF REFINEMENT WITH SIMULATED ANNEALING.
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Solvent computation | Bsol: 51.5279 Å2 / ksol: 0.385527 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.4 Å2
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Refinement step | Cycle: LAST / Resolution: 1.58→49.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.58→1.59 Å / Total num. of bins used: 50
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.6 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Lowest resolution: 1.64 Å |