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Yorodumi- PDB-1f9k: WINGED BEAN ACIDIC LECTIN COMPLEXED WITH METHYL-ALPHA-D-GALACTOSE -
+Open data
-Basic information
Entry | Database: PDB / ID: 1f9k | |||||||||
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Title | WINGED BEAN ACIDIC LECTIN COMPLEXED WITH METHYL-ALPHA-D-GALACTOSE | |||||||||
Components | ACIDIC LECTIN | |||||||||
Keywords | SUGAR BINDING PROTEIN / LEGUME LECTIN / GLYCOSYLATED PROTEIN / H-ANTIGENIC SPECIFICITY / AGGLUTININ | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Psophocarpus tetragonolobus (winged bean) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å | |||||||||
Authors | Manoj, N. / Srinivas, V.R. / Surolia, A. / Vijayan, M. / Suguna, K. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: Carbohydrate specificity and salt-bridge mediated conformational change in acidic winged bean agglutinin. Authors: Manoj, N. / Srinivas, V.R. / Surolia, A. / Vijayan, M. / Suguna, K. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1999 Title: Crystallization and Preliminary Crystallographic Analysis of Winged Bean Acidic Lectin Authors: Manoj, N. / Srinivas, V.R. / Satish, B. / Singha, N.C. / Suguna, K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1f9k.cif.gz | 98.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1f9k.ent.gz | 75.3 KB | Display | PDB format |
PDBx/mmJSON format | 1f9k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f9/1f9k ftp://data.pdbj.org/pub/pdb/validation_reports/f9/1f9k | HTTPS FTP |
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-Related 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: (-0.919856, -0.075705, -0.384881), Vector: |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 26390.123 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Psophocarpus tetragonolobus (winged bean) / Organ: LEGUMINOUS SEEDS / References: GenBank: 6018681, UniProt: Q9SM56*PLUS |
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-Sugars , 2 types, 3 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Sugar | ChemComp-AMG / | |
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-Non-polymers , 3 types, 45 molecules
#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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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: 2.72 Å3/Da / Density % sol: 54 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: liquid diffusion / pH: 7.2 Details: CRYSTALS WERE GROWN BY BATCH METHOD BY MIXING 35 MICROLITERS OF A SOLUTION CONTAINING 25 MG/ML PROTEIN SOLUTION IN 0.02 M PHOSPHATE BUFFER AT PH 7.2, CONTAINING 0.15 M SODIUM CHLORIDE, 0.025 ...Details: CRYSTALS WERE GROWN BY BATCH METHOD BY MIXING 35 MICROLITERS OF A SOLUTION CONTAINING 25 MG/ML PROTEIN SOLUTION IN 0.02 M PHOSPHATE BUFFER AT PH 7.2, CONTAINING 0.15 M SODIUM CHLORIDE, 0.025 (W/V) SODIUM NITRITE, 20 TIMES MOLAR EXCESS OF METHYL-ALPHA-D-GALACTOSE WITH 23 MICROLITRES OF 30% PEG4000 SOLUTION IN THE SAME BUFFER. PEG4000, Sodium Phosphate, sodium chloride, sodium azide, LIQUID DIFFUSION, temperature 298K | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: batch method / Details: Manoj, N., (1999) Acta Crystallogr., D55, 564. | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 20, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3→28 Å / Num. all: 47085 / Num. obs: 11152 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 38.1 Å2 / Rmerge(I) obs: 0.11 |
Reflection shell | Resolution: 3→3.1 Å / Rmerge(I) obs: 0.44 / Num. unique all: 1115 / % possible all: 98.2 |
Reflection | *PLUS Num. measured all: 47085 |
Reflection shell | *PLUS Lowest resolution: 3.1 Å / % possible obs: 98.2 % / Rmerge(I) obs: 0.442 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: WINGED BEAN BASIC LECTIN Resolution: 3→20 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 224886.48 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 31.83 Å2 / ksol: 0.2458 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | |||||||||||||||||||||||||
LS refinement shell | Resolution: 3→3.19 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.4 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 8.2 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 46.7 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.332 / % reflection Rfree: 7.8 % / Rfactor Rwork: 0.285 |