+Open data
-Basic information
Entry | Database: PDB / ID: 1qmj | ||||||
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Title | CG-16, a homodimeric agglutinin from chicken liver | ||||||
Components | BETA-GALACTOSIDE-BINDING LECTIN | ||||||
Keywords | SUGAR BINDING PROTEIN / GALECTIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | GALLUS GALLUS (chicken) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Varela, P.F. / Solis, D. / Diaz-Maurino, T. / Kaltner, H. / Gabius, H.-J. / Romero, A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1999 Title: The 2.15 A Crystal Structure of Cg-16, the Developmentally Regulated Homodimeric Chicken Galectin Authors: Varela, P.F. / Solis, D. / Diaz-Maurino, T. / Kaltner, H. / Gabius, H.-J. / Romero, A. #1: Journal: Biochem.Biophys.Res.Commun. / Year: 1976 Title: Developmentally Regulated Lectin in Embryonic Chick Muscle and a Myogenic Cell Line Authors: Nowak, T.P. / Haywood, P.L. / Barondes, S.H. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE ANTI-PARALLEL BETA-SHEET STRUCTURE OF EACH MONOMER IS ... SHEET DETERMINATION METHOD: DSSP THE ANTI-PARALLEL BETA-SHEET STRUCTURE OF EACH MONOMER IS EXTENDED AS THE TWO MONOMERS ASSOCIATE TO FORM A DIMER CONTAINING AN EXTENDED BETA-SANDWICH, EACH WITH THE SAME JELLY ROLL TOPOLOGY. STRANDS 1 OF EACH SHEET A1 AND B1 ARE CONNECTED AS ARE STRANS 5 OF EACH SHEET A2 AND B2. THE SHEET IS HOWEVER, PRESENT HERE PER MONOMER ONLY. THE SHEET STRUCTURE OF THIS MOLECULE IS ALSO BIFURCATED, WITH STRAND 5 OF SHEET A1 (B1) CONNECTED TO STRAND 1 OF SHEET A3 (B3). |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qmj.cif.gz | 67.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qmj.ent.gz | 50.1 KB | Display | PDB format |
PDBx/mmJSON format | 1qmj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qmj_validation.pdf.gz | 383.5 KB | Display | wwPDB validaton report |
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Full document | 1qmj_full_validation.pdf.gz | 386.7 KB | Display | |
Data in XML | 1qmj_validation.xml.gz | 7.1 KB | Display | |
Data in CIF | 1qmj_validation.cif.gz | 11.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qm/1qmj ftp://data.pdbj.org/pub/pdb/validation_reports/qm/1qmj | HTTPS FTP |
-Related structure data
Related structure data | 1slaS 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: (-0.95636, -0.28284, 0.07327), Vector: |
-Components
#1: Protein | Mass: 14692.690 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) GALLUS GALLUS (chicken) / Organ: LIVER / References: UniProt: P23668 #2: Chemical | ChemComp-BME / #3: Water | ChemComp-HOH / | Compound details | THE NUMBERING IS MADE ACCORDING TO THE BOVINE GAL-1 STRUCTURE. THERE IS A GAP BETWEEN RESIDUES ...THE NUMBERING IS MADE ACCORDING TO THE BOVINE GAL-1 STRUCTURE. THERE IS A GAP BETWEEN RESIDUES GLU102 AND VAL104 - MAXIMIZE THE STRUCTURAL | Sequence details | RESIDUES MET1 AND GLU2 ARE NOT MODELLED. NUMBERING IN THE PDB DATA BASE IS MADE ACCORDING TO THE ...RESIDUES MET1 AND GLU2 ARE NOT MODELLED. NUMBERING IN THE PDB DATA BASE IS MADE ACCORDING TO THE GAL-1 BOVINE STRUCTURE. THIS NUMBERING GIVES A GAP BETWEEN RESIDUES 102 AND 104. | |
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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: 2.8 Å3/Da / Density % sol: 55 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion / pH: 5.6 Details: CRYSTALS WERE OBTAINED IN HANGING OR SITTING DROPS BY MIXING EQUAL VOLUMES OF THE PROTEIN SOLUTION (10 MG/ML) AND THE PRECIPITATING BUFFER (2M AMMONIUM SULPHATE, 5% (V/V) ISOPROPANOL AND 1% ...Details: CRYSTALS WERE OBTAINED IN HANGING OR SITTING DROPS BY MIXING EQUAL VOLUMES OF THE PROTEIN SOLUTION (10 MG/ML) AND THE PRECIPITATING BUFFER (2M AMMONIUM SULPHATE, 5% (V/V) ISOPROPANOL AND 1% BETA-MERCAPTO ETHANOL, PH 5.6) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / pH: 7.2 / Method: vapor diffusionDetails: drop consists of equal volume of protein and precipitant solutions | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 1999 |
Radiation | Monochromator: GRAPHITE(002) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→30 Å / Num. obs: 15244 / % possible obs: 87.8 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Biso Wilson estimate: 31.5 Å2 / Rmerge(I) obs: 0.0307 / Rsym value: 0.056 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 2.15→2.25 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.0451 / Mean I/σ(I) obs: 4 / Rsym value: 0.204 / % possible all: 75 |
Reflection | *PLUS Rmerge(I) obs: 0.056 |
Reflection shell | *PLUS % possible obs: 75 % / Rmerge(I) obs: 0.204 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1SLA Resolution: 2.15→8 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 33.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.25 Å / Total num. of bins used: 8
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Xplor file |
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