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Yorodumi- PDB-2bve: Structure of the N-terminal of Sialoadhesin in complex with 2-Phe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2bve | ||||||
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Title | Structure of the N-terminal of Sialoadhesin in complex with 2-Phenyl- Prop5Ac | ||||||
Components | SIALOADHESIN | ||||||
Keywords | IMMUNE SYSTEM / IMMUNOGLOBULIN / LECTIN / SUPERFAMILY / CARBOHYDRATE BINDING / SIGLEC / INHIBITOR DESIGN / CELL ADHESION | ||||||
Function / homology | Function and homology information positive regulation of T cell apoptotic process / positive regulation of extrinsic apoptotic signaling pathway / virion binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of type I interferon production / late endosome / carbohydrate binding / clathrin-dependent endocytosis of virus by host cell / early endosome / cell adhesion ...positive regulation of T cell apoptotic process / positive regulation of extrinsic apoptotic signaling pathway / virion binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of type I interferon production / late endosome / carbohydrate binding / clathrin-dependent endocytosis of virus by host cell / early endosome / cell adhesion / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Zaccai, N.R. / May, A.P. / Robinson, R.C. / Burtnick, L.D. / Crocker, P. / Brossmer, R. / Kelm, S. / Jones, E.Y. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Crystallographic and in Silico Analysis of the Sialoside-Binding Characteristics of the Siglec Sialoadhesin. Authors: Zaccai, N.R. / May, A.P. / Robinson, R.C. / Burtnick, L.D. / Crocker, P. / Brossmer, R. / Kelm, S. / Jones, E.Y. | ||||||
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 | 2bve.cif.gz | 63.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bve.ent.gz | 46.8 KB | Display | PDB format |
PDBx/mmJSON format | 2bve.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bv/2bve ftp://data.pdbj.org/pub/pdb/validation_reports/bv/2bve | HTTPS FTP |
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-Related structure data
Related structure data | 1qfoS 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.35759, -0.82448, -0.43859), Vector: |
-Components
#1: Protein | Mass: 13319.107 Da / Num. of mol.: 2 Fragment: DOMAIN ONE, IG-LIKE V-TYPE DOMAIN, RESIDUES 20-138 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Cell: MACROPHAGE / Plasmid: PEE14 PLASMID / Production host: CRICETULUS GRISEUS (Chinese hamster) / References: UniProt: Q62230 #2: Sugar | #3: 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: 2.19 Å3/Da / Density % sol: 43.8 % Description: DATA COLLECTED TO 2.1 ANGSTROM. STRUCTURE ONLY REFINED TO 2.2 ANGSTROM. MOLECULAR REPLACEMENT WITH ALL DATA BETWEEN 20 AND 3 ANGSTROM. |
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Crystal grow | pH: 5.6 Details: 1:1 DROP WITH 10MG/ML PROTEIN, 10MM DTT AND 24% PEG4000, 0.16MM MGCL2, 0.08 TRIS PH 8.5, 25MM COMPOUND |
-Data collection
Diffraction | Mean temperature: 104 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. obs: 13244 / % possible obs: 92 % / Observed criterion σ(I): -3 / Redundancy: 4.95 % / Biso Wilson estimate: 11.4 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 10.45 |
Reflection shell | Resolution: 2.17→2.26 Å / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.3 / % possible all: 92 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QFO Resolution: 2.2→19.72 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 96148.69 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 54.0175 Å2 / ksol: 0.360159 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→19.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
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Xplor file |
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