+Open data
-Basic information
Entry | Database: PDB / ID: 1by2 | ||||||
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Title | STRUCTURE OF M2BP SCAVENGER RECEPTOR CYSTEINE-RICH DOMAIN | ||||||
Components | MAC-2 BINDING PROTEIN | ||||||
Keywords | EXTRACELLULAR MODULE / SCAVENGER RECEPTOR / TUMOUR-ASSOCIATED ANTIGEN / EXTRACELLULAR MATRIX / GLYCOSYLATED PROTEIN | ||||||
Function / homology | Function and homology information platelet dense granule lumen / scavenger receptor activity / cellular defense response / Platelet degranulation / collagen-containing extracellular matrix / blood microparticle / cell adhesion / signal transduction / extracellular space / extracellular exosome ...platelet dense granule lumen / scavenger receptor activity / cellular defense response / Platelet degranulation / collagen-containing extracellular matrix / blood microparticle / cell adhesion / signal transduction / extracellular space / extracellular exosome / extracellular region / membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MIRAS / Resolution: 2 Å | ||||||
Authors | Hohenester, E. / Sasaki, T. / Timpl, R. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1999 Title: Crystal structure of a scavenger receptor cysteine-rich domain sheds light on an ancient superfamily. Authors: Hohenester, E. / Sasaki, T. / Timpl, R. #1: Journal: Embo J. / Year: 1998 Title: Mac-2 Binding Protein is a Cell-Adhesive Protein of the Extracellular Matrix which Self-Assembles Into Ring-Like Structures and Binds Beta1 Integrins, Collagens and Fibronectin Authors: Sasaki, T. / Brakebusch, C. / Engel, J. / Timpl, R. #2: Journal: Trends Biochem.Sci. / Year: 1994 Title: The Srcr Superfamily: A Family Reminiscent of the Ig Superfamily Authors: Resnick, D. / Pearson, A. / Krieger, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1by2.cif.gz | 31.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1by2.ent.gz | 22.9 KB | Display | PDB format |
PDBx/mmJSON format | 1by2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1by2_validation.pdf.gz | 379.4 KB | Display | wwPDB validaton report |
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Full document | 1by2_full_validation.pdf.gz | 379.4 KB | Display | |
Data in XML | 1by2_validation.xml.gz | 3.7 KB | Display | |
Data in CIF | 1by2_validation.cif.gz | 5.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/by/1by2 ftp://data.pdbj.org/pub/pdb/validation_reports/by/1by2 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 12705.093 Da / Num. of mol.: 1 / Fragment: SCAVENGER RECEPTOR CYSTEINE-RICH (SRCR) DOMAIN / Mutation: N-TERMINAL APLA Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line: 293-EBNA / Organ: KIDNEY / Cell line (production host): 293-EBNA / Production host: Homo sapiens (human) / References: UniProt: Q08380 |
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#2: Sugar | ChemComp-NAG / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 50 % Description: TWO DERIVATIVES (SMCL3 AND UO2SO4) WERE USED AT 3.0 A | |||||||||||||||||||||||||
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Crystal grow | pH: 6 / Details: pH 6.0 | |||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
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: ELLIOTT GX-21 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 7, 1998 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 9843 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 6 % / Rmerge(I) obs: 0.186 / Mean I/σ(I) obs: 3.7 / % possible all: 100 |
Reflection | *PLUS Num. measured all: 60557 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 2→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0 Isotropic thermal model: INDIVIDUAL RESTRAINED, RMS BONDS 3.5 A**2 Cross valid method: FREE R-FACTOR / σ(F): 0
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Displacement parameters | Biso mean: 20 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati d res low obs: 6 Å / Luzzati sigma a obs: 0.18 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.09 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.84 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rwork: 0.27 |