+Open data
-Basic information
Entry | Database: PDB / ID: 1qr4 | ||||||
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Title | TWO FIBRONECTIN TYPE-III DOMAIN SEGMENT FROM CHICKEN TENASCIN | ||||||
Components | PROTEIN (TENASCIN) | ||||||
Keywords | STRUCTURAL PROTEIN / TENASCIN / FIBRONECTIN TYPE-III / HEPARIN / EXTRACELLULAR MATRIX / ADHESION / FUSION PROTEIN | ||||||
Function / homology | Function and homology information collagen-containing extracellular matrix / cell adhesion / signaling receptor binding / extracellular space Similarity search - Function | ||||||
Biological species | Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||
Authors | Piontek, K. / Bisig, D.A. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1999 Title: Purification, crystallization and preliminary crystallographic studies of a two fibronectin type-III domain segment from chicken tenascin encompassing the heparin- and contactin-binding regions. Authors: Bisig, D. / Weber, P. / Vaughan, L. / Winterhalter, K.H. / Piontek, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qr4.cif.gz | 81 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qr4.ent.gz | 60.7 KB | Display | PDB format |
PDBx/mmJSON format | 1qr4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qr4_validation.pdf.gz | 419.8 KB | Display | wwPDB validaton report |
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Full document | 1qr4_full_validation.pdf.gz | 426.5 KB | Display | |
Data in XML | 1qr4_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | 1qr4_validation.cif.gz | 21.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qr/1qr4 ftp://data.pdbj.org/pub/pdb/validation_reports/qr/1qr4 | HTTPS FTP |
-Related structure data
Related structure data | 1fnfS 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:
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-Components
#1: Protein | Mass: 20260.840 Da / Num. of mol.: 2 / Fragment: FNIII DOMAINS 5-6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Cellular location: EXTRACELLULAR MATRIX / Plasmid: PDS9/56 / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: P10039 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 47 % Description: DATA WERE COLLECTED AT THE SYNCHROTRON FACILITIES OF DESY/X31 AND ESRF/BM01A | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 5 Details: 27% PEG2000, 100MM NAAC PH 4.5-5.0, 10-100 MM MGCL2/CACL2, | ||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 4.5 / Method: vapor diffusion, hanging drop / Details: used to seeding | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Wavelength: 0.9 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→20 Å / Num. obs: 11344 / % possible obs: 94 % / Redundancy: 6 % / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.55→2.64 Å / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2 / Rsym value: 0.47 / % possible all: 70.1 |
Reflection | *PLUS Num. measured all: 68031 |
Reflection shell | *PLUS % possible obs: 75.5 % / Mean I/σ(I) obs: 2.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1FNF Resolution: 2.55→17.8 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 49.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.55→17.8 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.55→2.67 Å / Total num. of bins used: 8 /
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 17.8 Å / σ(F): 0 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 49.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.421 / Rfactor Rwork: 0.377 |