+Open data
-Basic information
Entry | Database: PDB / ID: 1zlg | ||||||
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Title | Solution structure of the extracellular matrix protein anosmin-1 | ||||||
Components | Anosmin 1 | ||||||
Keywords | HORMONE/GROWTH FACTOR / INSULIN-LIKE GROWTH FACTOR RECEPTOR CYS-RICH FOLD / WHEY ACIDIC PROTEIN FOLD / FIBRONECTIN TYPE III FOLD / HORMONE-GROWTH FACTOR COMPLEX | ||||||
Function / homology | Function and homology information FGFR1c ligand binding and activation / extracellular matrix structural constituent / extracellular matrix / axon guidance / Negative regulation of FGFR1 signaling / neuron differentiation / chemotaxis / serine-type endopeptidase inhibitor activity / heparin binding / cell adhesion ...FGFR1c ligand binding and activation / extracellular matrix structural constituent / extracellular matrix / axon guidance / Negative regulation of FGFR1 signaling / neuron differentiation / chemotaxis / serine-type endopeptidase inhibitor activity / heparin binding / cell adhesion / cell surface / extracellular space / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION SCATTERING / SYNCHROTRON | ||||||
Authors | Hu, Y. / Sun, Z. / Eaton, J.T. / Bouloux, P.M. / Perkins, S.J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: Extended and Flexible Domain Solution Structure of the Extracellular Matrix Protein Anosmin-1 by X-ray Scattering, Analytical Ultracentrifugation and Constrained Modelling. Authors: Hu, Y. / Sun, Z. / Eaton, J.T. / Bouloux, P.M. / Perkins, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zlg.cif.gz | 35.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zlg.ent.gz | 16.5 KB | Display | PDB format |
PDBx/mmJSON format | 1zlg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1zlg_validation.pdf.gz | 290.7 KB | Display | wwPDB validaton report |
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Full document | 1zlg_full_validation.pdf.gz | 293.2 KB | Display | |
Data in XML | 1zlg_validation.xml.gz | 1.2 KB | Display | |
Data in CIF | 1zlg_validation.cif.gz | 6.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zl/1zlg ftp://data.pdbj.org/pub/pdb/validation_reports/zl/1zlg | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 76545.117 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KAL1, ADMLX, KAL, KALIG1 / Plasmid: pMT/BIP/V5-His / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): Schneider 2 (S2) cells / References: UniProt: P23352 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION SCATTERING |
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-Data collection
Diffraction |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID2 | ||||||||||||
Detector |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength | Relative weight: 1 | ||||||||||||
Soln scatter | Type: x-ray / Buffer name: 12 MM NA PHOSPHATE, 220 MM NACL / Conc. range: 0.2-0.4 / Data analysis software list: SCTPL7, GNOM / Data reduction software list: MULTICCD / Detector type: FRELON CCD CAMERA / Mean guiner radius: 6.65 nm / Mean guiner radius esd: 0.49 nm / Min mean cross sectional radii gyration: 1.88 nm / Min mean cross sectional radii gyration esd: 0.77 nm / Num. of time frames: 1 / Protein length: 1 / Sample pH: 7.4 / Source beamline: ID02 / Source class: Y / Source type: ESRF BEAMLINE ID02 / Temperature: 288 K |
-Processing
Software |
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Refinement step | Cycle: LAST
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Soln scatter model | Method: CONSTRAINED SCATTERING FITTING OF HOMOLOGY MODELS Conformer selection criteria: THE MODELLED SCATTERING CURVES WERE ASSESSED BY CALCULATION OF THE RG, RSX-1 AND VALUES IN THE SAME Q RANGES USED IN THE EXPERIMENTAL GUINIER FITS. MODELS WERE THEN ...Conformer selection criteria: THE MODELLED SCATTERING CURVES WERE ASSESSED BY CALCULATION OF THE RG, RSX-1 AND VALUES IN THE SAME Q RANGES USED IN THE EXPERIMENTAL GUINIER FITS. MODELS WERE THEN RANKED USING A GOODNESS-OF-FIT R-FACTOR DEFINED BY ANALOGY WITH PROTEIN CRYSTALLOGRAPHY Details: HOMOLOGY MODELS WERE BUILT FOR THE CYS-BOX, WAP AND FOUR FNIII DOMAINS. THE POSITIONS OF THE DOMAINS WERE DETERMINED BY AN APPROACH THAT COMBINED RANDOMISED LINKER PEPTIDE STRUCTURES ...Details: HOMOLOGY MODELS WERE BUILT FOR THE CYS-BOX, WAP AND FOUR FNIII DOMAINS. THE POSITIONS OF THE DOMAINS WERE DETERMINED BY AN APPROACH THAT COMBINED RANDOMISED LINKER PEPTIDE STRUCTURES PRODUCED BY MOLECULAR DYNAMICS SIMULATIONS WITH CURVE-FITTING TO EXPERIMENTAL X-RAY SOLUTION SCATTERING DATA. A SINGLE ARRANGEMENT OF THE SIX DOMAINS IS PRESENTED, WHICH IS REPRESENTATIVE OF A FAMILY OF STRUCTURES THAT FIT THE SCATTERING DATA. MORE DETAILS ON THE MODELLING STRATEGY ARE CONTAINED IN THE PRIMARY REFERENCE. THE ALGORITHM RESULTED IN SEVERAL CLOSE APPROACHES BETWEEN ATOMS. THIS ENTRY CONTAINS FOUR SUCH PAIRS ALA 292 - PRO 318 PRO 291 - GLU 319 PRO 27 - PHE 122 TYR 225 - PHE 355 Num. of conformers calculated: 10000 / Num. of conformers submitted: 1 / Representative conformer: 1 / Software author list: ACCELRYS Software list: INSIGHT II, HOMOLOGY, DISCOVERY, BIOPOLYMER, DELPHI, O, SCTPL7, GNOM |