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- PDB-1zlg: Solution structure of the extracellular matrix protein anosmin-1 -

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Basic information

Entry
Database: PDB / ID: 1zlg
TitleSolution structure of the extracellular matrix protein anosmin-1
ComponentsAnosmin 1
KeywordsHORMONE/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 / serine-type endopeptidase inhibitor activity / neuron differentiation / chemotaxis / heparin binding / cell adhesion ...FGFR1c ligand binding and activation / extracellular matrix structural constituent / extracellular matrix / axon guidance / Negative regulation of FGFR1 signaling / serine-type endopeptidase inhibitor activity / neuron differentiation / chemotaxis / heparin binding / cell adhesion / cell surface / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Anosmin-1, cysteine rich domain / Anosmin-1 / Anosmin cysteine rich domain / WAP-type 'four-disulfide core' domain / Elafin-like superfamily / WAP-type (Whey Acidic Protein) 'four-disulfide core' / WAP-type 'four-disulfide core' domain profile. / Four-disulfide core domains / Fibronectin type III domain / Fibronectin type 3 domain ...Anosmin-1, cysteine rich domain / Anosmin-1 / Anosmin cysteine rich domain / WAP-type 'four-disulfide core' domain / Elafin-like superfamily / WAP-type (Whey Acidic Protein) 'four-disulfide core' / WAP-type 'four-disulfide core' domain profile. / Four-disulfide core domains / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION SCATTERING / SYNCHROTRON
AuthorsHu, Y. / Sun, Z. / Eaton, J.T. / Bouloux, P.M. / Perkins, S.J.
CitationJournal: 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
DepositionMay 6, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Dec 21, 2022Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Anosmin 1


Theoretical massNumber of molelcules
Total (without water)76,5451
Polymers76,5451
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Anosmin 1 / Kallmann syndrome protein / Adhesion molecule-like X-linked / Coordinate model: Cα atoms only


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

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Experiment

ExperimentMethod: SOLUTION SCATTERING

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12881
21
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID2
Detector
TypeIDDetectorDate
FRELON CCD CAMERA1CCDMay 1, 2003
FRELON CCD CAMERA2CCDDec 1, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
Soln scatterType: 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

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Processing

Software
NameVersionClassification
MULTICCDdata collection
SCTPL7data reduction
GNOMdata reduction
Insight IIII 98.0model building
SCTPL7model building
MULTICCDdata reduction
SCTPL7data scaling
GNOMdata scaling
SCTPL7phasing
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms680 0 0 0 680
Soln scatter modelMethod: 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

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