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- PDB-2ibb: Crystal Structure of the First and Second FNIII Domains of Ihog -

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Basic information

Entry
Database: PDB / ID: 2ibb
TitleCrystal Structure of the First and Second FNIII Domains of Ihog
ComponentsCG9211-PA
KeywordsPROTEIN BINDING / ihog / hedgehog / fibronectin type III
Function / homology
Function and homology information


maintenance of protein location in extracellular region / Myogenesis / cuticle pattern formation / Ligand-receptor interactions / cytoneme / Assembly of the 'signalling complexes' / Signaling by ROBO receptors / : / wing disc pattern formation / wing disc anterior/posterior pattern formation ...maintenance of protein location in extracellular region / Myogenesis / cuticle pattern formation / Ligand-receptor interactions / cytoneme / Assembly of the 'signalling complexes' / Signaling by ROBO receptors / : / wing disc pattern formation / wing disc anterior/posterior pattern formation / compound eye development / hedgehog family protein binding / homotypic cell-cell adhesion / segment specification / patched binding / smoothened signaling pathway / coreceptor activity / cell-cell adhesion / heparin binding / cell surface / protein homodimerization activity / membrane / identical protein binding / plasma membrane
Similarity search - Function
Immunoglobulin domain / Immunoglobulin domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype ...Immunoglobulin domain / Immunoglobulin domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Interference hedgehog
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMcLellan, J.S. / Leahy, D.J.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Structure of a heparin-dependent complex of Hedgehog and Ihog.
Authors: McLellan, J.S. / Yao, S. / Zheng, X. / Geisbrecht, B.V. / Ghirlando, R. / Beachy, P.A. / Leahy, D.J.
History
DepositionSep 11, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CG9211-PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4494
Polymers24,1611
Non-polymers2883
Water23413
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.380, 65.240, 84.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CG9211-PA / GH03927p


Mass: 24161.174 Da / Num. of mol.: 1 / Fragment: Extracellular FNIII Domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: iHog, CG9211 / Plasmid: pT7HMT / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q9VM64
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: 0.05M Tris-HCl pH 7.9, 23% PEG 3350, 0.2M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 29, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 8851 / % possible obs: 98.1 % / Redundancy: 5 % / Rmerge(I) obs: 0.126 / Χ2: 1.412 / Net I/σ(I): 7.5
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.801 / Num. unique all: 879 / Χ2: 0.99 / % possible all: 99.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: First FNIII domain Ihog and PDB Entry: 1FNF domain 7
Resolution: 2.4→21.57 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.275 457 5.1 %random
Rwork0.244 ---
all-8958 --
obs-8332 93 %-
Solvent computationBsol: 23.396 Å2
Displacement parametersBiso mean: 38.263 Å2
Baniso -1Baniso -2Baniso -3
1--3.049 Å20 Å20 Å2
2---2.847 Å20 Å2
3---5.896 Å2
Refinement stepCycle: LAST / Resolution: 2.4→21.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1670 0 15 13 1698
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.665
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:ion.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param

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