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- PDB-2ic2: Crystal Structure of the First FNIII Domain of Ihog -

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Basic information

Entry
Database: PDB / ID: 2ic2
TitleCrystal Structure of the First FNIII Domain of Ihog
ComponentsCG9211-PA
KeywordsPROTEIN BINDING / ihog / hedgehog / fibronectin type III
Function / homology
Function and homology information


Netrin-1 signaling / DCC mediated attractive signaling / Caspase activation via Dependence Receptors in the absence of ligand / maintenance of protein location in extracellular region / Myogenesis / cuticle pattern formation / Ligand-receptor interactions / cytoneme / Assembly of the 'signalling complexes' / Signaling by ROBO receptors ...Netrin-1 signaling / DCC mediated attractive signaling / Caspase activation via Dependence Receptors in the absence of ligand / 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 / membrane => GO:0016020 / 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 / Interference hedgehog
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.3 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 12, 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
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CG9211-PA
B: CG9211-PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3229
Polymers26,6492
Non-polymers6727
Water3,747208
1
A: CG9211-PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7095
Polymers13,3251
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CG9211-PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6134
Polymers13,3251
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.511, 39.480, 127.666
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a monomer, and the asymmetric unit contains two copies.

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Components

#1: Protein CG9211-PA / GH03927p


Mass: 13324.610 Da / Num. of mol.: 2 / Fragment: First FNIII Domain
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: Q2XY56, UniProt: Q9VM64*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 1.87 Å3/Da / Density % sol: 34.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.2
Details: 0.05M Citrate pH 3.2, 26% PEG 3350, 0.1M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDCrystal-ID
11
21
31
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9792, 0.9794, 0.9724
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 3, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.97941
30.97241
Reflection

D res high: 1.5 Å / D res low: 30 Å

Redundancy (%)IDAv σ(I) over netINumberRmerge(I) obsΧ2Num. obs% possible obs
9.7115.12991830.0671.053077093.3
9.9215.13053590.0731.213081093.6
9.9315.33066610.0711.173091893.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.23308310.0551.14210.1
2.563.2389.710.061.10510.3
2.242.5691.810.0671.12110.1
2.042.2493.310.0691.03310
1.892.0494.710.0761.1289.9
1.781.8994.810.0861.1579.8
1.691.7895.910.10219.7
1.621.6996.610.1130.9559.7
1.551.6297.210.1360.9639.4
1.51.5597.410.1440.9258.2
3.233083.420.0611.36810.3
2.563.2390.120.0651.31310.5
2.242.5692.320.0741.33210.3
2.042.2493.520.0751.22310.3
1.892.049520.0831.31510.1
1.781.8995.120.0931.31910
1.691.7896.120.111.13710
1.621.699720.1251.0489.9
1.551.6297.320.1461.0139.6
1.51.5597.620.1550.9758.2
3.233083.630.0591.28310.4
2.563.2390.230.0631.25510.5
2.242.5692.330.0721.27810.3
2.042.2493.630.0741.19510.3
1.892.049530.0821.29410.1
1.781.8995.130.0911.28410
1.691.7896.230.1081.10610
1.621.699730.121.00310
1.551.6297.430.1420.9919.5
1.51.5597.630.1490.9498.2
ReflectionResolution: 1.3→30 Å / Num. obs: 45209 / % possible obs: 90 % / Redundancy: 8.3 % / Rmerge(I) obs: 0.077 / Χ2: 0.992 / Net I/σ(I): 13.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.3-1.353.70.22832900.82367.2
1.35-1.44.60.20740000.87880.6
1.4-1.4660.18547630.95695.6
1.46-1.547.70.15348080.99597.7
1.54-1.649.30.13248591.03797.3
1.64-1.769.70.10747811.06596.3
1.76-1.949.80.08647660.9995.1
1.94-2.22100.07247231.00593.6
2.22-2.810.20.06846690.97691.4
2.8-3010.30.06945500.97285.2

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MADD res high: 1.6 Å / D res low: 30 Å / FOM : 0.58 / Reflection: 25235
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
13 wavelength10.97944.15-7.66
13 wavelength20.97924.64-6.38
13 wavelength30.97243.25-3.89
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
112.10625.24119.306SE9.90.58
212.42420.85213.138SE19.60.68
333.7533.0150.298SE5.80.33
433.0964.96730.832SE8.80.37
517.5343.34626.136SE30.40.82
Phasing MAD shell
Resolution (Å)FOM Reflection
5.78-300.661092
3.64-5.780.621973
2.84-3.640.642600
2.41-2.840.633100
2.13-2.410.583565
1.93-2.130.583937
1.77-1.930.564309
1.65-1.770.524659
Phasing dmFOM : 0.7 / FOM acentric: 0.7 / FOM centric: 0.65 / Reflection: 25236 / Reflection acentric: 22670 / Reflection centric: 2566
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
4.6-28.9390.890.910.851033785248
2.9-4.60.870.880.8332432785458
2.3-2.90.780.790.741963733463
2-2.30.720.720.6542673870397
1.7-20.640.640.5476927054638
1.6-1.70.550.560.4548054443362

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVE2.03phasing
CNSrefinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 1.3→28.9 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.234 2222 4.4 %random
Rwork0.215 ---
obs-44255 88.3 %-
Solvent computationBsol: 44.704 Å2
Displacement parametersBiso mean: 11.884 Å2
Baniso -1Baniso -2Baniso -3
1--1.703 Å20 Å20 Å2
2---0.072 Å20 Å2
3---1.775 Å2
Refinement stepCycle: LAST / Resolution: 1.3→28.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1801 0 35 208 2044
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.495
X-RAY DIFFRACTIONc_mcbond_it1.3821.5
X-RAY DIFFRACTIONc_scbond_it2.8032
X-RAY DIFFRACTIONc_mcangle_it1.9592
X-RAY DIFFRACTIONc_scangle_it3.4842.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top

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