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- PDB-3d34: Structure of the F-spondin domain of mindin -

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Basic information

Entry
Database: PDB / ID: 3d34
TitleStructure of the F-spondin domain of mindin
ComponentsSpondin-2
KeywordsIMMUNE SYSTEM / F-spondin domain of mindin / Cell adhesion / Extracellular matrix / Immune response / Polymorphism / Secreted
Function / homology
Function and homology information


mast cell mediated immunity / Defective B3GALTL causes PpS / O-glycosylation of TSR domain-containing proteins / opsonization / induction of bacterial agglutination / positive regulation of macrophage cytokine production / defense response to fungus / extracellular matrix / lipopolysaccharide binding / antigen binding ...mast cell mediated immunity / Defective B3GALTL causes PpS / O-glycosylation of TSR domain-containing proteins / opsonization / induction of bacterial agglutination / positive regulation of macrophage cytokine production / defense response to fungus / extracellular matrix / lipopolysaccharide binding / antigen binding / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / cellular response to lipopolysaccharide / defense response to virus / cell adhesion / innate immune response / extracellular exosome / metal ion binding
Similarity search - Function
F-spondin domain / Spondin, N-terminal / Spondin, N-terminal domain superfamily / Spondin_N / Spondin domain profile. / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / Immunoglobulin-like ...F-spondin domain / Spondin, N-terminal / Spondin, N-terminal domain superfamily / Spondin_N / Spondin domain profile. / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
NICKEL (II) ION / Spondin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsLi, Y. / Mariuzza, R.A.
CitationJournal: Embo J. / Year: 2009
Title: Structure of the F-spondin domain of mindin, an integrin ligand and pattern recognition molecule.
Authors: Li, Y. / Cao, C. / Jia, W. / Yu, L. / Mo, M. / Wang, Q. / Huang, Y. / Lim, J.M. / Ishihara, M. / Wells, L. / Azadi, P. / Robinson, H. / He, Y.W. / Zhang, L. / Mariuzza, R.A.
History
DepositionMay 9, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.classification / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Spondin-2
B: Spondin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,77110
Polymers49,3392
Non-polymers4328
Water5,747319
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-10.6 kcal/mol
Surface area19240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.600, 68.027, 110.130
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Spondin-2 / Mindin / Differentially expressed in cancerous and non-cancerous lung cells 1 / DIL-1


Mass: 24669.549 Da / Num. of mol.: 2 / Fragment: F-spondin domain, UNP residues 27-249
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPON2, DIL1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BUD6
#2: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / 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: 1.92 Å3/Da / Density % sol: 35.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0-6% PEG2000, 100mM Tris-HCl, 10mM NiCl2, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→29.73 Å / Num. obs: 35173 / % possible obs: 97.3 % / Redundancy: 3.08 % / Rmerge(I) obs: 0.052 / Χ2: 0.98 / Net I/σ(I): 13.5 / Scaling rejects: 1319
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2.96 % / Rmerge(I) obs: 0.163 / Mean I/σ(I) obs: 5.8 / Num. measured all: 9255 / Num. unique all: 35173 / Χ2: 0.95 / % possible all: 93.7

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Processing

Software
NameVersionClassificationNB
d*TREK9.2SSIdata scaling
CNSrefinement
PDB_EXTRACT3.005data extraction
DENZOdata reduction
SCALEPACKdata scaling
RefinementHighest resolution: 1.8 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.215 1757 4.9 %
Rwork0.189 --
obs-34285 95.2 %
Solvent computationBsol: 56.5 Å2
Displacement parametersBiso mean: 19.306 Å2
Baniso -1Baniso -2Baniso -3
1--0.181 Å20 Å20 Å2
2--0.185 Å20 Å2
3----0.005 Å2
Refinement stepCycle: LAST / Highest resolution: 1.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3279 0 8 319 3606
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.0951.5
X-RAY DIFFRACTIONc_scbond_it1.792
X-RAY DIFFRACTIONc_mcangle_it1.5922
X-RAY DIFFRACTIONc_scangle_it2.5652.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param

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