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- PDB-6rk1: Crystal structure of TSP1 domain from CCN3 -

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Basic information

Entry
Database: PDB / ID: 6rk1
TitleCrystal structure of TSP1 domain from CCN3
ComponentsCCN family member 3
KeywordsSTRUCTURAL PROTEIN / extra-cellular matrix / CCN family / matricellular protein / signalling
Function / homology
Function and homology information


negative regulation of sensory perception of pain / endothelial cell-cell adhesion / bone regeneration / smooth muscle cell proliferation / negative regulation of monocyte chemotaxis / negative regulation of chondrocyte proliferation / : / hematopoietic stem cell homeostasis / negative regulation of myotube differentiation / endothelial cell chemotaxis ...negative regulation of sensory perception of pain / endothelial cell-cell adhesion / bone regeneration / smooth muscle cell proliferation / negative regulation of monocyte chemotaxis / negative regulation of chondrocyte proliferation / : / hematopoietic stem cell homeostasis / negative regulation of myotube differentiation / endothelial cell chemotaxis / type B pancreatic cell proliferation / fibroblast migration / gap junction / negative regulation of non-canonical NF-kappaB signal transduction / Notch binding / cell adhesion mediated by integrin / smooth muscle cell migration / negative regulation of SMAD protein signal transduction / positive regulation of Notch signaling pathway / negative regulation of insulin secretion / chondrocyte differentiation / cell chemotaxis / extracellular matrix / growth factor activity / negative regulation of cell growth / negative regulation of inflammatory response / integrin binding / heparin binding / regulation of gene expression / angiogenesis / collagen-containing extracellular matrix / cell adhesion / axon / intracellular membrane-bounded organelle / neuronal cell body / dendrite / signal transduction / extracellular region / cytoplasm
Similarity search - Function
IGFBP-related, CNN / CCN, TSP1 domain / CCN3 Nov like TSP1 domain / Insulin-like growth factor binding protein, N-terminal, Cys-rich conserved site / Insulin-like growth factor-binding protein (IGFBP) N-terminal domain signature. / Glycoprotein hormone subunit beta / Cystine-knot domain / Insulin-like growth factor binding protein / Insulin-like growth factor-binding protein, IGFBP / Insulin-like growth factor-binding protein (IGFBP) N-terminal domain profile. ...IGFBP-related, CNN / CCN, TSP1 domain / CCN3 Nov like TSP1 domain / Insulin-like growth factor binding protein, N-terminal, Cys-rich conserved site / Insulin-like growth factor-binding protein (IGFBP) N-terminal domain signature. / Glycoprotein hormone subunit beta / Cystine-knot domain / Insulin-like growth factor binding protein / Insulin-like growth factor-binding protein, IGFBP / Insulin-like growth factor-binding protein (IGFBP) N-terminal domain profile. / Insulin growth factor-binding protein homologues / C-terminal cystine knot signature. / C-terminal cystine knot domain profile. / Cystine knot, C-terminal / C-terminal cystine knot-like domain (CTCK) / von Willebrand factor type C domain / VWFC domain signature. / VWFC domain profile. / von Willebrand factor (vWF) type C domain / VWFC domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / Growth factor receptor cysteine-rich domain superfamily
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.63 Å
AuthorsXu, E.-R. / Hyvonen, M.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2020
Title: The thrombospondin module 1 domain of the matricellular protein CCN3 shows an atypical disulfide pattern and incomplete CWR layers.
Authors: Xu, E.R. / Lafita, A. / Bateman, A. / Hyvonen, M.
History
DepositionApr 29, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CCN family member 3
B: CCN family member 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,27612
Polymers12,9032
Non-polymers37410
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-88 kcal/mol
Surface area6910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.860, 52.860, 102.390
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-461-

HOH

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Components

#1: Protein CCN family member 3 / Cellular communication network factor 3 / Nephroblastoma-overexpressed gene protein homolog / ...Cellular communication network factor 3 / Nephroblastoma-overexpressed gene protein homolog / Protein NOV homolog / NovH


Mass: 6451.354 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: TSP1 domain of CCN3 / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ccn3, Nov / Plasmid: pHAT4
Details (production host): T7 promoter driven vector with TEV_cleavable hexa-His tag
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pUBS520 / References: UniProt: Q9QZQ5
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 3.2 Å3/Da / Density % sol: 61.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8 / Details: 3.0 M NaCl, 0.1 M Tris pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.63→34.13 Å / Num. obs: 2082 / % possible obs: 100 % / Observed criterion σ(F): 2 / Redundancy: 7.6 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 13
Reflection shellResolution: 1.63→1.66 Å / Num. unique obs: 220

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 1.63→34.13 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 16.02
RfactorNum. reflection% reflection
Rfree0.1844 1050 4.92 %
Rwork0.1615 --
obs0.1626 21339 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.63→34.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms710 0 15 140 865
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005762
X-RAY DIFFRACTIONf_angle_d0.7511028
X-RAY DIFFRACTIONf_dihedral_angle_d10.97506
X-RAY DIFFRACTIONf_chiral_restr0.044116
X-RAY DIFFRACTIONf_plane_restr0.004132
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6301-1.70430.23161420.21442491X-RAY DIFFRACTION100
1.7043-1.79410.19371200.16812488X-RAY DIFFRACTION100
1.7941-1.90650.18981320.15562508X-RAY DIFFRACTION100
1.9065-2.05370.15641320.12412474X-RAY DIFFRACTION100
2.0537-2.26030.14651420.13752508X-RAY DIFFRACTION100
2.2603-2.58730.19581370.15692533X-RAY DIFFRACTION100
2.5873-3.25930.16681260.16582571X-RAY DIFFRACTION100
3.2593-34.13750.20931190.17272716X-RAY DIFFRACTION100

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