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- PDB-2cg6: Second and third fibronectin type I module pair (crystal form I). -

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Basic information

Entry
Database: PDB / ID: 2cg6
TitleSecond and third fibronectin type I module pair (crystal form I).
ComponentsHUMAN FIBRONECTIN
KeywordsSIGNALING PROTEIN / CELL ADHESION / GLYCOPROTEIN / HEPARIN-BINDING / ACUTE PHASE / ALTERNATIVE SPLICING / PHOSPHORYLATION / PYRROLIDONE CARBOXYLIC ACID / SULFATION
Function / homology
Function and homology information


negative regulation of monocyte activation / calcium-independent cell-matrix adhesion / negative regulation of transforming growth factor beta production / Fibronectin matrix formation / Extracellular matrix organization / positive regulation of substrate-dependent cell migration, cell attachment to substrate / neural crest cell migration involved in autonomic nervous system development / peptidase activator activity / fibrinogen complex / peptide cross-linking ...negative regulation of monocyte activation / calcium-independent cell-matrix adhesion / negative regulation of transforming growth factor beta production / Fibronectin matrix formation / Extracellular matrix organization / positive regulation of substrate-dependent cell migration, cell attachment to substrate / neural crest cell migration involved in autonomic nervous system development / peptidase activator activity / fibrinogen complex / peptide cross-linking / integrin activation / ALK mutants bind TKIs / cell-substrate junction assembly / biological process involved in interaction with symbiont / proteoglycan binding / Molecules associated with elastic fibres / extracellular matrix structural constituent / MET activates PTK2 signaling / Syndecan interactions / p130Cas linkage to MAPK signaling for integrins / endodermal cell differentiation / endoplasmic reticulum-Golgi intermediate compartment / GRB2:SOS provides linkage to MAPK signaling for Integrins / Non-integrin membrane-ECM interactions / basement membrane / ECM proteoglycans / Integrin cell surface interactions / positive regulation of axon extension / collagen binding / Degradation of the extracellular matrix / Integrin signaling / extracellular matrix / substrate adhesion-dependent cell spreading / regulation of ERK1 and ERK2 cascade / cell-matrix adhesion / platelet alpha granule lumen / acute-phase response / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / Post-translational protein phosphorylation / wound healing / regulation of protein phosphorylation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / response to wounding / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / positive regulation of fibroblast proliferation / GPER1 signaling / Signaling by BRAF and RAF1 fusions / Signaling by ALK fusions and activated point mutants / integrin binding / Platelet degranulation / heparin binding / heart development / nervous system development / regulation of cell shape / protease binding / Interleukin-4 and Interleukin-13 signaling / angiogenesis / collagen-containing extracellular matrix / blood microparticle / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell adhesion / apical plasma membrane / endoplasmic reticulum lumen / signaling receptor binding / positive regulation of cell population proliferation / positive regulation of gene expression / extracellular space / extracellular exosome / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Fibronectin type I domain / : / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / Complement Module, domain 1 / Complement Module; domain 1 / Fibronectin type II domain / Fibronectin type II domain superfamily ...Fibronectin type I domain / : / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / Complement Module, domain 1 / Complement Module; domain 1 / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / Kringle-like fold / EGF-like domain signature 1. / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Ribbon / Immunoglobulin-like fold / Mainly Beta
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.55 Å
AuthorsRudino-Pinera, E. / Ravelli, R.B.G. / Sheldrick, G.M. / Nanao, M.H. / Werner, J.M. / Schwarz-Linek, U. / Potts, J.R. / Garman, E.F.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: The Solution and Crystal Structures of a Module Pair from the Staphylococcus Aureus-Binding Site of Human Fibronectin-A Tale with a Twist.
Authors: Rudino-Pinera, E. / Ravelli, R.B.G. / Sheldrick, G.M. / Nanao, M.H. / Korostelev, V.V. / Werner, J.M. / Schwarz-Linek, U. / Potts, J.R. / Garman, E.F.
History
DepositionFeb 27, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.4Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HUMAN FIBRONECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2162
Polymers10,1201
Non-polymers961
Water1,26170
1
A: HUMAN FIBRONECTIN
hetero molecules

A: HUMAN FIBRONECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4334
Polymers20,2412
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)37.855, 37.855, 108.419
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein HUMAN FIBRONECTIN / FN / COLD-INSOLUBLE GLOBULIN / CIG


Mass: 10120.389 Da / Num. of mol.: 1 / Fragment: RESIDUES 93-182 (62-151 IN COORDINATES)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: PICHIA PASTORIS (fungus) / References: UniProt: P02751
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.98 Å3/Da / Density % sol: 38.01 %
Description: THE PHASES FOR THE STRUCTURE WERE OBTAINED BY COMBINING RIP AND S-SAD PHASES TO 2.1A RESOLUTION. BEFORE BURN RIP DATA SET, AT 1.55A RESOLUTION, IS DEPOSITED HERE.
Crystal growpH: 4.5
Details: 0.2 M AMMONIUM SULPHATE, 0.1M NA ACETATE PH 4.5, 2% MPD, 5% PEG MME 550

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9756
DetectorType: ADSC / Detector: CCD / Date: May 24, 2004
Details: A ZEISS MIRROR WITH DIMENSIONS OF 800X95X78 MM3. MADE OF MONOCRYSTALLINE SILICON AND COATED WITH 20-50 NM RH. SPECIFICATIONS SAGITTAL RADIUS 77.15. BENDING RADIUS 9KM.
RadiationMonochromator: KHOZU MONOCHROMATOR WITH A MCLENNON CONTROLLER CONTAINING A LN2 COOLED SI111 CRYSTAL
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9756 Å / Relative weight: 1
ReflectionResolution: 1.55→35.74 Å / Num. obs: 12021 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 24.27 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 6
Reflection shellResolution: 1.55→1.63 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 1.8 / % possible all: 93.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing
RefinementMethod to determine structure: OTHER / Resolution: 1.55→35.74 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.631 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.231 579 4.8 %RANDOM
Rwork0.188 ---
obs0.191 11400 98.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.76 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20 Å2
2--0.08 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.55→35.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms703 0 5 70 778
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.021792
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6961.9381077
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6515101
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.0321.31638
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.42715136
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3631511
X-RAY DIFFRACTIONr_chiral_restr0.1280.2103
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02628
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2270.2313
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.2533
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.255
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2990.258
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1780.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4051.5487
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.4592770
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.9683351
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.8934.5307
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.296 39
Rwork0.22 727

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