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- PDB-2vxp: The fourth FAS1 domain structure of human Bigh3 -

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Basic information

Entry
Database: PDB / ID: 2vxp
TitleThe fourth FAS1 domain structure of human Bigh3
ComponentsTRANSFORMING GROWTH FACTOR-BETA-INDUCED PROTEIN IG-H3
KeywordsCELL ADHESION / RGD-CONTAINING COLLAGEN-ASSOCIATED PROTEIN / FAS1 / BIGH3 / VISION / AMYLOID / RGD-CAP / SECRETED / DISEASE MUTATION / KERATO-EPITHELIN / FASCICLIN 1 / POLYMORPHISM / SENSORY TRANSDUCTION / EXTRACELLULAR MATRIX
Function / homology
Function and homology information


negative regulation of cell adhesion / response to stimulus / extracellular matrix binding / extracellular matrix structural constituent / basement membrane / localization / chondrocyte differentiation / cell adhesion molecule binding / collagen binding / visual perception ...negative regulation of cell adhesion / response to stimulus / extracellular matrix binding / extracellular matrix structural constituent / basement membrane / localization / chondrocyte differentiation / cell adhesion molecule binding / collagen binding / visual perception / extracellular matrix organization / extracellular matrix / trans-Golgi network / integrin binding / angiogenesis / collagen-containing extracellular matrix / cell population proliferation / cell adhesion / Amyloid fiber formation / extracellular space / extracellular exosome / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
FAS1 domain / FAS1 domain / TGF beta-induced protein/periostin / EMI domain / EMI domain profile. / FAS1 domain / FAS1 domain superfamily / Fasciclin domain / FAS1/BIgH3 domain profile. / Four repeated domains in the Fasciclin I family of proteins, present in many other contexts. ...FAS1 domain / FAS1 domain / TGF beta-induced protein/periostin / EMI domain / EMI domain profile. / FAS1 domain / FAS1 domain superfamily / Fasciclin domain / FAS1/BIgH3 domain profile. / Four repeated domains in the Fasciclin I family of proteins, present in many other contexts. / Roll / Mainly Beta
Similarity search - Domain/homology
Transforming growth factor-beta-induced protein ig-h3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsYoo, J.-H. / Cho, H.-S.
CitationJournal: To be Published
Title: The Structural Analysis of the Fas1 Domain 4 of Big-H3 for Relationship with Corneal Dystrophy
Authors: Yoo, J.-H. / Kim, E. / Kim, J. / Cho, H.-S.
History
DepositionJul 8, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2009Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
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

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Assembly

Deposited unit
A: TRANSFORMING GROWTH FACTOR-BETA-INDUCED PROTEIN IG-H3
B: TRANSFORMING GROWTH FACTOR-BETA-INDUCED PROTEIN IG-H3


Theoretical massNumber of molelcules
Total (without water)28,5132
Polymers28,5132
Non-polymers00
Water57632
1
A: TRANSFORMING GROWTH FACTOR-BETA-INDUCED PROTEIN IG-H3


Theoretical massNumber of molelcules
Total (without water)14,2561
Polymers14,2561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: TRANSFORMING GROWTH FACTOR-BETA-INDUCED PROTEIN IG-H3


Theoretical massNumber of molelcules
Total (without water)14,2561
Polymers14,2561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)62.934, 62.934, 143.290
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein TRANSFORMING GROWTH FACTOR-BETA-INDUCED PROTEIN IG-H3 / BETA IG-H3 / KERATO-EPITHELIN / RGD-CONTAINING COLLAGEN-ASSOCIATED PROTEIN / RGD-CAP


Mass: 14256.435 Da / Num. of mol.: 2 / Fragment: FOURTH FAS1 DOMAIN, RESIDUES 502-633
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15582
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 57.9 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.97939
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97939 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 21986 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 16.9 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 35.38
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 15.5 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 5.04 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→50 Å / Cross valid method: RANDOM / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.285 1062 4.8 %
Rwork0.27 --
obs0.27 21536 98 %
Solvent computationBsol: 56.56 Å2 / ksol: 0.36 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.85 Å2-6.801 Å20 Å2
2---1.85 Å20 Å2
3---3.7 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1978 0 0 32 2010
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.97
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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