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- PDB-7asg: TGFBIp mutant R555W -

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Basic information

Entry
Database: PDB / ID: 7asg
TitleTGFBIp mutant R555W
ComponentsTransforming growth factor-beta-induced protein ig-h3
KeywordsPROTEIN FIBRIL / granular corneal dystrophy / lattice corneal dystrophy / protein aggregation / extracellular matrix protein
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
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.
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 Å
AuthorsNielsen, N.S. / Gadeberg, T.A.F. / Andersen, G.R.
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Mutation-induced dimerization of transforming growth factor-beta-induced protein may drive protein aggregation in granular corneal dystrophy.
Authors: Nielsen, N.S. / Gadeberg, T.A.F. / Poulsen, E.T. / Harwood, S.L. / Weberskov, C.E. / Pedersen, J.S. / Andersen, G.R. / Enghild, J.J.
History
DepositionOct 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)65,1321
Polymers65,1321
Non-polymers00
Water4,612256
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area28390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.060, 98.490, 207.840
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-708-

HOH

21A-902-

HOH

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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: 65132.379 Da / Num. of mol.: 1 / Mutation: R555W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TGFBI, BIGH3 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q15582
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 3.07 Å3/Da / Density % sol: 59.89 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 7
Details: 0.5 M Succinic acid pH 7.0, 0.1 M BIS-TRIS propane pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2→49.24 Å / Num. obs: 54442 / % possible obs: 99.82 % / Redundancy: 10.4 % / Biso Wilson estimate: 40.78 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.1883 / Rrim(I) all: 0.198 / Net I/σ(I): 8.38
Reflection shellResolution: 2→2.071 Å / Redundancy: 10.5 % / Num. unique obs: 5356 / CC1/2: 0.53 / CC star: 0.833 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5nv6

5nv6


Resolution: 2→49.24 Å / SU ML: 0.3219 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.2167
RfactorNum. reflection% reflection
Rfree0.2463 1998 3.68 %
Rwork0.2059 52366 -
obs0.2074 54364 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.76 Å2
Refinement stepCycle: LAST / Resolution: 2→49.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4554 0 0 256 4810
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01634634
X-RAY DIFFRACTIONf_angle_d1.46746295
X-RAY DIFFRACTIONf_chiral_restr0.0702747
X-RAY DIFFRACTIONf_plane_restr0.0087811
X-RAY DIFFRACTIONf_dihedral_angle_d6.25612806
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.51181410.48783683X-RAY DIFFRACTION99.48
2.05-2.110.38121410.37863687X-RAY DIFFRACTION99.66
2.11-2.170.3131420.31293730X-RAY DIFFRACTION99.64
2.17-2.240.32331420.27973687X-RAY DIFFRACTION99.71
2.24-2.320.32231400.26983685X-RAY DIFFRACTION99.84
2.32-2.410.27071420.24253723X-RAY DIFFRACTION99.9
2.41-2.520.23521400.23813706X-RAY DIFFRACTION99.87
2.52-2.650.28851420.21183715X-RAY DIFFRACTION99.92
2.65-2.820.2341420.20983724X-RAY DIFFRACTION99.9
2.82-3.040.21271430.19983739X-RAY DIFFRACTION99.95
3.04-3.340.24781430.20653763X-RAY DIFFRACTION99.92
3.34-3.830.23311430.193759X-RAY DIFFRACTION99.97
3.83-4.820.19651470.1523828X-RAY DIFFRACTION100
4.82-49.240.24551500.18663937X-RAY DIFFRACTION99.8
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.892560307730.1843671372.118414055911.37389644546-0.07565226668973.02326869074-0.3106978436010.1830777389521.10550316142-0.379979257498-0.637972982197-0.293631136497-0.6754544050310.1052446553870.5367125736861.014608176330.00642713911437-0.3498874375450.7934724387790.06134102584031.08786370948.7088123852281.00398137330.7093865362
23.155043804340.1687640730110.2675345118941.531922207610.4507668068452.48085796911-0.0434877502904-0.02725342625950.124899518610.02652153555230.0129682349785-0.01369411855080.04948951815530.09344434888870.04626656029350.3682940471080.00168174457252-0.03646013033840.4033394446490.03801771753820.3448598437274.7020456129959.812473878620.107728337
32.15487632644-0.2645794705782.036252793680.0775288195735-0.4493963813672.86394618234-0.0317985162598-0.08347226271460.0945099970748-0.01400517991930.000288359759902-0.0129976213159-0.0204408934314-0.05210292750020.003567765994620.4174231943620.02492906921540.006781623526850.483602243118-0.007008467613540.41405888011715.567438476255.457693603143.6934236184
40.0303117465534-0.140385867632-0.008540671758631.084175345181.592117881553.06110505466-0.02589970588540.05039829355610.0714672569413-0.08892893022570.209968565874-0.119260763207-0.1201442857970.706071567795-0.1434730467070.336256388382-0.0508580066499-0.006608204169020.596363043998-0.03329941740260.35853579789928.73891350565.677737480482.038329049
51.11239407809-0.178146363230.6154528961612.192334606361.185025473342.67340924583-0.0672942568665-0.2481697991570.03180597932130.06531562615190.07215512737190.3132220943330.0215731751721-0.1025132509930.005641745066820.394960291895-0.07171140246310.03185138391380.568314875395-0.04815350620810.45789443868120.334965863484.1958540511109.022683967
61.526337022111.392890990940.5974306776942.974919555520.04519367754462.65601772069-0.04198844404660.1413087090170.222370028366-0.3641866051090.0476405737960.487190569749-0.255499197036-0.05613163731840.02494438829550.433908650353-0.0507251790343-0.02252413978950.495328283943-0.0460012436930.46146960601616.989905072382.829649191495.2283945545
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 47 through 94 )
2X-RAY DIFFRACTION2chain 'A' and (resid 95 through 189 )
3X-RAY DIFFRACTION3chain 'A' and (resid 190 through 367 )
4X-RAY DIFFRACTION4chain 'A' and (resid 368 through 524 )
5X-RAY DIFFRACTION5chain 'A' and (resid 525 through 572 )
6X-RAY DIFFRACTION6chain 'A' and (resid 573 through 637 )

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