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- PDB-1g1c: I1 DOMAIN FROM TITIN -

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Basic information

Entry
Database: PDB / ID: 1g1c
TitleI1 DOMAIN FROM TITIN
ComponentsIMMUNOGLOBULIN-LIKE DOMAIN I1 FROM TITIN
KeywordsSTRUCTURAL PROTEIN / immunoglobulin domain / Beta-sandwhich / I-set
Function / homology
Function and homology information


sarcomerogenesis / structural molecule activity conferring elasticity / telethonin binding / skeletal muscle myosin thick filament assembly / cardiac myofibril assembly / detection of muscle stretch / muscle alpha-actinin binding / cardiac muscle tissue morphogenesis / regulation of catalytic activity / Striated Muscle Contraction ...sarcomerogenesis / structural molecule activity conferring elasticity / telethonin binding / skeletal muscle myosin thick filament assembly / cardiac myofibril assembly / detection of muscle stretch / muscle alpha-actinin binding / cardiac muscle tissue morphogenesis / regulation of catalytic activity / Striated Muscle Contraction / mitotic chromosome condensation / cardiac muscle hypertrophy / M band / actinin binding / I band / cardiac muscle cell development / regulation of protein kinase activity / structural constituent of muscle / sarcomere organization / skeletal muscle thin filament assembly / striated muscle thin filament / striated muscle contraction / protein kinase A signaling / cardiac muscle contraction / muscle contraction / condensed nuclear chromosome / positive regulation of protein secretion / Z disc / response to calcium ion / : / actin filament binding / Platelet degranulation / protein tyrosine kinase activity / protease binding / calmodulin binding / non-specific serine/threonine protein kinase / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / calcium ion binding / positive regulation of gene expression / protein kinase binding / enzyme binding / extracellular exosome / extracellular region / ATP binding / identical protein binding / cytosol
Similarity search - Function
PPAK motif / PPAK motif / Titin, Z repeat / Titin Z / MyBP-C, tri-helix bundle domain / Tri-helix bundle domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain ...PPAK motif / PPAK motif / Titin, Z repeat / Titin Z / MyBP-C, tri-helix bundle domain / Tri-helix bundle domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Tyrosine-protein kinase, active site / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Protein kinase domain / Immunoglobulins / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsMayans, O. / Wuerges, J. / Gautel, M. / Wilmanns, M.
CitationJournal: Structure / Year: 2001
Title: Structural evidence for a possible role of reversible disulphide bridge formation in the elasticity of the muscle protein titin.
Authors: Mayans, O. / Wuerges, J. / Canela, S. / Gautel, M. / Wilmanns, M.
History
DepositionOct 11, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 11, 2019Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: citation / diffrn_source ...citation / diffrn_source / pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / struct_ref_seq_dif
Item: _citation.pdbx_database_id_DOI / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IMMUNOGLOBULIN-LIKE DOMAIN I1 FROM TITIN
B: IMMUNOGLOBULIN-LIKE DOMAIN I1 FROM TITIN


Theoretical massNumber of molelcules
Total (without water)22,4792
Polymers22,4792
Non-polymers00
Water3,567198
1
A: IMMUNOGLOBULIN-LIKE DOMAIN I1 FROM TITIN


Theoretical massNumber of molelcules
Total (without water)11,2401
Polymers11,2401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: IMMUNOGLOBULIN-LIKE DOMAIN I1 FROM TITIN


Theoretical massNumber of molelcules
Total (without water)11,2401
Polymers11,2401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.3, 78.6, 79.6
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein IMMUNOGLOBULIN-LIKE DOMAIN I1 FROM TITIN


Mass: 11239.681 Da / Num. of mol.: 2 / Fragment: MOST N-TERMINAL IG DOMAIN, RESIDUES 2027-2125
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Organ: HEART / Plasmid: PET8C / Production host: Escherichia coli (E. coli) / References: UniProt: Q10466, UniProt: Q8WZ42*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.66 Å3/Da / Density % sol: 53.82 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 3.25 M NaCl, 0.1 M Tris-HCL pH 8.0, 1mM EDTA, 1mM DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP at 294K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
13 mg/mlprotein1drop
23.25 M1reservoirNaCl
30.1 MTris-HCl1reservoir
41 mMEDTA1reservoir
51 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.906
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.906 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 14589 / % possible obs: 99.6 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 10.9
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.274 / Num. unique all: 966 / % possible all: 99.9
Reflection shell
*PLUS
% possible obs: 99.9 % / Num. unique obs: 966 / Mean I/σ(I) obs: 2.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.9refinement
RefinementResolution: 2.1→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.248 859 5.9 %random
Rwork0.202 ---
obs-14589 --
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1564 0 0 198 1762
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5.9 % / Rfactor obs: 0.202
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it

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