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- PDB-3b43: I-band fragment I65-I70 from titin -

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Basic information

Entry
Database: PDB / ID: 3b43
TitleI-band fragment I65-I70 from titin
ComponentsTitin
KeywordsSTRUCTURAL PROTEIN / I-set Ig fold / extended poly-Ig filament / titin / elastic filament
Function / homology
Function and homology information


non-specific serine/threonine protein kinase / protein serine/threonine kinase activity
Similarity search - Function
Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold ...Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 3.3 Å
Authorsvon Castelmur, E. / Marino, M. / Labeit, D. / Labeit, S. / Mayans, O.
Citation
Journal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: A regular pattern of Ig super-motifs defines segmental flexibility as the elastic mechanism of the titin chain
Authors: von Castelmur, E. / Marino, M. / Svergun, D.I. / Kreplak, L. / Ucurum-Fotiadis, Z. / Konarev, P.V. / Urzhumtsev, A. / Labeit, D. / Labeit, S. / Mayans, O.
#1: Journal: J.Muscle Res.Cell.Motil. / Year: 2005
Title: Poly-Ig tandems from I-band titin share extended domain arrangements irrespective of the distinct features of their modular constituents
Authors: Marino, M. / Svergun, D.I. / Kreplak, L. / Konarev, P.V. / Maco, B. / Labeit, D. / Mayans, O.
History
DepositionOct 23, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Titin


Theoretical massNumber of molelcules
Total (without water)62,8891
Polymers62,8891
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)141.430, 141.430, 166.010
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Titin


Mass: 62888.961 Da / Num. of mol.: 1 / Fragment: I65-I70
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Plasmid: pETM-11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Rosetta
References: UniProt: D0VWS0*PLUS, non-specific serine/threonine protein kinase
Has protein modificationY
Sequence detailsTHE DATABASE SEQUENCE ENTRY COVERING THIS CONSTRUCT IS EMBL Y14852, RABBIT SOLEUS TITIN MRNA, BASES ...THE DATABASE SEQUENCE ENTRY COVERING THIS CONSTRUCT IS EMBL Y14852, RABBIT SOLEUS TITIN MRNA, BASES 11881-13578. THE CLOSEST HOMOLOG IS HUMAN TITIN SWISSPROT ENTRY Q8WZ42, RESIDUES 7946-8511.

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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: 3.81 Å3/Da / Density % sol: 67.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.9
Details: pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 3, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.3→17 Å / Num. obs: 14953 / % possible obs: 98.57 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 82.5 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 19.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
3.3-3.350.4784.3436763997.3
3.35-3.40.4115434162098.9
3.4-3.50.3535.67888112899.2
3.5-3.750.2627.616213232099.2
3.75-40.14712.612465178799.1
4-60.06624.140989595098.7
6-80.04432.59977149597.8
8-100.0339.9327554296.6
10-120.02159155424695.7
12-140.02356.577513095.6
14-160.02156.94027195.9
160.019541402513.8

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Phasing

PhasingMethod: MIRAS

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Processing

Software
NameVersionClassificationNB
XSCALEdata processing
SHARPphasing
PHENIXrefinement
PDB_EXTRACT3data extraction
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MIRAS / Resolution: 3.3→16.985 Å / FOM work R set: 0.794 / SU ML: 0.46 / Phase error: 26.76 / Stereochemistry target values: ML / Details: This structure was refined using TLS in PHENIX.
RfactorNum. reflection% reflection
Rfree0.267 757 5.06 %
Rwork0.22 --
obs0.222 14953 98.57 %
Solvent computationShrinkage radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.059 Å2 / ksol: 0.281 e/Å3
Displacement parametersBiso max: 219.59 Å2 / Biso min: 46.99 Å2
Baniso -1Baniso -2Baniso -3
1--9.466 Å2-0 Å20 Å2
2---9.466 Å2-0 Å2
3---18.932 Å2
Refinement stepCycle: LAST / Resolution: 3.3→16.985 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4412 0 0 0 4412
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONf_angle_d0.94461081
X-RAY DIFFRACTIONf_bond_d0.00645061
X-RAY DIFFRACTIONf_chiral_restr0.0636881
X-RAY DIFFRACTIONf_dihedral_angle_d20.25416591
X-RAY DIFFRACTIONf_plane_restr0.0047911
X-RAY DIFFRACTIONf_nbd_refined4.131
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree: 0.307 / Rfactor Rwork: 0.273 / Total num. of bins used: 5

Resolution (Å)Num. reflection RfreeNum. reflection Rwork% reflection obs (%)
3.3002-3.5529150277498.78
3.5529-3.9065155279599.23
3.9065-4.4628131284899.17
4.4628-5.5892159283898.49
5.589-16.9854162294197.27
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)
15.37880.9633-2.14583.08310.63452.9430.07440.1555-1.19650.1582-0.3137-0.2880.48840.41110.00070.74340.09460.07050.8763-0.03850.533827.67591.879616.0823
23.64312.7595-2.77084.6185-1.53443.57060.07170.0239-0.0409-0.21330.12670.32420.3329-0.192-0.00030.5939-0.0064-0.02180.51740.12710.3289-18.81680.263325.3669
32.74281.67150.10830.63990.76090.9449-0.04750.4341-1.0795-0.2243-0.16960.0810.5788-0.00850.00011.3658-0.15580.03780.5616-0.17371.3647-35.9529-44.468536.5522
40.38440.21660.9705-0.50761.48151.0145-0.0896-0.16340.909-0.25480.0277-0.7657-0.31181.1110.00012.0353-0.0433-0.16730.99950.06932.3785-23.6753-87.034842.4776
51.9385-0.1681-1.33672.7677-2.39891.301-0.36570.00450.1103-0.21360.0281-1.4982-0.80870.135501.65140.25460.02820.78780.05281.2399-28.4356-129.128340.129
62.71680.4182-0.67780.77470.5580.1827-0.163-0.5454-0.86310.5221-0.0545-0.55340.01990.6583-0.00011.63780.44270.08781.09070.35611.7929-10.691-168.696947.0476
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resid -2:94A-2 - 94
2X-RAY DIFFRACTION2chain A and resid 95:190A95 - 190
3X-RAY DIFFRACTION3chain A and resid 191:284A191 - 284
4X-RAY DIFFRACTION4chain A and resid 285:378A285 - 378
5X-RAY DIFFRACTION5chain A and resid 379:471A379 - 471
6X-RAY DIFFRACTION6chain A and resid 472:566A472 - 566

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