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- PDB-2rik: I-band fragment I67-I69 from titin -

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Basic information

Entry
Database: PDB / ID: 2rik
TitleI-band fragment I67-I69 from titin
ComponentsTitin
KeywordsSTRUCTURAL PROTEIN / I-set Ig fold / poly-Ig linear array
Function / homology
Function and homology information


Titin, Z repeat / Titin Z / Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain ...Titin, Z repeat / Titin Z / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsMarino, M. / von Castelmur, E. / 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 11, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2023Group: 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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _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)31,3231
Polymers31,3231
Non-polymers00
Water8,629479
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.686, 86.294, 44.698
Angle α, β, γ (deg.)90.000, 104.970, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Titin


Mass: 31322.566 Da / Num. of mol.: 1 / Fragment: I67-I69
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: O97791*PLUS, non-specific serine/threonine protein kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 479 / Source method: isolated from a natural source / Formula: H2O
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 12457-13296. THE CLOSEST HOMOLOG IS HUMAN TITIN SWISSPROT ENTRY Q8WZ42, RESIDUES 8137-84.

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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: 2.58 Å3/Da / Density % sol: 52.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: pH 4.6, 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: 1.6→19 Å / Num. obs: 41644 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 4.57 % / Biso Wilson estimate: 25.981 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 15.25
Reflection shellResolution: 1.6→1.62 Å / Redundancy: 3.75 % / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 3.5 / Num. unique all: 1312 / % possible all: 87.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMAC5.2.0005refinement
PDB_EXTRACT3data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: trimmed poly-Ala model of 1TLK

1tlk


Resolution: 1.6→18.97 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.014 / SU ML: 0.056 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.216 1042 2.5 %RANDOM
Rwork0.171 ---
obs-41644 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.022 Å2
Baniso -1Baniso -2Baniso -3
1-1.11 Å20 Å20.8 Å2
2---0.25 Å20 Å2
3----0.45 Å2
Refinement stepCycle: LAST / Resolution: 1.6→18.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2191 0 0 479 2670
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222243
X-RAY DIFFRACTIONr_angle_refined_deg1.5071.9683034
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9975282
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.8124.83591
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.08315404
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.399159
X-RAY DIFFRACTIONr_chiral_restr0.1160.2339
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021664
X-RAY DIFFRACTIONr_nbd_refined0.2180.2899
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21504
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2324
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1690.244
X-RAY DIFFRACTIONr_mcbond_it1.2051.51463
X-RAY DIFFRACTIONr_mcangle_it1.78222290
X-RAY DIFFRACTIONr_scbond_it2.8613900
X-RAY DIFFRACTIONr_scangle_it4.364.5743
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 73 -
Rwork0.21 2815 -
all-2888 -
obs-2815 100 %
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)
10.85370.2356-0.67870.4776-0.46471.9666-0.07280.0149-0.0503-0.0370.079-0.0348-0.0240.0869-0.0062-0.0326-0.0176-0.0029-0.0184-0.0034-0.02384.73467.987417.2591
20.48820.1901-0.22733.5479-1.77711.2590.0273-0.01860.0208-0.1770.06040.17570.0976-0.1037-0.0877-0.03-0.0294-0.0173-0.02250.0342-0.037514.82940.4355-11.9279
30.9138-0.1359-0.50441.3944-0.70461.1317-0.03820.0412-0.04720.0689-0.0171-0.0123-0.0227-0.01920.0553-0.02440.0192-0.0165-0.02760.0303-0.02427.81165.2411-44.4707
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-1 - 913 - 95
2X-RAY DIFFRACTION2AA94 - 18698 - 190
3X-RAY DIFFRACTION3AA188 - 280192 - 284

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