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- PDB-2ill: Anomalous substructure of Titin-A168169 -

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Basic information

Entry
Database: PDB / ID: 2ill
TitleAnomalous substructure of Titin-A168169
ComponentsTitin
KeywordsTRANSFERASE / long wavelength
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 / FOURIER SYNTHESIS / Resolution: 2.2 Å
AuthorsMueller-Dieckmann, C. / Weiss, M.S.
CitationJournal: ACTA CRYSTALLOGR.,SECT.D / Year: 2007
Title: On the routine use of soft X-rays in macromolecular crystallography. Part IV. Efficient determination of anomalous substructures in biomacromolecules using longer X-ray wavelengths
Authors: Mueller-Dieckmann, C. / Panjikar, S. / Schmidt, A. / Mueller, S. / Kuper, J. / Geerlof, A. / Wilmanns, M. / Singh, R.K. / Tucker, P.A. / Weiss, M.S.
History
DepositionOct 3, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Titin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7093
Polymers21,6381
Non-polymers712
Water1,69394
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.260, 89.120, 103.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Titin / / Connectin / Rhabdomyosarcoma antigen MU-RMS-40.14


Mass: 21637.691 Da / Num. of mol.: 1 / Fragment: Titin-A168169
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
References: UniProt: Q8WZ42, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 3.69 Å3/Da / Density % sol: 66.67 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 2 Å
DetectorType: MAR CCD 165 mm / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2 Å / Relative weight: 1
ReflectionResolution: 2.2→99 Å / Num. all: 16570 / Num. obs: 16486 / % possible obs: 99 % / Redundancy: 11.8 % / Biso Wilson estimate: 47.5 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 34.1
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 4.3 / % possible all: 92

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.92 / SU B: 8.818 / SU ML: 0.118 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.193 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24266 323 2 %RANDOM
Rwork0.21176 ---
obs0.21237 16151 99.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 42.868 Å2
Baniso -1Baniso -2Baniso -3
1-2.78 Å20 Å20 Å2
2---1.77 Å20 Å2
3----1 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1524 0 2 94 1620
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0221566
X-RAY DIFFRACTIONr_bond_other_d0.0010.021426
X-RAY DIFFRACTIONr_angle_refined_deg2.2241.9492125
X-RAY DIFFRACTIONr_angle_other_deg0.93633328
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1865198
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.77724.36671
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.78615270
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.374159
X-RAY DIFFRACTIONr_chiral_restr0.1240.2238
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021747
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02308
X-RAY DIFFRACTIONr_nbd_refined0.2370.2285
X-RAY DIFFRACTIONr_nbd_other0.2070.21353
X-RAY DIFFRACTIONr_nbtor_refined0.180.2724
X-RAY DIFFRACTIONr_nbtor_other0.0950.21013
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3440.292
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3160.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2760.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0880.27
X-RAY DIFFRACTIONr_mcbond_it2.0381.51218
X-RAY DIFFRACTIONr_mcbond_other0.3571.5402
X-RAY DIFFRACTIONr_mcangle_it2.72.51578
X-RAY DIFFRACTIONr_scbond_it6.0195686
X-RAY DIFFRACTIONr_scangle_it7.51210545
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.416 21 -
Rwork0.282 1137 -
obs--95.39 %
Refinement TLS params.Method: refined / Origin x: 11.0123 Å / Origin y: 56.0772 Å / Origin z: -6.4602 Å
111213212223313233
T-0.0671 Å2-0.0719 Å2-0.0313 Å2--0.1167 Å20.0066 Å2---0.0564 Å2
L0.2485 °2-0.0832 °21.0478 °2-0.1803 °2-0.073 °2--5.7382 °2
S0.0265 Å °0.0409 Å °-0.0078 Å °-0.0234 Å °0.1126 Å °-0.0913 Å °0.271 Å °-0.0015 Å °-0.1391 Å °

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