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- PDB-2bk8: M1 domain from titin -

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Basic information

Entry
Database: PDB / ID: 2bk8
TitleM1 domain from titin
ComponentsTITIN HEART ISOFORM N2-B
KeywordsIG DOMAIN / TITIN / M-BAND / STRUCTURAL PROTEIN / MUSCLE / ANTIBODY
Function / homology
Function and homology information


sarcomerogenesis / structural molecule activity conferring elasticity / telethonin binding / skeletal muscle myosin thick filament assembly / cardiac myofibril assembly / muscle alpha-actinin binding / detection of muscle stretch / cardiac muscle tissue morphogenesis / regulation of catalytic activity / cardiac muscle hypertrophy ...sarcomerogenesis / structural molecule activity conferring elasticity / telethonin binding / skeletal muscle myosin thick filament assembly / cardiac myofibril assembly / muscle alpha-actinin binding / detection of muscle stretch / cardiac muscle tissue morphogenesis / regulation of catalytic activity / cardiac muscle hypertrophy / mitotic chromosome condensation / Striated Muscle Contraction / M band / actinin binding / I band / cardiac muscle cell development / regulation of protein kinase activity / sarcomere organization / structural constituent of muscle / 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 / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsMueller, S. / Kursula, I. / Wilmanns, M.
CitationJournal: To be Published
Title: Structure of M1 Domain from Titin
Authors: Mueller, S. / Kursula, I. / Wilmanns, M.
History
DepositionFeb 11, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 9, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 12, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TITIN HEART ISOFORM N2-B


Theoretical massNumber of molelcules
Total (without water)11,0431
Polymers11,0431
Non-polymers00
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)68.780, 68.780, 48.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein TITIN HEART ISOFORM N2-B / CONNECTIN / M1


Mass: 11043.252 Da / Num. of mol.: 1 / Fragment: RESIDUES 25073-25166 (IG-LIKE DOMAIN)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: MUSCLESkeletal muscle / Plasmid: PETM11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8WZ42, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.21 Å3/Da / Density % sol: 44 %
Crystal growpH: 7 / Details: 2.2 M AMMONIUM SULFATE 0.1 M BIS TRIS PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8128
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 16, 2004 / Details: MIRRORS
RadiationMonochromator: TRIANGULAR MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8128 Å / Relative weight: 1
ReflectionResolution: 1.69→17.74 Å / Num. obs: 24619 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 18.1
Reflection shellResolution: 1.69→1.8 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3.89 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
AMoREphasing
CaspRphasing
REFMAC5.2.0005refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HOMOLOGY MODEL

Resolution: 1.69→17.74 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.939 / SU ML: 0.085 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.234 632 5 %RANDOM
Rwork0.189 ---
obs0.191 11995 99.6 %-
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: 37.37 Å2
Baniso -1Baniso -2Baniso -3
1--1.83 Å20 Å20 Å2
2---1.83 Å20 Å2
3---3.67 Å2
Refinement stepCycle: LAST / Resolution: 1.69→17.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms776 0 0 129 905
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022803
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3931.9481081
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.045596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.22725.12241
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.05715148
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.415153
X-RAY DIFFRACTIONr_chiral_restr0.1040.2115
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02607
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2530.2305
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.2513
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.269
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4610.220
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.040.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8843502
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.3794770
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.964364
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3935311
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.69→1.73 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.272 46
Rwork0.235 871
Refinement TLS params.Method: refined / Origin x: 23.2947 Å / Origin y: -1.8454 Å / Origin z: 34.8834 Å
111213212223313233
T-0.1665 Å2-0.0061 Å2-0.033 Å2--0.1432 Å2-0.0213 Å2---0.1569 Å2
L2.1986 °20.4704 °2-0.8696 °2-3.4849 °2-1.7812 °2--4.1068 °2
S-0.021 Å °0.0812 Å °0.0263 Å °-0.1107 Å °-0.0135 Å °-0.0098 Å °-0.0983 Å °0.0011 Å °0.0345 Å °

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