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- PDB-3puc: Atomic resolution structure of titin domain M7 -

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Basic information

Entry
Database: PDB / ID: 3puc
TitleAtomic resolution structure of titin domain M7
ComponentsTitin
KeywordsTRANSFERASE / I-set Ig-like domain / M-band
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 / actinin binding / M band / 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 / cardiac muscle contraction / protein kinase A signaling / condensed nuclear chromosome / muscle contraction / positive regulation of protein secretion / Z disc / response to calcium ion / : / actin filament binding / Platelet degranulation / protein tyrosine kinase activity / protease binding / non-specific serine/threonine protein kinase / calmodulin binding / 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: 0.96 Å
AuthorsSauer, F. / Wilmanns, M.
CitationJournal: To be Published
Title: structure of titin M7
Authors: Sauer, F. / Wilmanns, M.
History
DepositionDec 4, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2016Group: Other
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / 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

Downloads & links

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Assembly

Deposited unit
A: Titin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5183
Polymers10,3261
Non-polymers1922
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)22.830, 68.570, 24.180
Angle α, β, γ (deg.)90.000, 100.940, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 10325.693 Da / Num. of mol.: 1 / Fragment: domain M7 (UNP RESIDUES 33774-33871)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTN / Plasmid: pETM14 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 star pRARE2
References: UniProt: Q8WZ42, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 1.8 Å3/Da / Density % sol: 31.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Tris pH 8.0, 3.2M ammonium sulfate, 1mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.82653 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 15, 2010
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.82653 Å / Relative weight: 1
ReflectionResolution: 0.96→30 Å / Num. all: 44457 / Num. obs: 44303 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.98 % / Biso Wilson estimate: 10.093 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 14.38
Reflection shell

Diffraction-ID: 1

Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique allNum. unique obsRrim(I) all% possible all
0.96-0.980.3860.3974.1111203258326032600.468100
0.98-1.010.2940.3185109723208320232020.37699.8
1.01-1.040.2320.2356.3108093140312831280.27799.6
1.04-1.070.1810.1937.5103232975297829780.228100
1.07-1.110.1350.1519.4101932949293729370.17899.6
1.11-1.150.1140.12810.798702855284628460.15199.7
1.15-1.190.0990.1111.893692711270927090.1399.9
1.19-1.240.090.10612.590852619260826080.12599.6
1.24-1.290.0810.09513.287322530251525150.11299.4
1.29-1.360.0770.0913.983582434241924190.10799.4
1.36-1.430.0640.08115.179032306229122910.09699.3
1.43-1.520.0610.07716.474252165215421540.09199.5
1.52-1.620.060.0917.569672033202120210.10699.4
1.62-1.750.0530.07318.966281911189018900.08698.9
1.75-1.920.0290.06426.5124841751174617460.06999.7
1.92-2.150.0260.05331.1112401584158315830.05799.9
2.15-2.480.0240.05233.898591404140514050.056100
2.48-3.040.0230.04934.777801189118611860.05499.7
3.04-4.290.020.03736.347419199189180.04299.9
4.29-300.0180.03235.923275165075070.03798.3

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Processing

Software
NameVersionClassificationNB
XSCALEdata processing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3KNB

3knb


Resolution: 0.96→19.518 Å / Occupancy max: 1 / Occupancy min: 0.1 / SU ML: 0.06 / σ(F): 0.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1354 1998 4.51 %RANDOM
Rwork0.1155 ---
obs0.1164 44284 99.66 %-
all-44457 --
Solvent computationShrinkage radii: 0 Å / VDW probe radii: 0.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 113.182 Å2 / ksol: 0.6 e/Å3
Displacement parametersBiso max: 104.4 Å2 / Biso mean: 12.4334 Å2 / Biso min: 3.87 Å2
Baniso -1Baniso -2Baniso -3
1--0.4563 Å2-0 Å21.7995 Å2
2--2.2992 Å20 Å2
3----1.843 Å2
Refinement stepCycle: LAST / Resolution: 0.96→19.518 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms706 0 10 160 876
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012832
X-RAY DIFFRACTIONf_angle_d1.4511146
X-RAY DIFFRACTIONf_chiral_restr0.082135
X-RAY DIFFRACTIONf_plane_restr0.008146
X-RAY DIFFRACTIONf_dihedral_angle_d10.696304
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
0.9601-0.99440.18071990.163342334432423399.9
0.9944-1.03420.14141950.133542224417422299.9
1.0342-1.08130.16132050.116142014406420199.9
1.0813-1.13830.13271950.105542394434423999.8
1.1383-1.20960.12542070.102242444451424499.6
1.2096-1.30290.12352030.09641804383418099.6
1.3029-1.4340.12981980.102942264424422699.4
1.434-1.64140.14061930.107342214414422199.4
1.6414-2.06770.13261990.107142384437423899.5
2.0677-19.52230.13292040.126642824486428299.8

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