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- PDB-1waa: IG27 protein domain -

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Basic information

Entry
Database: PDB / ID: 1waa
TitleIG27 protein domain
Components(TITIN) x 3
KeywordsMETAL BINDING PROTEIN / CALMODULIN-BINDING / CYTOSKELETON / IMMUNOGLOBULIN DOMAIN / MUSCLE PROTEIN / PHOSPHORYLATION / SERINE/THREONINE- PROTEIN KINASE / STRUCTURAL PROTEIN.
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: 1.8 Å
AuthorsVega, M.C. / Valencia, L. / Zou, P. / Wilmanns, M.
CitationJournal: Plos Comput.Biol. / Year: 2009
Title: Mechanical Network in Titin Immunoglobulin from Force Distribution Analysis.
Authors: Stacklies, W. / Vega, M.C. / Wilmanns, M. / Grater, F.
History
DepositionOct 25, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2006Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Version format compliance
Revision 1.2Jul 24, 2019Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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
B: TITIN
C: TITIN
D: TITIN
E: TITIN
F: TITIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,34530
Polymers60,7766
Non-polymers1,57024
Water8,647480
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10740 Å2
ΔGint-757.7 kcal/mol
Surface area24860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.240, 75.990, 134.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
TITIN / / I27 DOMAIN FROM TITIN / HEART ISOFORM N2-B


Mass: 10124.597 Da / Num. of mol.: 4 / Fragment: IG DOMAIN, RESIDUES 12801-12889
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: MUSCLESkeletal muscle / Organ: HEART / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q8WZ42, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Protein TITIN / / I27 DOMAIN FROM TITIN / HEART ISOFORM N2-B


Mass: 10138.623 Da / Num. of mol.: 1 / Fragment: IG DOMAIN, RESIDUES 12801-12889
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: MUSCLESkeletal muscle / Organ: HEART / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q8WZ42, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#3: Protein TITIN / / I27 DOMAIN FROM TITIN / HEART ISOFORM N2-B


Mass: 10138.622 Da / Num. of mol.: 1 / Fragment: IG DOMAIN, RESIDUES 12801-12889
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: MUSCLESkeletal muscle / Organ: HEART / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q8WZ42, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#4: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 480 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFUNCTION: THIS MUSCLE PROTEIN MAY BE INVOLVED IN MUSCLE ASSEMBLY AND MAINTAINING THE STRUCTURAL ...FUNCTION: THIS MUSCLE PROTEIN MAY BE INVOLVED IN MUSCLE ASSEMBLY AND MAINTAINING THE STRUCTURAL INTEGRITY OF SARCOMERES

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.9 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.84
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.84 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 53298 / % possible obs: 89.2 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.3
Reflection shellResolution: 1.8→2 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 5.4 / % possible all: 92.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TIT

1tit


Resolution: 1.8→15 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.904 / SU B: 13.244 / SU ML: 0.16 / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.268 3714 7.2 %RANDOM
Rwork0.207 ---
obs0.211 47862 86.5 %-
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: 29.07 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2---0.12 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4215 0 24 480 4719
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224189
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6461.9645648
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7935546
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.2726.604159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.5115713
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1210.2649
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023058
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.260.21879
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.22778
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2348
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.241
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1810.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.28722793
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.09434344
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.8674.51542
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.80261304
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: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.2 1
Rwork0.231 4055
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)
12.89351.9134-0.55136.1637-1.47981.6813-0.00970.0622-0.0367-0.21540.00990.04170.1178-0.0163-0.0001-0.150.0115-0.0171-0.13960.0097-0.114151.531738.814692.6619
23.1817-0.00722.24251.1946-0.89155.999-0.01310.22450.1673-0.05210.0123-0.0768-0.20730.1340.0008-0.10860.01490.0115-0.0952-0.0129-0.129751.116166.182571.003
32.39462.39850.97186.84931.45161.7958-0.09150.07850.1393-0.23460.00960.1335-0.1137-0.03560.0819-0.11970.005-0.0112-0.1228-0.0099-0.092742.818578.648889.9914
44.1636-0.5316-2.2542.3610.96244.7045-0.02570.1826-0.2281-0.09550.02040.03540.2656-0.07490.0053-0.11450.0205-0.0341-0.0989-0.0293-0.116243.192748.752172.4666
54.925-2.94382.27724.7246-1.94854.8237-0.1037-0.3677-0.11240.48660.20790.1890.2061-0.013-0.1042-0.01780.00040.0238-0.06320.0228-0.097642.752248.8668106.4446
63.7266-2.2217-1.73654.12352.37713.4532-0.0621-0.272-0.09650.2530.0397-0.00120.0595-0.05150.0224-0.1123-0.001-0.0227-0.0628-0.0184-0.120651.211971.0214105.3923
70.271-0.02150.02650.69060.00630.2749-0.0126-0.0071-0.00170.0097-0.0150.00010.00830.01610.02770.01620.0079-0.00270.0369-0.0110.034147.936258.437388.8532
80.6215-0.3057-0.16650.92720.02461.2811-0.0604-0.0563-0.06980.01750.02790.03560.1835-0.03470.0324-0.08550.0053-0.0222-0.0537-0.0134-0.027546.268457.073589.7216
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-3 - 89
2X-RAY DIFFRACTION2B1 - 89
3X-RAY DIFFRACTION3C-2 - 89
4X-RAY DIFFRACTION4D-3 - 89
5X-RAY DIFFRACTION5E-3 - 89
6X-RAY DIFFRACTION6F-3 - 89
7X-RAY DIFFRACTION7A2001 - 2105
8X-RAY DIFFRACTION7B2001 - 2088
9X-RAY DIFFRACTION7C2001 - 2075
10X-RAY DIFFRACTION7D2001 - 2073
11X-RAY DIFFRACTION7E2001 - 2062
12X-RAY DIFFRACTION7F2001 - 2077
13X-RAY DIFFRACTION8A1090 - 1094
14X-RAY DIFFRACTION8B1090 - 1094
15X-RAY DIFFRACTION8C1090 - 1094
16X-RAY DIFFRACTION8D1090 - 1092
17X-RAY DIFFRACTION8E1089 - 1091
18X-RAY DIFFRACTION8F1090 - 1092

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