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- PDB-5wj7: Crystal Structure of Amino Acids 1733-1797 of Human Beta Cardiac ... -

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Basic information

Entry
Database: PDB / ID: 5wj7
TitleCrystal Structure of Amino Acids 1733-1797 of Human Beta Cardiac Myosin Fused to Xrcc4
ComponentsDNA repair protein XRCC4,Myosin-7
KeywordsActin/DNA Binding Protein / Myosin / Xrcc4 / Coiled-Coil / Actin-DNA Binding Protein complex
Function / homology
Function and homology information


FHA domain binding / regulation of slow-twitch skeletal muscle fiber contraction / regulation of the force of skeletal muscle contraction / positive regulation of ligase activity / DNA ligase IV complex / DNA ligation involved in DNA repair / muscle myosin complex / muscle filament sliding / DNA-dependent protein kinase-DNA ligase 4 complex / immunoglobulin V(D)J recombination ...FHA domain binding / regulation of slow-twitch skeletal muscle fiber contraction / regulation of the force of skeletal muscle contraction / positive regulation of ligase activity / DNA ligase IV complex / DNA ligation involved in DNA repair / muscle myosin complex / muscle filament sliding / DNA-dependent protein kinase-DNA ligase 4 complex / immunoglobulin V(D)J recombination / nonhomologous end joining complex / regulation of the force of heart contraction / protein localization to site of double-strand break / transition between fast and slow fiber / myosin filament / myosin II complex / adult heart development / cardiac muscle hypertrophy in response to stress / myosin complex / sarcomere organization / microfilament motor activity / ventricular cardiac muscle tissue morphogenesis / myofibril / cellular response to lithium ion / 2-LTR circle formation / skeletal muscle contraction / response to X-ray / striated muscle contraction / SUMOylation of DNA damage response and repair proteins / ATP metabolic process / stress fiber / cardiac muscle contraction / regulation of heart rate / sarcomere / muscle contraction / Nonhomologous End-Joining (NHEJ) / Z disc / double-strand break repair via nonhomologous end joining / double-strand break repair / actin filament binding / site of double-strand break / calmodulin binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #370 / DNA double-strand break repair and VJ recombination XRCC4, N-terminal / Dna Repair Protein Xrcc4; Chain: A, domain 1 / XRCC4, N-terminal domain superfamily / DNA repair protein XRCC4 / DNA double-strand break repair and V(D)J recombination protein XRCC4 / XRCC4-like, N-terminal domain superfamily / DNA repair protein XRCC4-like, C-terminal / Myosin tail / Myosin tail ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #370 / DNA double-strand break repair and VJ recombination XRCC4, N-terminal / Dna Repair Protein Xrcc4; Chain: A, domain 1 / XRCC4, N-terminal domain superfamily / DNA repair protein XRCC4 / DNA double-strand break repair and V(D)J recombination protein XRCC4 / XRCC4-like, N-terminal domain superfamily / DNA repair protein XRCC4-like, C-terminal / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Myosin S1 fragment, N-terminal / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Short calmodulin-binding motif containing conserved Ile and Gln residues. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / IQ motif, EF-hand binding site / Kinesin motor domain superfamily / Beta Complex / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Myosin-7 / DNA repair protein XRCC4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsAndreas, M.P. / Ajay, G. / Gellings, J. / Rayment, I.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R21 HL111237 United States
CitationJournal: J. Struct. Biol. / Year: 2017
Title: Design considerations in coiled-coil fusion constructs for the structural determination of a problematic region of the human cardiac myosin rod.
Authors: Andreas, M.P. / Ajay, G. / Gellings, J.A. / Rayment, I.
History
DepositionJul 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software
Item: _pdbx_audit_support.funding_organization / _software.classification
Revision 1.2Dec 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA repair protein XRCC4,Myosin-7
B: DNA repair protein XRCC4,Myosin-7


Theoretical massNumber of molelcules
Total (without water)45,1912
Polymers45,1912
Non-polymers00
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4740 Å2
ΔGint-58 kcal/mol
Surface area22340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.032, 71.506, 173.056
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 DNA repair protein XRCC4,Myosin-7 / / X-ray repair cross-complementing protein 4 / Myosin heavy chain 7 / Myosin heavy chain slow isoform ...X-ray repair cross-complementing protein 4 / Myosin heavy chain 7 / Myosin heavy chain slow isoform / MyHC-slow / Myosin heavy chain / cardiac muscle beta isoform / MyHC-beta


Mass: 22595.488 Da / Num. of mol.: 2
Fragment: UNP Q13426 residues 2-132, UNP P12883 residues 1733-1797
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XRCC4, MYH7, MYHCB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): CodonPlus / References: UniProt: Q13426, UniProt: P12883
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 145 / 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 Å3/Da / Density % sol: 59.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 16% (w/v) Methyl-Ether PEG 5K, 300 mM glycine, 100 mM triethanolamine pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.43→100 Å / Num. obs: 21429 / % possible obs: 99.6 % / Redundancy: 12 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 53.6
Reflection shellResolution: 2.43→2.47 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.185 / Mean I/σ(I) obs: 7.86 / Num. unique obs: 1036 / % possible all: 97.2

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
REFMAC5.6refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IK9

1ik9


Resolution: 2.5→39.243 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.26
RfactorNum. reflection% reflection
Rfree0.2492 982 5 %
Rwork0.2034 --
obs0.2058 19647 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→39.243 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3104 0 0 145 3249
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023151
X-RAY DIFFRACTIONf_angle_d0.3724231
X-RAY DIFFRACTIONf_dihedral_angle_d11.6771939
X-RAY DIFFRACTIONf_chiral_restr0.035469
X-RAY DIFFRACTIONf_plane_restr0.002548
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.63180.31751390.25472643X-RAY DIFFRACTION100
2.6318-2.79670.29691360.24932604X-RAY DIFFRACTION100
2.7967-3.01250.30311390.24412622X-RAY DIFFRACTION100
3.0125-3.31560.31821380.22432637X-RAY DIFFRACTION100
3.3156-3.7950.26461410.20292665X-RAY DIFFRACTION100
3.795-4.77990.19931420.16512694X-RAY DIFFRACTION100
4.7799-39.24790.19691470.18182800X-RAY DIFFRACTION99
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)
13.0479-2.39020.9015.2135-0.24372.94930.12680.1228-0.0723-0.212-0.15940.23670.1796-0.23710.03960.1946-0.06030.01020.2015-0.00140.188-1.2249-3.7801-12.7005
20.3111-0.02630.40140.14280.88562.4670.00430.08350.0302-0.00440.0710.03290.00970.3098-0.08030.2645-0.04390.01170.22110.0750.34813.2936-13.013-48.2226
33.5895-1.5521-0.9446.52581.46695.6920.26330.5071-0.2807-0.6441-0.3062-0.22960.49140.35940.02630.44480.143-0.02580.34480.01510.301620.1317-33.2194-21.3586
40.2899-0.20410.67160.0608-0.52853.4343-0.16080.0960.1202-0.014-0.0865-0.0933-0.74130.03570.32740.32630.0342-0.02520.36410.01380.30492.8002-14.3139-61.1326
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 0 through 93 )
2X-RAY DIFFRACTION2chain 'B' and (resid 94 through 1795 )
3X-RAY DIFFRACTION3chain 'A' and (resid 0 through 118 )
4X-RAY DIFFRACTION4chain 'A' and (resid 119 through 1794 )

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