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- PDB-5fm4: Structure of the C-terminally extended domain My4 of human myomes... -

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Basic information

Entry
Database: PDB / ID: 5fm4
TitleStructure of the C-terminally extended domain My4 of human myomesin (space group P21)
ComponentsMYOMESIN-1
KeywordsSTRUCTURAL PROTEIN / SARCOMERE / M-BAND / FIBRONECTIN DOMAIN
Function / homology
Function and homology information


extraocular skeletal muscle development / striated muscle myosin thick filament / protein kinase A signaling / M band / structural constituent of muscle / sarcomere organization / positive regulation of protein secretion / kinase binding / positive regulation of gene expression / protein homodimerization activity / identical protein binding
Similarity search - Function
: / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily ...: / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsPernigo, S. / Steiner, R.A.
CitationJournal: Structure / Year: 2017
Title: Binding of Myomesin to Obscurin-Like-1 at the Muscle M-Band Provides a Strategy for Isoform-Specific Mechanical Protection.
Authors: Pernigo, S. / Fukuzawa, A. / Beedle, A.E. / Holt, M. / Round, A. / Pandini, A. / Garcia-Manyes, S. / Gautel, M. / Steiner, R.A.
History
DepositionOct 30, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2016Group: Database references
Revision 1.2Dec 28, 2016Group: Database references
Revision 1.3Mar 1, 2017Group: Database references
Revision 2.0Oct 23, 2019Group: Atomic model / Data collection / Other / Category: atom_site / pdbx_database_status
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_database_status.status_code_sf
Revision 2.1Jan 10, 2024Group: 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: MYOMESIN-1
B: MYOMESIN-1
C: MYOMESIN-1
D: MYOMESIN-1
E: MYOMESIN-1
F: MYOMESIN-1


Theoretical massNumber of molelcules
Total (without water)73,1226
Polymers73,1226
Non-polymers00
Water66737
1
A: MYOMESIN-1


Theoretical massNumber of molelcules
Total (without water)12,1871
Polymers12,1871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: MYOMESIN-1


Theoretical massNumber of molelcules
Total (without water)12,1871
Polymers12,1871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: MYOMESIN-1


Theoretical massNumber of molelcules
Total (without water)12,1871
Polymers12,1871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: MYOMESIN-1


Theoretical massNumber of molelcules
Total (without water)12,1871
Polymers12,1871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: MYOMESIN-1


Theoretical massNumber of molelcules
Total (without water)12,1871
Polymers12,1871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: MYOMESIN-1


Theoretical massNumber of molelcules
Total (without water)12,1871
Polymers12,1871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.530, 156.840, 48.260
Angle α, β, γ (deg.)90.00, 94.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
MYOMESIN-1 / 190 KDA CONNECTIN-ASSOCIATED PROTEIN / 190 KDA TITIN-ASSOCIATED PROTEIN / MYOMESIN FAMILY MEMBER 1 / MYOMESIN


Mass: 12186.966 Da / Num. of mol.: 6
Fragment: MY4 EXTENDED AT ITS C-TERMINUS, UNP RESIDUES 510-618
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P52179
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.25 Å3/Da / Density % sol: 45.3 % / Description: NONE
Crystal growpH: 5.5 / Details: 25 % (W/V) PEG 3350 100 MM BIS-TRIS PH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 2.8→39.21 Å / Num. obs: 15138 / % possible obs: 95.3 % / Observed criterion σ(I): -1 / Redundancy: 3.1 % / Biso Wilson estimate: 38.45 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.8
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 3.1 / % possible all: 89.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5FM5

5fm5


Resolution: 2.8→39.21 Å / SU ML: 0.4 / σ(F): 0.02 / Phase error: 31.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.287 1448 4.8 %
Rwork0.2608 --
obs0.2621 15106 95.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.3 Å2
Refinement stepCycle: LAST / Resolution: 2.8→39.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4726 0 0 37 4763
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054845
X-RAY DIFFRACTIONf_angle_d1.0726589
X-RAY DIFFRACTIONf_dihedral_angle_d11.3731787
X-RAY DIFFRACTIONf_chiral_restr0.043729
X-RAY DIFFRACTIONf_plane_restr0.004854
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8002-2.90030.34461270.31692758X-RAY DIFFRACTION92
2.9003-3.01640.35931360.29992989X-RAY DIFFRACTION99
3.0164-3.15360.29891690.31412836X-RAY DIFFRACTION97
3.1536-3.31980.36511350.29942930X-RAY DIFFRACTION97
3.3198-3.52760.27561150.29232787X-RAY DIFFRACTION94
3.5276-3.79980.3171500.28412772X-RAY DIFFRACTION93
3.7998-4.18180.31651560.26462846X-RAY DIFFRACTION95
4.1818-4.7860.24071370.21732894X-RAY DIFFRACTION96
4.786-6.02630.24791570.22242737X-RAY DIFFRACTION93
6.0263-39.21380.24051660.21742830X-RAY DIFFRACTION96

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