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- PDB-3rbs: Crystal structure of the myomesin domains 10 and 11 -

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Basic information

Entry
Database: PDB / ID: 3rbs
TitleCrystal structure of the myomesin domains 10 and 11
ComponentsMyomesin-1
KeywordsCONTRACTILE PROTEIN / Immunoglobulin C-set domain
Function / homology
Function and homology information


extraocular skeletal muscle development / striated muscle myosin thick filament / M band / structural constituent of muscle / protein kinase A signaling / 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 subtype ...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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / NITRATE ION / Myomesin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsChatziefthimiou, S.D. / Pinotsis, N. / Wilmanns, M.
CitationJournal: Plos Biol. / Year: 2012
Title: Superhelical architecture of the Myosin filament-linking protein myomesin with unusual elastic properties.
Authors: Pinotsis, N. / Chatziefthimiou, S.D. / Berkemeier, F. / Beuron, F. / Mavridis, I.M. / Konarev, P.V. / Svergun, D.I. / Morris, E. / Rief, M. / Wilmanns, M.
History
DepositionMar 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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: Myomesin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5846
Polymers24,2261
Non-polymers3585
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.187, 74.693, 89.414
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 Myomesin-1 / / 190 kDa connectin-associated protein / 190 kDa titin-associated protein / Myomesin family member 1


Mass: 24225.660 Da / Num. of mol.: 1
Fragment: Myomesin-1 Domains 10 and 11, UNP residues 1247-1447
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYOM1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Codon Plus-RP / References: UniProt: P52179
#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS
#3: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.63 Å3/Da / Density % sol: 53.26 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M NaNO3, 18% w/v polyethylene glycol 3350, 5% w/w ethylene glycol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.91508 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 10, 2007
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91508 Å / Relative weight: 1
ReflectionResolution: 1.85→25 Å / Num. all: 22541 / Num. obs: 22541 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Rmerge(I) obs: 0.47 / Net I/σ(I): 33.9

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Processing

Software
NameVersionClassification
DNAdata collection
SHELXSphasing
PHENIX(phenix.refine: dev_530)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.85→23.495 Å / SU ML: 0.25 / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.239 716 3.18 %
Rwork0.1888 --
obs0.1903 22541 99.99 %
all-22541 -
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40 Å2 / ksol: 0.335 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.6252 Å20 Å20 Å2
2--1.7744 Å20 Å2
3---1.5877 Å2
Refinement stepCycle: LAST / Resolution: 1.85→23.495 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1656 0 20 178 1854
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071711
X-RAY DIFFRACTIONf_angle_d1.0242288
X-RAY DIFFRACTIONf_dihedral_angle_d14.519651
X-RAY DIFFRACTIONf_chiral_restr0.071244
X-RAY DIFFRACTIONf_plane_restr0.003293
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.99280.26791330.22964303X-RAY DIFFRACTION100
1.9928-2.19320.25361490.18924269X-RAY DIFFRACTION100
2.1932-2.51020.23831430.19984333X-RAY DIFFRACTION100
2.5102-3.16140.27191500.20034362X-RAY DIFFRACTION100
3.1614-23.49730.21911410.17824558X-RAY DIFFRACTION100
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)
11.4986-0.28240.28032.42170.89762.49880.11580.0254-0.08230.1855-0.08010.1594-0.0472-0.1745-0.00090.2046-0.01320.00930.20450.01640.2392-3.751455.157526.8126
20.83120.1795-0.45491.0841-0.48352.34930.05870.08940.00450.3098-0.0062-0.1168-0.2763-0.05680.00030.2902-0.0214-0.01270.23370.00260.234914.286371.8043-6.9576
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 0:1346)
2X-RAY DIFFRACTION2(chain A and resid 1347:1446)

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