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- PDB-2y23: CRYSTAL STRUCTURE OF THE MYOMESIN DOMAINS MY9-MY11 -

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Basic information

Entry
Database: PDB / ID: 2y23
TitleCRYSTAL STRUCTURE OF THE MYOMESIN DOMAINS MY9-MY11
ComponentsMYOMESIN
KeywordsSTRUCTURAL PROTEIN / SARCOMERE / M-BAND / IMMUNOGLOBULIN- LIKE 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 / Myomesin-1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPinotsis, N. / Chatziefthimiou, S.D. / 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
DepositionDec 13, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2012Group: Other
Revision 1.2Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

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Assembly

Deposited unit
A: MYOMESIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4005
Polymers36,0461
Non-polymers3554
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.471, 41.487, 84.862
Angle α, β, γ (deg.)90.00, 88.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 36045.805 Da / Num. of mol.: 1 / Fragment: DOMAINS MY9, MY10, MY11, RESIDUES 1141-1447
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: MUSCLESkeletal muscle / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / 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-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000 / 2-(2-Methoxyethoxy)ethanol


Mass: 120.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 3.11 Å3/Da / Density % sol: 60.5 % / Description: NONE
Crystal growpH: 7.5
Details: 0.18M MAGNESIUM ACETATE 20% W/V POLYETHYLENE GLYCOL 3350, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.97699
DetectorType: MARRESEARCH / Detector: CCD / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL SI(111), HORIZONTALLY FOCUSSING
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97699 Å / Relative weight: 1
ReflectionResolution: 2.49→25 Å / Num. obs: 15174 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 58.3 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.6
Reflection shellResolution: 2.49→2.53 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 1.8 / % possible all: 89.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MYOMESIN DOMAINS MY10-MY11, PDB ENTRY 2R15

2r15


Resolution: 2.5→25 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.928 / SU B: 23.84 / SU ML: 0.283 / Cross valid method: THROUGHOUT / ESU R: 0.434 / ESU R Free: 0.292 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.271 465 3.1 %RANDOM
Rwork0.20934 ---
obs0.21127 14571 100 %-
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: 59.363 Å2
Baniso -1Baniso -2Baniso -3
1--1.51 Å20 Å2-2.33 Å2
2---3.1 Å20 Å2
3---4.74 Å2
Refinement stepCycle: LAST / Resolution: 2.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2443 0 17 182 2642
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222509
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5771.9633369
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1985303
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.53225.702121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.51715483
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.588159
X-RAY DIFFRACTIONr_chiral_restr0.0940.2371
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021848
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2530.2899
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21604
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2104
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2330.234
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1910.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6671.51560
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.07122444
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.63331082
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.6214.5925
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: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.492 43 -
Rwork0.315 1013 -
obs--100 %
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)
13.3184-2.1412-0.07525.5134-0.35681.94580.10880.0754-0.2717-0.146-0.13860.34350.1095-0.12790.0298-0.07860.0223-0.0274-0.0963-0.0363-0.045248.1272-31.277732.6518
23.3651-0.91750.11252.1791-0.94163.92280.0680.1382-0.2387-0.09730.04940.2615-0.08360.0973-0.1174-0.1253-0.0119-0.0059-0.0865-0.0386-0.116411.27420.106522.7737
33.7763-3.17092.90624.1814-4.76039.2892-0.1614-0.778-0.02750.55450.50690.3472-0.4535-0.9719-0.34540.09240.03030.02070.26720.00390.0959-19.160420.8727-0.276
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1141 - 1243
2X-RAY DIFFRACTION2A1244 - 1357
3X-RAY DIFFRACTION3A1358 - 1447

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