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- PDB-9doz: Myocilin OLF oligomers -

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Basic information

Entry
Database: PDB / ID: 9doz
TitleMyocilin OLF oligomers
ComponentsMyocilin
KeywordsCELL ADHESION / OLF
Function / homology
Function and homology information


skeletal muscle hypertrophy / clustering of voltage-gated sodium channels / myosin light chain binding / non-canonical Wnt signaling pathway / myelination in peripheral nervous system / frizzled binding / node of Ranvier / negative regulation of stress fiber assembly / negative regulation of Rho protein signal transduction / ERBB2-ERBB3 signaling pathway ...skeletal muscle hypertrophy / clustering of voltage-gated sodium channels / myosin light chain binding / non-canonical Wnt signaling pathway / myelination in peripheral nervous system / frizzled binding / node of Ranvier / negative regulation of stress fiber assembly / negative regulation of Rho protein signal transduction / ERBB2-ERBB3 signaling pathway / positive regulation of mitochondrial depolarization / regulation of MAPK cascade / fibronectin binding / negative regulation of cell-matrix adhesion / positive regulation of focal adhesion assembly / rough endoplasmic reticulum / positive regulation of stress fiber assembly / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of JNK cascade / bone development / receptor tyrosine kinase binding / mitochondrial intermembrane space / neuron projection development / osteoblast differentiation / cytoplasmic vesicle / : / mitochondrial outer membrane / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / mitochondrial inner membrane / cilium / positive regulation of cell migration / endoplasmic reticulum / Golgi apparatus / signal transduction / extracellular space / extracellular exosome / metal ion binding
Similarity search - Function
: / Olfactomedin-like domain / Olfactomedin-like domain / Olfactomedin-like domain profile. / Olfactomedin-like domains
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.454 Å
AuthorsScelsi, H.F. / Huard, D.J.E. / Lieberman, R.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)R01EY021205 United States
CitationJournal: Protein Sci. / Year: 2025
Title: Detection of non-native species formed during fibrillization of the myocilin olfactomedin domain.
Authors: Scelsi, H.F. / Close, E.G.S. / Huard, D.J.E. / Dunn, E. / Bogdanovic, N. / Mudiyanselage, S.H.W. / Grant, A. / Stagg, S.M. / Schmidt-Krey, I. / Van Horn, W.D. / Lieberman, R.L.
History
DepositionSep 20, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2025Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Myocilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2603
Polymers31,1971
Non-polymers632
Water3,477193
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.268, 50.895, 50.490
Angle α, β, γ (deg.)90.000, 96.680, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Myocilin / Myocilin 55 kDa subunit / Trabecular meshwork-induced glucocorticoid response protein


Mass: 31196.980 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYOC, GLC1A, TIGR / Production host: Escherichia coli (E. coli) / Strain (production host): RG2 / References: UniProt: Q99972
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 1.98 Å3/Da / Density % sol: 38.97 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 10% PEG8000, 0.1M magnesium chloride

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 4, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.454→37.26 Å / Num. obs: 42816 / % possible obs: 97.74 % / Redundancy: 5.8 % / Biso Wilson estimate: 10.68 Å2 / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.1482 / Rpim(I) all: 0.06597 / Rrim(I) all: 0.1626 / Net I/σ(I): 13.49
Reflection shellResolution: 1.454→1.506 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.7241 / Mean I/σ(I) obs: 2.83 / Num. unique obs: 3909 / CC1/2: 0.715 / CC star: 0.913 / Rpim(I) all: 0.362 / Rrim(I) all: 0.8123 / % possible all: 89.54

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.17.1_3660phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.454→37.26 Å / SU ML: 0.1367 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 19.2705
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1964 2006 4.69 %
Rwork0.1672 40753 -
obs0.1686 42759 97.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.69 Å2
Refinement stepCycle: LAST / Resolution: 1.454→37.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2065 0 2 193 2260
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00512156
X-RAY DIFFRACTIONf_angle_d0.86472949
X-RAY DIFFRACTIONf_chiral_restr0.0837328
X-RAY DIFFRACTIONf_plane_restr0.0049372
X-RAY DIFFRACTIONf_dihedral_angle_d6.4647299
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.454-1.490.25891280.21662585X-RAY DIFFRACTION86.76
1.49-1.530.21661420.19722844X-RAY DIFFRACTION96.89
1.53-1.580.25841390.18132902X-RAY DIFFRACTION97.5
1.58-1.630.21431410.18182884X-RAY DIFFRACTION97.74
1.63-1.680.21021410.17372923X-RAY DIFFRACTION98.14
1.68-1.750.19891460.16882885X-RAY DIFFRACTION97.68
1.75-1.830.19781420.16242924X-RAY DIFFRACTION98.74
1.83-1.930.19391490.15922916X-RAY DIFFRACTION98.84
1.93-2.050.16121390.15832956X-RAY DIFFRACTION98.88
2.05-2.210.20591500.15952964X-RAY DIFFRACTION99.33
2.21-2.430.19041430.1692966X-RAY DIFFRACTION99.55
2.43-2.780.24141470.17642976X-RAY DIFFRACTION99.74
2.78-3.50.20221460.16672996X-RAY DIFFRACTION99.65
3.5-37.260.1581530.15543032X-RAY DIFFRACTION99.01

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