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- PDB-7t8d: Myocilin OLF mutant V449I -

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Basic information

Entry
Database: PDB / ID: 7t8d
TitleMyocilin OLF mutant V449I
ComponentsMyocilin, C-terminal fragment
KeywordsCELL ADHESION / olfactomedin / beta-propeller
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 / node of Ranvier / frizzled binding / negative regulation of stress fiber assembly / negative regulation of Rho protein signal transduction / positive regulation of mitochondrial depolarization ...skeletal muscle hypertrophy / clustering of voltage-gated sodium channels / myosin light chain binding / non-canonical Wnt signaling pathway / myelination in peripheral nervous system / node of Ranvier / frizzled binding / negative regulation of stress fiber assembly / negative regulation of Rho protein signal transduction / positive regulation of mitochondrial depolarization / negative regulation of cell-matrix adhesion / ERBB2-ERBB3 signaling pathway / positive regulation of focal adhesion assembly / regulation of MAPK cascade / fibronectin binding / rough endoplasmic reticulum / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of stress fiber assembly / positive regulation of JNK cascade / bone development / mitochondrial intermembrane space / cilium / receptor tyrosine kinase binding / osteoblast differentiation / neuron projection development / cytoplasmic vesicle / collagen-containing extracellular matrix / mitochondrial outer membrane / mitochondrial inner membrane / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of cell migration / Golgi apparatus / endoplasmic reticulum / 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: 1.38 Å
AuthorsScelsi, H.S. / Barlow, B.M. / Lieberman, R.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI) United States
CitationJournal: Dis Model Mech / Year: 2023
Title: Quantitative differentiation of benign and misfolded glaucoma-causing myocilin variants on the basis of protein thermal stability.
Authors: Scelsi, H.F. / Hill, K.R. / Barlow, B.M. / Martin, M.D. / Lieberman, R.L.
History
DepositionDec 16, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title ..._citation.journal_volume / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Myocilin, C-terminal fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3664
Polymers31,2111
Non-polymers1553
Water3,891216
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.408, 50.865, 50.458
Angle α, β, γ (deg.)90.000, 97.008, 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, C-terminal fragment / / Myocilin 35 kDa N-terminal fragment


Mass: 31211.008 Da / Num. of mol.: 1 / Mutation: V449I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYOC, GLC1A, TIGR / Production host: Escherichia coli (E. coli) / 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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.97 Å3/Da / Density % sol: 37.49 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 0.05 M magnesium chloride, 10% PEG 8000

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Data collection

DiffractionMean temperature: 273 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.38→35.69 Å / Num. obs: 50378 / % possible obs: 98.68 % / Redundancy: 6.7 % / Biso Wilson estimate: 9.74 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.0661 / Rpim(I) all: 0.0274 / Rrim(I) all: 0.07168 / Net I/σ(I): 17.82
Reflection shellResolution: 1.38→1.429 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.4149 / Mean I/σ(I) obs: 6.52 / Num. unique obs: 4924 / CC1/2: 0.935 / CC star: 0.983 / Rpim(I) all: 0.182 / Rrim(I) all: 0.4541 / % possible all: 97.45

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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
Starting model: 6PKE

6pke


Resolution: 1.38→35.69 Å / SU ML: 0.1173 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 18.1856
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1842 2004 3.97 %
Rwork0.1633 48505 -
obs0.1642 50378 98.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 12.97 Å2
Refinement stepCycle: LAST / Resolution: 1.38→35.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2066 0 8 216 2290
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00532208
X-RAY DIFFRACTIONf_angle_d0.88663022
X-RAY DIFFRACTIONf_chiral_restr0.0873332
X-RAY DIFFRACTIONf_plane_restr0.005385
X-RAY DIFFRACTIONf_dihedral_angle_d6.6637307
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.38-1.410.25151330.21493233X-RAY DIFFRACTION92.02
1.41-1.450.20131420.19563443X-RAY DIFFRACTION99.39
1.45-1.490.22591450.18153523X-RAY DIFFRACTION99.4
1.49-1.540.18861470.17653455X-RAY DIFFRACTION98.98
1.54-1.60.21581380.16763458X-RAY DIFFRACTION98.95
1.6-1.660.18321440.16793411X-RAY DIFFRACTION97.37
1.66-1.740.17821380.16023464X-RAY DIFFRACTION98.07
1.74-1.830.16211440.16113505X-RAY DIFFRACTION99.92
1.83-1.940.18971420.16163516X-RAY DIFFRACTION99.86
1.94-2.090.14081470.1533470X-RAY DIFFRACTION98.83
2.09-2.30.19741430.15223449X-RAY DIFFRACTION97.64
2.3-2.640.17631510.1663477X-RAY DIFFRACTION98.67
2.64-3.320.19921440.16263550X-RAY DIFFRACTION99.92
3.32-35.690.17461460.15613551X-RAY DIFFRACTION98.06

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