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- PDB-7sjv: Myocilin OLF mutant T353I -

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Basic information

Entry
Database: PDB / ID: 7sjv
TitleMyocilin OLF mutant T353I
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 / frizzled binding / node of Ranvier / 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 / frizzled binding / node of Ranvier / negative regulation of stress fiber assembly / negative regulation of Rho protein signal transduction / positive regulation of mitochondrial depolarization / ERBB2-ERBB3 signaling pathway / 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: 1.39 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
DepositionOct 19, 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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)31,2723
Polymers31,2091
Non-polymers632
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.365, 50.702, 50.644
Angle α, β, γ (deg.)90.000, 96.852, 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: 31209.035 Da / Num. of mol.: 1 / Mutation: T353I
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.02 Å3/Da / Density % sol: 39.11 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 8% PEG 8000, 0.1M magnesium chloride

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 4, 2021
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.39→35.24 Å / Num. obs: 49251 / % possible obs: 98.31 % / Redundancy: 6 % / Biso Wilson estimate: 6.92 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.1226 / Rpim(I) all: 0.05351 / Rrim(I) all: 0.1341 / Net I/σ(I): 16.62
Reflection shellResolution: 1.39→1.44 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.5567 / Num. unique obs: 4798 / CC1/2: 0.892 / CC star: 0.971 / Rpim(I) all: 0.2599 / Rrim(I) all: 0.6166 / % possible all: 96.03

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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: 1.39→35.24 Å / SU ML: 0.1084 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18.1575
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1891 1988 4.03 %
Rwork0.1731 47329 -
obs0.1738 49251 97.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 10.41 Å2
Refinement stepCycle: LAST / Resolution: 1.39→35.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2066 0 2 126 2194
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00472208
X-RAY DIFFRACTIONf_angle_d0.87153031
X-RAY DIFFRACTIONf_chiral_restr0.0844334
X-RAY DIFFRACTIONf_plane_restr0.0049389
X-RAY DIFFRACTIONf_dihedral_angle_d15.7706309
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.39-1.420.221250.20723023X-RAY DIFFRACTION88.68
1.42-1.460.22011360.1883428X-RAY DIFFRACTION98.43
1.46-1.50.20611440.18933374X-RAY DIFFRACTION98.68
1.5-1.550.20431440.17493401X-RAY DIFFRACTION98.86
1.55-1.610.18711370.17263406X-RAY DIFFRACTION98.88
1.61-1.670.17471390.17713336X-RAY DIFFRACTION97.39
1.67-1.750.1991560.16933383X-RAY DIFFRACTION97.84
1.75-1.840.20721430.17213404X-RAY DIFFRACTION99.63
1.84-1.960.18561480.16483460X-RAY DIFFRACTION99.67
1.96-2.110.17781420.16553406X-RAY DIFFRACTION99.08
2.11-2.320.19161430.16853378X-RAY DIFFRACTION97.67
2.32-2.650.18231410.18023391X-RAY DIFFRACTION97.68
2.65-3.340.20931460.18393465X-RAY DIFFRACTION99.7
3.34-35.240.16281440.15913474X-RAY DIFFRACTION97.84

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