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- PDB-7skd: Myocilin OLF mutant S331L -

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Basic information

Entry
Database: PDB / ID: 7skd
TitleMyocilin OLF mutant S331L
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: 1.712 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 20, 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 1.3Oct 23, 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)31,2863
Polymers31,2231
Non-polymers632
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.180, 50.600, 50.280
Angle α, β, γ (deg.)90.000, 97.148, 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: 31223.062 Da / Num. of mol.: 1 / Fragment: Olfactomedin Domain / Mutation: S331L
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.: 84 / 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: 1.99 Å3/Da / Density % sol: 38.28 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 10% PEG 8000, 0.05M 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 20, 2021
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.712→35.13 Å / Num. obs: 21742 / % possible obs: 80.84 % / Redundancy: 6.1 % / Biso Wilson estimate: 18.33 Å2 / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.09655 / Rpim(I) all: 0.04307 / Rrim(I) all: 0.1062 / Net I/σ(I): 10.58
Reflection shellResolution: 1.712→1.773 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 2.24 / Num. unique obs: 1000 / CC1/2: 0.934 / CC star: 0.983 / Rpim(I) all: 0.1665 / Rrim(I) all: 0.3573 / % possible all: 37.78

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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: 1.712→35.13 Å / SU ML: 0.2531 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.6324
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.282 3781 9.25 %
Rwork0.2268 37089 -
obs0.232 21742 78.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.48 Å2
Refinement stepCycle: LAST / Resolution: 1.712→35.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2067 0 2 84 2153
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00672172
X-RAY DIFFRACTIONf_angle_d0.88912968
X-RAY DIFFRACTIONf_chiral_restr0.0564327
X-RAY DIFFRACTIONf_plane_restr0.0047377
X-RAY DIFFRACTIONf_dihedral_angle_d16.0017298
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.712-1.730.3844330.4262334X-RAY DIFFRACTION18.52
1.73-1.760.4138820.3918747X-RAY DIFFRACTION44.74
1.76-1.780.4107840.3618840X-RAY DIFFRACTION48.58
1.78-1.810.3952990.33551001X-RAY DIFFRACTION56.24
1.81-1.830.48421020.3181974X-RAY DIFFRACTION57.66
1.83-1.860.38471020.34461169X-RAY DIFFRACTION65.58
1.86-1.890.56461070.36311039X-RAY DIFFRACTION60.51
1.89-1.920.6381760.4554631X-RAY DIFFRACTION36.29
1.92-1.960.4207970.3979980X-RAY DIFFRACTION56.65
1.96-20.41991570.26961541X-RAY DIFFRACTION88.35
2-2.040.24211760.26831698X-RAY DIFFRACTION96.85
2.04-2.080.41881560.37631401X-RAY DIFFRACTION81.31
2.08-2.130.31021540.29281616X-RAY DIFFRACTION91.24
2.13-2.180.32381760.24571706X-RAY DIFFRACTION99.52
2.18-2.240.37351500.2881505X-RAY DIFFRACTION86.47
2.24-2.310.37511130.29791248X-RAY DIFFRACTION69.87
2.31-2.380.30571830.23051687X-RAY DIFFRACTION99.1
2.38-2.470.35711580.23271705X-RAY DIFFRACTION97.08
2.47-2.570.3671880.2331685X-RAY DIFFRACTION96.4
2.57-2.680.30141760.2421690X-RAY DIFFRACTION98.47
2.68-2.830.25291920.22051742X-RAY DIFFRACTION99.23
2.83-30.24211700.22181731X-RAY DIFFRACTION99.53
3-3.230.27681780.20921718X-RAY DIFFRACTION98.8
3.23-3.560.25331640.19931635X-RAY DIFFRACTION93.65
3.56-4.070.24451590.2041610X-RAY DIFFRACTION92.86
4.07-5.130.13871780.13221744X-RAY DIFFRACTION99.12
5.13-35.130.21211710.14631712X-RAY DIFFRACTION98.12

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