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- PDB-7skf: Myocilin OLF mutant A445V -

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Basic information

Entry
Database: PDB / ID: 7skf
TitleMyocilin OLF mutant A445V
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: 1.282 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 16, 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)31,3804
Polymers31,2251
Non-polymers1553
Water4,360242
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.349, 50.653, 50.629
Angle α, β, γ (deg.)90.000, 96.493, 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: 31225.035 Da / Num. of mol.: 1 / Fragment: Olfactomedin Domain / Mutation: A445V
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CA / CALCIUM ION


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


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


Mass: 18.015 Da / Num. of mol.: 242 / 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: 39.06 %
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: Jun 24, 2021
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.282→33.28 Å / Num. obs: 62664 / % possible obs: 98.42 % / Redundancy: 6.3 % / Biso Wilson estimate: 8.15 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.04734 / Rpim(I) all: 0.02039 / Rrim(I) all: 0.05169 / Net I/σ(I): 25.72
Reflection shellResolution: 1.282→1.328 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.1573 / Mean I/σ(I) obs: 8.92 / Num. unique obs: 6143 / CC1/2: 0.983 / CC star: 0.996 / Rpim(I) all: 0.06826 / Rrim(I) all: 0.172 / % possible all: 96.74

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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: 1.282→33.28 Å / SU ML: 0.0901 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 16.5726
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1663 1987 3.17 %
Rwork0.162 60675 -
obs0.1621 62662 98.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 11.87 Å2
Refinement stepCycle: LAST / Resolution: 1.282→33.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2067 0 8 242 2317
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00452271
X-RAY DIFFRACTIONf_angle_d0.86283123
X-RAY DIFFRACTIONf_chiral_restr0.0844344
X-RAY DIFFRACTIONf_plane_restr0.0048402
X-RAY DIFFRACTIONf_dihedral_angle_d12.1533321
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.282-1.310.19471310.18514178X-RAY DIFFRACTION95.65
1.31-1.350.17881440.18144366X-RAY DIFFRACTION99.3
1.35-1.390.1821440.17144325X-RAY DIFFRACTION98.89
1.39-1.430.20051380.16714339X-RAY DIFFRACTION98.76
1.43-1.490.17771430.16914307X-RAY DIFFRACTION98.47
1.49-1.550.16211390.1644235X-RAY DIFFRACTION96.58
1.55-1.620.17931480.16114350X-RAY DIFFRACTION99.45
1.62-1.70.16151370.1574396X-RAY DIFFRACTION99.43
1.7-1.810.15821460.16054365X-RAY DIFFRACTION99.25
1.81-1.950.16761430.1564325X-RAY DIFFRACTION98.24
1.95-2.140.16481380.15484248X-RAY DIFFRACTION96.65
2.14-2.450.15261480.15964407X-RAY DIFFRACTION99.87
2.45-3.090.17021440.17434431X-RAY DIFFRACTION99.83
3.09-33.280.15781440.15274403X-RAY DIFFRACTION97.53

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