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- PDB-7sij: Myocilin OLF mutant E352K -

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Basic information

Entry
Database: PDB / ID: 7sij
TitleMyocilin OLF mutant E352K
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: 1.54 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 14, 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)31,3524
Polymers31,1971
Non-polymers1553
Water3,801211
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.336, 50.734, 50.490
Angle α, β, γ (deg.)90.000, 96.604, 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: 31197.047 Da / Num. of mol.: 1 / Mutation: E352K
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.: 211 / 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: 2.01 Å3/Da / Density % sol: 38.96 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 10% PEG 8000, 0.25M 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: Mar 30, 2021
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.54→37.26 Å / Num. obs: 36260 / % possible obs: 98.57 % / Redundancy: 6.4 % / Biso Wilson estimate: 10.2 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.050569 / Rpim(I) all: 0.02186 / Rrim(I) all: 0.05536 / Net I/σ(I): 22.48
Reflection shellResolution: 1.54→1.595 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.1528 / Mean I/σ(I) obs: 8.21 / Num. unique obs: 3465 / CC1/2: 0.985 / CC star: 0.996 / Rpim(I) all: 0.06553 / Rrim(I) all: 0.1668 / % possible all: 95.58

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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: 1.54→37.26 Å / SU ML: 0.1325 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 16.8842
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1778 2005 5.53 %
Rwork0.155 34255 -
obs0.1563 36260 98.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.37 Å2
Refinement stepCycle: LAST / Resolution: 1.54→37.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2065 0 8 211 2284
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00542197
X-RAY DIFFRACTIONf_angle_d0.86713005
X-RAY DIFFRACTIONf_chiral_restr0.0578330
X-RAY DIFFRACTIONf_plane_restr0.005383
X-RAY DIFFRACTIONf_dihedral_angle_d12.2575305
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.580.20931320.15992257X-RAY DIFFRACTION91.39
1.58-1.620.17741420.1532446X-RAY DIFFRACTION99.35
1.62-1.670.20161450.15072453X-RAY DIFFRACTION99.27
1.67-1.720.19321450.14872430X-RAY DIFFRACTION99.54
1.72-1.780.17181460.15282480X-RAY DIFFRACTION99.58
1.78-1.850.18931400.14992438X-RAY DIFFRACTION98.32
1.85-1.940.16141390.15122414X-RAY DIFFRACTION97.22
1.94-2.040.1751460.15212459X-RAY DIFFRACTION99.24
2.04-2.170.17081420.15332471X-RAY DIFFRACTION99.5
2.17-2.340.19551420.15352476X-RAY DIFFRACTION99.77
2.34-2.570.17661470.16592491X-RAY DIFFRACTION99.1
2.57-2.940.19031410.16692416X-RAY DIFFRACTION97.37
2.94-3.710.17731510.1552494X-RAY DIFFRACTION99.51
3.71-37.260.15791470.15012530X-RAY DIFFRACTION98.42

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