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- PDB-6pke: Myocilin OLF mutant N428E/D478S -

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Basic information

Entry
Database: PDB / ID: 6pke
TitleMyocilin OLF mutant N428E/D478S
ComponentsMyocilin
KeywordsCELL ADHESION / 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 / negative regulation of cell-matrix adhesion ...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 / negative regulation of cell-matrix adhesion / positive regulation of mitochondrial depolarization / ERBB2-ERBB3 signaling pathway / positive regulation of focal adhesion assembly / regulation of MAPK cascade / fibronectin binding / positive regulation of substrate adhesion-dependent cell spreading / rough endoplasmic reticulum / positive regulation of stress fiber assembly / positive regulation of JNK cascade / bone development / cilium / receptor tyrosine kinase binding / mitochondrial intermembrane space / 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 / signal transduction / endoplasmic reticulum / 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: 1.88 Å
AuthorsLieberman, R.L. / Hill, S.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)R01EY021205 United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Calcium-ligand variants of the myocilin olfactomedin propeller selected from invertebrate phyla reveal cross-talk with N-terminal blade and surface helices.
Authors: Hill, S.E. / Cho, H. / Raut, P. / Lieberman, R.L.
History
DepositionJun 29, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Myocilin
B: Myocilin


Theoretical massNumber of molelcules
Total (without water)62,3682
Polymers62,3682
Non-polymers00
Water5,531307
1
A: Myocilin


Theoretical massNumber of molelcules
Total (without water)31,1841
Polymers31,1841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Myocilin


Theoretical massNumber of molelcules
Total (without water)31,1841
Polymers31,1841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.222, 47.294, 97.020
Angle α, β, γ (deg.)90.000, 100.281, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

#1: Protein Myocilin / Myocilin 55 kDa subunit / Trabecular meshwork-induced glucocorticoid response protein


Mass: 31183.984 Da / Num. of mol.: 2 / Fragment: Olfactomedin domain, residues 228-504 / Mutation: N428E, D478S / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q99972
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / Source method: isolated from a natural source / Formula: H2O
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: 1.81 Å3/Da / Density % sol: 31.95 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG 8000, MgCl2

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Data collection

DiffractionMean temperature: 100 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 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.88→50 Å / Num. obs: 34580 / % possible obs: 97.8 % / Redundancy: 3.1 % / Biso Wilson estimate: 25.49 Å2 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.073 / Rrim(I) all: 0.139 / Χ2: 0.763 / Net I/σ(I): 5.9 / Num. measured all: 108492
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.88-1.912.80.45916410.6930.3120.5580.4895
1.91-1.952.80.4417020.630.3010.5360.4996.6
1.95-1.982.80.40616900.7610.2760.4940.51496
1.98-2.032.90.34917100.8160.2360.4240.51497.5
2.03-2.072.90.35316760.8290.2360.4270.54896.5
2.07-2.122.80.35617540.8470.2380.4310.53398.3
2.12-2.172.70.32216930.8330.2170.390.59196.9
2.17-2.232.80.31816800.8290.2110.3830.61696.5
2.23-2.293.20.2817620.910.1760.3330.64898.9
2.29-2.373.30.26417350.9060.160.3110.799.4
2.37-2.453.40.26617540.9180.1630.3140.67599.6
2.45-2.553.50.26717570.8970.1640.3150.69399.5
2.55-2.673.50.27317530.8930.1650.320.73999.3
2.67-2.813.40.2217600.9290.1360.260.75599.3
2.81-2.983.20.16917480.9590.1070.2010.82398.8
2.98-3.2130.14417080.9610.0930.1720.97596.2
3.21-3.543.60.09917580.9840.060.1171.07599
3.54-4.053.60.07717650.9920.0460.091.20499
4.05-5.13.20.05417500.9940.0360.0651.16896.9
5.1-503.20.05517840.9970.0330.0651.0795.9

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 6ou2

6ou2


Resolution: 1.88→33.6 Å / SU ML: 0.1657 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.8298
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2185 1992 5.77 %
Rwork0.1761 32544 -
obs0.1786 34536 97.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.14 Å2
Refinement stepCycle: LAST / Resolution: 1.88→33.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4070 0 0 307 4377
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00644198
X-RAY DIFFRACTIONf_angle_d0.77365730
X-RAY DIFFRACTIONf_chiral_restr0.055640
X-RAY DIFFRACTIONf_plane_restr0.0051722
X-RAY DIFFRACTIONf_dihedral_angle_d19.03141502
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.930.23251520.21282212X-RAY DIFFRACTION93.96
1.93-1.980.26431280.20562255X-RAY DIFFRACTION95.86
1.98-2.040.22991310.19622303X-RAY DIFFRACTION97.48
2.04-2.10.25381510.19592299X-RAY DIFFRACTION97.03
2.1-2.180.24571280.19042312X-RAY DIFFRACTION97.33
2.18-2.260.25921450.1852300X-RAY DIFFRACTION97.33
2.26-2.370.23481390.17292354X-RAY DIFFRACTION99.36
2.37-2.490.20511460.18032352X-RAY DIFFRACTION99.52
2.49-2.650.20521440.17532379X-RAY DIFFRACTION99.53
2.65-2.850.20421540.18192355X-RAY DIFFRACTION99.29
2.85-3.140.21421370.1752317X-RAY DIFFRACTION97
3.14-3.590.20681420.16722368X-RAY DIFFRACTION98.9
3.59-4.520.18011530.15082366X-RAY DIFFRACTION98.59
4.52-33.60.24711420.18322372X-RAY DIFFRACTION95.44

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