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- PDB-6pkd: Myocilin OLF mutant N428D/D478H -

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Basic information

Entry
Database: PDB / ID: 6pkd
TitleMyocilin OLF mutant N428D/D478H
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 / regulation of MAPK cascade / positive regulation of focal adhesion assembly / 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 / endoplasmic reticulum / 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: 1.9 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.4Nov 6, 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

Downloads & links

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Assembly

Deposited unit
A: Myocilin
B: Myocilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4884
Polymers62,4422
Non-polymers462
Water6,089338
1
A: Myocilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2442
Polymers31,2211
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Myocilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2442
Polymers31,2211
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.547, 47.342, 97.076
Angle α, β, γ (deg.)90.000, 100.196, 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: 31221.027 Da / Num. of mol.: 2 / Fragment: Olfactomedin domain, residues 228-504 / Mutation: N428D, D478H / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q99972
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / 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: 1.82 Å3/Da / Density % sol: 32.27 %
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: 1.9→50 Å / Num. obs: 33873 / % possible obs: 98.6 % / Redundancy: 4.1 % / Biso Wilson estimate: 19.27 Å2 / Rmerge(I) obs: 0.144 / Rpim(I) all: 0.081 / Rrim(I) all: 0.166 / Χ2: 1.352 / Net I/σ(I): 6.4 / Num. measured all: 137258
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.933.50.49616880.6660.3010.5840.62996.6
1.93-1.973.60.44216120.7930.2580.5150.72297.1
1.97-2.013.60.4316380.7520.2610.5060.70597.4
2.01-2.053.60.40617010.7840.2460.4780.76697.9
2.05-2.093.50.42116400.7510.2620.4990.79597.6
2.09-2.143.70.36216580.8280.2180.4250.81697.4
2.14-2.1940.36616980.8290.210.4240.84398.9
2.19-2.254.40.31316970.8750.1730.3590.88899.2
2.25-2.324.30.316990.8920.1660.3440.96999.6
2.32-2.394.30.27716770.9040.1530.3181.0299.6
2.39-2.484.40.28317160.9090.1540.3241.10599.5
2.48-2.584.30.26216910.9190.1430.31.22699.6
2.58-2.74.30.23217270.9380.1280.2661.30899.3
2.7-2.844.20.19216940.9430.1070.2211.44999.6
2.84-3.023.80.15516770.9650.0910.1811.69498.2
3.02-3.254.20.13517160.9770.0740.1551.87399
3.25-3.584.60.11217160.9810.0590.1272.11599.4
3.58-4.094.40.09417160.9880.050.1072.38699.4
4.09-5.164.10.07517320.9910.0420.0862.53699.1
5.16-5040.07517800.9930.0430.0872.37898.5

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Processing

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

6ou2


Resolution: 1.9→33.63 Å / SU ML: 0.1658 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.913
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2081 2002 5.94 %
Rwork0.1819 31705 -
obs0.1834 33707 98.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.58 Å2
Refinement stepCycle: LAST / Resolution: 1.9→33.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4193 0 2 338 4533
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00664329
X-RAY DIFFRACTIONf_angle_d0.87975902
X-RAY DIFFRACTIONf_chiral_restr0.0558651
X-RAY DIFFRACTIONf_plane_restr0.0042745
X-RAY DIFFRACTIONf_dihedral_angle_d17.4431560
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.24351480.21512157X-RAY DIFFRACTION94.35
1.95-20.25521300.20882241X-RAY DIFFRACTION97.13
2-2.060.22761410.20932227X-RAY DIFFRACTION97.93
2.06-2.130.28621430.21182222X-RAY DIFFRACTION96.41
2.13-2.210.21261310.20232270X-RAY DIFFRACTION98.64
2.21-2.290.23651560.18962246X-RAY DIFFRACTION99.3
2.29-2.40.22881300.18852288X-RAY DIFFRACTION99.38
2.4-2.520.25141530.19082296X-RAY DIFFRACTION99.27
2.52-2.680.25991460.18862253X-RAY DIFFRACTION99.17
2.68-2.890.20581400.19162295X-RAY DIFFRACTION98.98
2.89-3.180.18281420.18162248X-RAY DIFFRACTION96.68
3.18-3.640.16131450.15692304X-RAY DIFFRACTION98.99
3.64-4.580.14891460.14882293X-RAY DIFFRACTION98.91
4.58-33.630.2281510.18562365X-RAY DIFFRACTION98.09

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