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- PDB-6nax: Olfactomedin domain of mouse myocilin -

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Basic information

Entry
Database: PDB / ID: 6nax
TitleOlfactomedin domain of mouse myocilin
ComponentsMyocilin
KeywordsPROTEIN BINDING / murine / olfactomedin
Function / homology
Function and homology information


: / mesaxon / skeletal muscle hypertrophy / : / clustering of voltage-gated sodium channels / myosin light chain binding / myelin sheath abaxonal region / Schmidt-Lanterman incisure / myelination in peripheral nervous system / node of Ranvier ...: / mesaxon / skeletal muscle hypertrophy / : / clustering of voltage-gated sodium channels / myosin light chain binding / myelin sheath abaxonal region / Schmidt-Lanterman incisure / 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 / bone development / mitochondrial intermembrane space / receptor tyrosine kinase binding / cilium / 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 / cytoplasm
Similarity search - Function
Olfactomedin-like domain / Olfactomedin-like domain / Olfactomedin-like domain profile. / Olfactomedin-like domains
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.551 Å
AuthorsPatterson-Orazem, A.C. / Hill, S.E. / Lieberman, R.L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)R01EY021205 United States
Other privateG2016027 United States
CitationJournal: Biochemistry / Year: 2019
Title: Differential Misfolding Properties of Glaucoma-Associated Olfactomedin Domains from Humans and Mice.
Authors: Patterson-Orazem, A.C. / Hill, S.E. / Wang, Y. / Dominic, I.M. / Hall, C.K. / Lieberman, R.L.
History
DepositionDec 6, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.2Apr 10, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Myocilin
B: Myocilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,98811
Polymers62,4542
Non-polymers5349
Water11,223623
1
A: Myocilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5136
Polymers31,2271
Non-polymers2865
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Myocilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4745
Polymers31,2271
Non-polymers2474
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)111.955, 111.955, 44.129
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 31227.043 Da / Num. of mol.: 2 / Fragment: residues 214-490
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Tissue: trabecular meshwork / Gene: Myoc, Tigr / Organ: eye / Plasmid: pMAL-c4x / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta Gami II DE3 pLysS / References: UniProt: O70624

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Non-polymers , 5 types, 632 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 623 / Source method: isolated from a natural source / Formula: H2O

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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: 2.21 Å3/Da / Density % sol: 44.45 % / Description: rectangular prism
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1:1 drop ratio of 30 mg/mL mouse OLF in 10 mM Na/K Phosphate pH 7.2 and mother liquor comprising 10% PEG 8000, 200 mM magnesium chloride

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→33.1 Å / Num. obs: 79283 / % possible obs: 98.5 % / Redundancy: 4.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.06705 / Rpim(I) all: 0.03524 / Rrim(I) all: 0.07602 / Net I/σ(I): 18.04
Reflection shellResolution: 1.551→1.607 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.2099 / Mean I/σ(I) obs: 6.06 / Num. unique obs: 7499 / CC1/2: 0.95 / Rpim(I) all: 0.1183 / Rrim(I) all: 0.2419 / % possible all: 95.2

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX(1.11.1_2575)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WXQ

4wxq


Resolution: 1.551→33.1 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.42
RfactorNum. reflection% reflection
Rfree0.1779 2000 2.55 %
Rwork0.1576 --
obs0.1582 78413 98.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.551→33.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4124 0 29 623 4776
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084348
X-RAY DIFFRACTIONf_angle_d0.8735932
X-RAY DIFFRACTIONf_dihedral_angle_d4.3583430
X-RAY DIFFRACTIONf_chiral_restr0.061647
X-RAY DIFFRACTIONf_plane_restr0.005750
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5513-1.59010.21021360.17545130X-RAY DIFFRACTION94
1.5901-1.63310.19571420.16995469X-RAY DIFFRACTION99
1.6331-1.68120.17441440.15555449X-RAY DIFFRACTION99
1.6812-1.73550.171460.15555457X-RAY DIFFRACTION99
1.7355-1.79750.18931440.15865511X-RAY DIFFRACTION100
1.7975-1.86940.21171450.15555488X-RAY DIFFRACTION99
1.8694-1.95450.16891460.165460X-RAY DIFFRACTION99
1.9545-2.05760.18421430.15035498X-RAY DIFFRACTION100
2.0576-2.18640.17171420.15345529X-RAY DIFFRACTION100
2.1864-2.35520.21420.16115477X-RAY DIFFRACTION99
2.3552-2.59220.20551500.17435498X-RAY DIFFRACTION99
2.5922-2.96710.19431420.16815444X-RAY DIFFRACTION98
2.9671-3.73750.16841450.15445474X-RAY DIFFRACTION98
3.7375-34.66390.13911330.14465530X-RAY DIFFRACTION96

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