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- PDB-9etn: Crystal structure of murine CRTAC1 -

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Basic information

Entry
Database: PDB / ID: 9etn
TitleCrystal structure of murine CRTAC1
ComponentsCartilage acidic protein 1
KeywordsSIGNALING PROTEIN / beta-propeller / potassium binding / calcium binding
Function / homology
Function and homology information


olfactory bulb development / axonal fasciculation / regulation of synapse assembly / growth cone / postsynaptic density / glutamatergic synapse / calcium ion binding / extracellular region
Similarity search - Function
ASPIC/UnbV / Cartilage acidic protein 1 / ASPIC and UnbV / FG-GAP-like repeat / : / FG-GAP repeat / Calcium-binding EGF domain / Integrin alpha, N-terminal / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. ...ASPIC/UnbV / Cartilage acidic protein 1 / ASPIC and UnbV / FG-GAP-like repeat / : / FG-GAP repeat / Calcium-binding EGF domain / Integrin alpha, N-terminal / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain
Similarity search - Domain/homology
: / Cartilage acidic protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.584 Å
AuthorsBeugelink, J.W. / Hof, H. / Janssen, B.J.C.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO) Netherlands
CitationJournal: J.Mol.Biol. / Year: 2024
Title: CRTAC1 has a Compact beta-propeller-TTR Core Stabilized by Potassium Ions.
Authors: Beugelink, J.W. / Hof, H. / Janssen, B.J.C.
History
DepositionMar 26, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cartilage acidic protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,10912
Polymers64,1581
Non-polymers95111
Water5,657314
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-13 kcal/mol
Surface area20940 Å2
Unit cell
Length a, b, c (Å)167.514, 84.204, 59.718
Angle α, β, γ (deg.)90.000, 102.702, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-978-

HOH

21A-1100-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Cartilage acidic protein 1 / 68 kDa chondrocyte-expressed protein / CEP-68 / ASPIC / Protein CRTAC1-B


Mass: 64157.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Crtac1, Aspic1, Cep68 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q8R555
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 324 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 314 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.2 Å3/Da / Density % sol: 61.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 100 mM sodium-malonate pH 5.0, 12% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.6702 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Aug 6, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6702 Å / Relative weight: 1
ReflectionResolution: 1.582→81.707 Å / Num. obs: 54952 / % possible obs: 86.5 % / Redundancy: 4.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.042 / Rrim(I) all: 0.099 / Net I/σ(I): 10.9
Reflection shellResolution: 1.582→1.786 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.777 / Num. unique obs: 2748 / CC1/2: 0.667 / Rpim(I) all: 0.409 / Rrim(I) all: 0.885 / % possible all: 67.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.584→81.707 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.194 / WRfactor Rwork: 0.149 / Average fsc free: 0.9742 / Average fsc work: 0.9849 / Cross valid method: FREE R-VALUE / ESU R: 0.2 / ESU R Free: 0.117
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1946 2798 5.092 %
Rwork0.1501 52152 -
all0.152 --
obs-54950 49.996 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 24.695 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å20 Å2-0.569 Å2
2---1.047 Å2-0 Å2
3---1.927 Å2
Refinement stepCycle: LAST / Resolution: 1.584→81.707 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4231 0 48 314 4593
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0124380
X-RAY DIFFRACTIONr_bond_other_d0.0020.0163962
X-RAY DIFFRACTIONr_angle_refined_deg1.2981.6565955
X-RAY DIFFRACTIONr_angle_other_deg0.7251.5819101
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6025563
X-RAY DIFFRACTIONr_dihedral_angle_other_1_deg0.022202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg15.703538
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.72310.09666
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.61810222
X-RAY DIFFRACTIONr_chiral_restr0.060.2643
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025364
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021079
X-RAY DIFFRACTIONr_nbd_refined0.2340.2800
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2110.23868
X-RAY DIFFRACTIONr_nbtor_refined0.1720.22179
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.22313
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2309
X-RAY DIFFRACTIONr_metal_ion_refined0.0970.236
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.20.29
X-RAY DIFFRACTIONr_nbd_other0.2050.233
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1770.215
X-RAY DIFFRACTIONr_mcbond_it1.4652.4662206
X-RAY DIFFRACTIONr_mcbond_other1.4512.4662206
X-RAY DIFFRACTIONr_mcangle_it2.1854.4282755
X-RAY DIFFRACTIONr_mcangle_other2.1864.4292756
X-RAY DIFFRACTIONr_scbond_it1.6412.7922174
X-RAY DIFFRACTIONr_scbond_other1.642.7932175
X-RAY DIFFRACTIONr_scangle_it2.4024.9993198
X-RAY DIFFRACTIONr_scangle_other2.40253199
X-RAY DIFFRACTIONr_lrange_it3.72924.4624874
X-RAY DIFFRACTIONr_lrange_other3.47424.2654804
X-RAY DIFFRACTIONr_rigid_bond_restr2.83438342
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.584-1.6250.30650.2391050.24281140.9740.9461.35570.232
1.625-1.6690.297220.2224140.22678610.9390.9645.54640.215
1.669-1.7180.294310.2257330.22876700.9460.9679.96090.219
1.718-1.770.247470.21410370.21574610.9680.97114.52890.205
1.77-1.8280.256630.20513550.20772230.9640.97619.63170.193
1.828-1.8930.229720.19811660.269550.9640.97717.80010.179
1.893-1.9640.224770.17516700.17767780.9650.98225.77460.147
1.964-2.0440.2151850.17535640.17765160.9730.98257.53530.147
2.044-2.1350.212130.16440150.16662610.9720.98567.52910.136
2.135-2.2390.212290.15939110.16259600.9740.98669.46310.13
2.239-2.360.2091850.14936390.15256600.9750.98767.56180.121
2.36-2.5030.2052450.15349490.15653710.9780.98796.70450.126
2.503-2.6760.2132620.14947780.15250450.9750.98899.90090.127
2.676-2.890.2022370.14544590.14847000.9760.98899.91490.131
2.89-3.1650.2052420.1540930.15343450.9690.98799.76990.143
3.165-3.5380.1842050.1537190.15239280.980.98799.89820.149
3.538-4.0840.1811320.13623580.13834830.9820.9971.49010.144
4.084-4.9990.1411610.11627910.11829540.990.99399.93230.133
4.999-7.0570.1961250.15821530.1622850.9790.98899.69370.178
7.057-81.7070.216600.18312430.18413080.9540.96299.61770.226

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