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- PDB-6b4a: Crystal structure of the C-Terminal Domain of Doublecortin (TgDCX... -

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Basic information

Entry
Database: PDB / ID: 6b4a
TitleCrystal structure of the C-Terminal Domain of Doublecortin (TgDCX) from Toxoplasma gondii ME49
ComponentsDoublecortin
KeywordsSTRUCTURAL PROTEIN / Structural Genomics / SSGCID / Toxoplasma gondii / Doublecortin / TgDCX / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


intracellular signal transduction
Similarity search - Function
P25-alpha / p25-alpha / Doublecortin / Doublecortin domain profile. / Domain in the Doublecortin (DCX) gene product / Doublecortin domain / Doublecortin domain superfamily
Similarity search - Domain/homology
FORMIC ACID / Doublecortin / Doublecortin
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SAD / molecular replacement / Resolution: 2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Bmc Mol Cell Biol / Year: 2020
Title: A doublecortin-domain protein of Toxoplasma and its orthologues bind to and modify the structure and organization of tubulin polymers.
Authors: Leung, J.M. / Nagayasu, E. / Hwang, Y.C. / Liu, J. / Pierce, P.G. / Phan, I.Q. / Prentice, R.A. / Murray, J.M. / Hu, K.
History
DepositionSep 26, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Doublecortin
B: Doublecortin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5384
Polymers24,4462
Non-polymers922
Water1,874104
1
A: Doublecortin


Theoretical massNumber of molelcules
Total (without water)12,2231
Polymers12,2231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Doublecortin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3153
Polymers12,2231
Non-polymers922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.860, 53.230, 96.380
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Doublecortin /


Mass: 12222.916 Da / Num. of mol.: 2 / Fragment: UNP Residues 148-243
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Strain: ATCC 50861 / VEG / Gene: BN1205_078130 / Plasmid: TogoA.17199.a.B3 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A086LLU6, UniProt: B6KAS6*PLUS
#2: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 1.94 Å3/Da / Density % sol: 36.5 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Rigaku Reagents PACT screen, optimized condition e6: 24.09% (w/v) PEG 3350, 50 mM sodium formate: TogoA.17199.a.B3.PW38274 at 15 mg/mL: cryo: 20% EG: tray 293956a11: puck utu4-1. For ...Details: Rigaku Reagents PACT screen, optimized condition e6: 24.09% (w/v) PEG 3350, 50 mM sodium formate: TogoA.17199.a.B3.PW38274 at 15 mg/mL: cryo: 20% EG: tray 293956a11: puck utu4-1. For phasing, a crystal from Rigaku Reagents PACT screen condition e6 (18% (w/v) PEG 3350, 200 mM sodium formate) was soaked in reservoir plus 20% 2.5 M NaI in ethylene glycol and vitrified. Anomalous data was collected at the home source. Tray 292844e6: puck hly3-2.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Aug 3, 2017
RadiationMonochromator: Rigaku Varimax / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→35.725 Å / Num. obs: 13417 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.112 % / Biso Wilson estimate: 30.77 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rrim(I) all: 0.064 / Χ2: 0.997 / Net I/σ(I): 17.97
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2-2.053.9160.5572.659800.8420.64599.8
2.05-2.114.420.4593.579290.890.52399.3
2.11-2.174.950.3384.999310.9390.379100
2.17-2.245.3280.2716.588860.9670.30199.9
2.24-2.315.5130.2467.238780.9680.27299.9
2.31-2.396.1460.2138.638270.9860.23299.9
2.39-2.486.950.2219.18200.9880.23999.9
2.48-2.587.0640.17910.867770.9890.19399.9
2.58-2.76.980.14913.067630.9920.16199.9
2.7-2.837.0570.12314.737390.9960.133100
2.83-2.987.0430.08719.736740.9970.09499.9
2.98-3.167.0520.07222.366570.9980.078100
3.16-3.387.0350.05826.996320.9990.062100
3.38-3.656.8250.04834.195780.9990.052100
3.65-46.5930.03841.935400.9990.04199.8
4-4.476.5990.03249.414910.9990.034100
4.47-5.166.7570.02949.64370.9990.03199.8
5.16-6.326.7010.03343.613840.9990.035100
6.32-8.946.4080.02745.6530910.029100
8.94-35.7255.4490.02155.1318510.02395.4

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Phasing

Phasing
Method
SAD
molecular replacement
Phasing MRModel details: Phaser MODE: EP_AUTO

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASER2.7.17phasing
PHENIXdev_2499refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
ARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 2→35.725 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.81
RfactorNum. reflection% reflection
Rfree0.2607 1423 10.64 %
Rwork0.1857 --
obs0.1935 13372 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 96.67 Å2 / Biso mean: 45.6687 Å2 / Biso min: 16.45 Å2
Refinement stepCycle: final / Resolution: 2→35.725 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1463 0 6 104 1573
Biso mean--55.3 45.29 -
Num. residues----186
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071518
X-RAY DIFFRACTIONf_angle_d0.7842068
X-RAY DIFFRACTIONf_chiral_restr0.054222
X-RAY DIFFRACTIONf_plane_restr0.006271
X-RAY DIFFRACTIONf_dihedral_angle_d10.252907
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.0002-2.07160.32291220.247711851307
2.0716-2.15460.33871440.230311651309
2.1546-2.25260.32111240.225411731297
2.2526-2.37140.28361390.202411761315
2.3714-2.51990.30791580.210311691327
2.5199-2.71440.26231490.205611741323
2.7144-2.98740.29481510.199411811332
2.9874-3.41940.27311490.188512021351
3.4194-4.3070.231330.157312271360
4.307-35.73040.22121540.166712971451
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.3683-4.83892.99226.3893-2.84437.20920.34551.01770.355-0.6324-0.6939-1.2955-0.11180.32550.43420.67730.05720.19160.42510.05530.37836.6091-1.26021.3407
20.15760.39750.7590.80911.54182.8243-0.21330.80.3394-0.9436-0.15730.5991-0.9104-1.4543-0.44281.13820.48170.07230.91760.2305-0.48425.48799.6414.2387
34.70222.45985.23096.33923.5185.91990.35151.3915-0.3646-0.88910.4483-1.9133-0.24681.3781-0.86340.84750.06830.4310.72390.05560.625243.64970.23881.4436
42.82261.3092.71236.841.02252.7901-0.62050.5741-0.3905-0.63790.92350.3399-0.97450.5628-0.26210.5348-0.08280.0910.5430.12230.595442.40836.70786.7612
52.49130.44112.11651.82631.48422.6783-0.6015-0.35371.6674-0.757-0.1659-0.4008-1.8194-0.5660.58270.63910.0317-0.06170.3388-0.06710.720737.853312.936110.4728
62.79060.8213.5642.56-1.41967.26450.1145-0.4485-0.71320.2167-0.2819-0.34520.66660.24470.18620.38040.00040.03040.32180.03330.333533.9131-1.278114.0387
74.99034.62864.3054.39924.16063.9986-0.021-0.512-1.1197-0.4715-0.3171-1.15631.11190.68340.38010.47740.13250.08440.49920.13730.486439.2494-6.97156.5616
87.6773-3.2687-1.87459.2944-2.41631.77660.21-0.49240.3031-0.0455-0.1975-0.7069-0.28240.11780.08490.2734-0.0180.02760.3568-0.00310.185131.18695.300411.9575
98.7972-2.0586-1.62425.6484-5.09448.06020.13510.6279-0.5668-1.0312-0.17320.6138-0.3279-1.36950.04120.44280.0707-0.10910.46660.00240.233721.31713.71388.5408
101.89891.13241.34251.12741.90786.72890.4938-0.648-0.10291.2468-0.0665-0.3822-0.1440.3969-0.17190.5507-0.0539-0.09090.3229-0.02440.25721.17311.573535.0754
111.174-0.5489-2.33838.26090.02935.5889-0.4516-0.2590.08510.98130.00511.07530.5809-1.08810.15910.4376-0.05590.08340.44040.01060.296613.183-1.249231.8379
121.2394-0.10462.32824.43723.06397.29390.2073-0.2092-0.43381.71510.4022-1.04990.92861.0832-0.43870.89960.1204-0.4760.5313-0.0740.903332.2636-4.974535.5953
133.6223.452-3.98593.5268-3.94077.24230.3128-0.6959-0.45741.0409-0.4667-0.49540.5290.20310.3040.496-0.0214-0.08740.30880.07290.401124.2565-8.2330.0847
143.7841-0.2067-0.71756.4169-1.52126.8502-0.14950.0666-0.2907-0.39110.0779-0.30520.39060.20670.05510.1578-0.0056-0.00530.1882-0.00960.175721.3158-0.893522.5582
156.9579-1.42432.85575.9583-1.2797.2540.02460.25710.0859-0.0369-0.1272-0.3649-0.04280.41660.05480.2804-0.03710.01290.18340.03970.181520.96051.738925.7489
163.65621.36282.58227.1817-2.35254.0293-0.0902-0.53440.73890.7478-0.02221.3559-0.5987-1.4791-0.38740.3260.07970.12010.44040.04230.4419.60717.441627.0986
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 148 through 158 )A148 - 158
2X-RAY DIFFRACTION2chain 'A' and (resid 159 through 166 )A159 - 166
3X-RAY DIFFRACTION3chain 'A' and (resid 167 through 177 )A167 - 177
4X-RAY DIFFRACTION4chain 'A' and (resid 178 through 189 )A178 - 189
5X-RAY DIFFRACTION5chain 'A' and (resid 190 through 197 )A190 - 197
6X-RAY DIFFRACTION6chain 'A' and (resid 198 through 209 )A198 - 209
7X-RAY DIFFRACTION7chain 'A' and (resid 210 through 216 )A210 - 216
8X-RAY DIFFRACTION8chain 'A' and (resid 217 through 229 )A217 - 229
9X-RAY DIFFRACTION9chain 'A' and (resid 230 through 239 )A230 - 239
10X-RAY DIFFRACTION10chain 'B' and (resid 149 through 158 )B149 - 158
11X-RAY DIFFRACTION11chain 'B' and (resid 159 through 171 )B159 - 171
12X-RAY DIFFRACTION12chain 'B' and (resid 172 through 177 )B172 - 177
13X-RAY DIFFRACTION13chain 'B' and (resid 178 through 189 )B178 - 189
14X-RAY DIFFRACTION14chain 'B' and (resid 190 through 209 )B190 - 209
15X-RAY DIFFRACTION15chain 'B' and (resid 210 through 229 )B210 - 229
16X-RAY DIFFRACTION16chain 'B' and (resid 230 through 242 )B230 - 242

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