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- PDB-6fnz: Crystal Structure of domain-swapped C-terminal domain of human do... -

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Basic information

Entry
Database: PDB / ID: 6fnz
TitleCrystal Structure of domain-swapped C-terminal domain of human doublecortin
Components
  • Neuronal migration protein doublecortin
  • possible peptide
KeywordsSIGNALING PROTEIN / DCX DOMAIN / UBIQUITIN-LIKE FOLD / MICROTUBULE ASSOCIATED / DOMAIN SWAP / ANALYTICAL ULTRACENTRIFUGATION
Function / homology
Function and homology information


axoneme assembly / Neurofascin interactions / microtubule associated complex / central nervous system development / neuron migration / nervous system development / retina development in camera-type eye / microtubule binding / microtubule / cytoskeleton ...axoneme assembly / Neurofascin interactions / microtubule associated complex / central nervous system development / neuron migration / nervous system development / retina development in camera-type eye / microtubule binding / microtubule / cytoskeleton / neuron projection / intracellular signal transduction / protein kinase binding / cytosol
Similarity search - Function
Neuronal migration protein doublecortin, chordata / Doublecortin / Doublecortin domain profile. / Domain in the Doublecortin (DCX) gene product / Doublecortin domain / Doublecortin domain superfamily
Similarity search - Domain/homology
Neuronal migration protein doublecortin
Similarity search - Component
Biological speciesHomo sapiens (human)
unidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsStihle, M. / Benz, J. / Rudolph, M.G.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2018
Title: Domain swap in the C-terminal ubiquitin-like domain of human doublecortin.
Authors: Rufer, A.C. / Kusznir, E. / Burger, D. / Stihle, M. / Ruf, A. / Rudolph, M.G.
History
DepositionFeb 5, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1May 9, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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 / _citation_author.name
Revision 1.2Oct 24, 2018Group: Data collection / Derived calculations / Category: struct_conn
Revision 1.3Jan 17, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neuronal migration protein doublecortin
B: Neuronal migration protein doublecortin
C: Neuronal migration protein doublecortin
D: Neuronal migration protein doublecortin
E: possible peptide
F: possible peptide
G: possible peptide


Theoretical massNumber of molelcules
Total (without water)38,1687
Polymers38,1687
Non-polymers00
Water72140
1
A: Neuronal migration protein doublecortin
C: Neuronal migration protein doublecortin
F: possible peptide


Theoretical massNumber of molelcules
Total (without water)18,7823
Polymers18,7823
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Neuronal migration protein doublecortin
D: Neuronal migration protein doublecortin
E: possible peptide
G: possible peptide


Theoretical massNumber of molelcules
Total (without water)19,3864
Polymers19,3864
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.450, 98.450, 114.810
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11G-3-

SER

21B-403-

HOH

31D-405-

HOH

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Components

#1: Protein
Neuronal migration protein doublecortin / Doublin / Lissencephalin-X / Lis-X


Mass: 9088.683 Da / Num. of mol.: 4
Fragment: C-terminal ubiquitin-like domain, UNP residues 174-254
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DCX, DBCN, LISX / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O43602
#2: Protein/peptide possible peptide


Mass: 604.565 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 3.64 Å3/Da / Density % sol: 66.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: 20 mg/mL protein and 3x cmc CHAPS in 20mM CAPS/NaOH pH10.5, 100mM NaCl, 5mM TCEP mixed 60-70% with 40-30% reservoir consisting of 0.1M HEPES/NaOH pH7.0, 10% PEG 5000 MME, 5% Tacsimate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.18→44.028 Å / Num. obs: 29591 / % possible obs: 97.5 % / Redundancy: 8.26 % / Biso Wilson estimate: 60.08 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.086 / Rrim(I) all: 0.092 / Χ2: 1.038 / Net I/σ(I): 12.86 / Num. measured all: 244277 / Scaling rejects: 23
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible allCC1/2
2.18-2.233.9094.7690.275691218814565.46966.5
2.23-2.297.6633.2260.716491216121523.45999.60.331
2.29-2.368.9562.3291.0618620208120792.47199.90.489
2.36-2.438.8491.8471.3317848201720171.9611000.524
2.43-2.518.5921.3351.8517107199119911.421000.731
2.51-2.68.3881.0122.3715803188418841.0791000.776
2.6-2.78.8880.723.3816497185618560.7641000.899
2.7-2.818.9750.4695.0416030178617860.4981000.957
2.81-2.938.7990.3267.1114923169616960.3461000.973
2.93-3.088.3870.21110.0713863165316530.2251000.986
3.08-3.248.3540.15413.2313066156415640.1641000.992
3.24-3.448.9010.11517.6113192148414820.12299.90.995
3.44-3.688.6550.07325.0912143140314030.0771000.998
3.68-3.978.2920.0629.9710829130613060.0641000.998
3.97-4.358.0470.05134.069793121712170.0551000.998
4.35-4.868.5590.04439.379501111011100.0461000.999
4.86-5.628.2240.04438.6581429909900.0471000.998
5.62-6.887.7340.04137.966208578560.04499.90.998
6.88-9.737.9410.03341.7953766776770.0351000.999
9.73-44.0286.5910.02939.3127424264160.03197.71

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.12rc1_2801refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: modified PDB entry 5ip4

5ip4


Resolution: 2.23→44.028 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2313 1428 5.08 %random
Rwork0.2075 26673 --
obs0.2088 28101 99.79 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 188.69 Å2 / Biso mean: 78.9177 Å2 / Biso min: 40.38 Å2
Refinement stepCycle: final / Resolution: 2.23→44.028 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2598 0 0 40 2638
Biso mean---60.92 -
Num. residues----333
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072687
X-RAY DIFFRACTIONf_angle_d0.9223618
X-RAY DIFFRACTIONf_chiral_restr0.058435
X-RAY DIFFRACTIONf_plane_restr0.005452
X-RAY DIFFRACTIONf_dihedral_angle_d13.0841648
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2298-2.30950.38471310.37772586271799
2.3095-2.4020.38971380.344326492787100
2.402-2.51130.39231450.32926102755100
2.5113-2.64370.30931390.301626092748100
2.6437-2.80930.31831410.277226532794100
2.8093-3.02620.27991540.261126412795100
3.0262-3.33060.27331520.238826462798100
3.3306-3.81230.21881560.213226682824100
3.8123-4.80220.20721370.158527312868100
4.8022-44.03670.16651350.168328803015100
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)
10.5824-0.36050.28650.1047-0.14770.12250.1871-0.5416-0.3620.1047-0.2665-0.99120.512-0.2963-0.00870.4913-0.05690.14790.4147-0.06360.7653-32.9486-6.0124-28.2105
20.3214-0.4694-0.6285-0.15140.0890.25990.0013-0.6976-0.27930.29060.2513-0.0083-0.21010.09210.00050.4809-0.00790.0570.64810.05440.4969-40.3658-3.6286-15.7578
30.0999-0.04690.00160.11950.10290.11270.47740.12130.0729-0.197-0.6376-0.97680.82921.1614-0.00120.8480.08760.22510.8213-0.28351.3276-31.0244-17.2981-30.4427
40.57010.1836-0.2855-0.0253-0.15360.48720.133-0.114-0.61740.63330.7762-0.45310.97290.23920.00010.6906-0.0467-0.05460.4864-0.04760.6353-36.1119-14.3001-17.2591
50.09710.6120.21060.93140.5970.42890.5792-0.75780.7022-0.1425-0.30250.0034-1.36030.80670.01190.5547-0.18270.04910.97520.01110.5807-35.8121-1.82448.7626
61.03-0.75220.32581.14750.44050.47960.1843-0.75370.42810.715-0.1077-0.165-1.21090.70270.00120.5658-0.0702-0.07670.89980.04210.4806-38.0883-6.898612.7236
70.8887-0.1851-0.90170.1676-0.19762.0211.2797-1.5430.1023-0.0244-1.31210.25941.74221.7965-0.06381.07870.0814-0.02780.8299-0.17080.7594-47.3298-28.069414.946
8-0.1770.1171-0.99821.2098-0.87521.07790.00330.19720.0492-0.1750.12440.1897-0.2412-0.3529-0.00010.4750.0191-0.03950.47680.00230.6053-46.7291-34.6275-0.2427
90.47970.70380.72121.09981.01391.02680.17630.3403-0.5861-0.41320.15860.8653-1.0510.02660.050.61330.23070.04080.61230.04760.6284-51.4348-29.7268-3.4434
101.2101-0.6853-0.10210.41390.17150.1443-0.26110.2197-0.7114-0.54240.5619-1.179-0.35640.62050.00810.7059-0.27990.02050.8731-0.16980.745-42.6948-37.5803-29.7232
110.33560.33960.32620.298-0.03540.0632-0.1280.6201-0.8359-0.8204-0.0611-0.03050.44561.3361-0.02650.8307-0.1952-0.04270.6758-0.01720.5133-47.7798-35.7945-33.9583
120.96550.18240.08080.54140.66290.8540.30950.21150.19270.0223-0.0010.1012-0.07690.61470.00070.60090.08810.02470.52110.0040.4414-43.3967-10.81254.8804
130.2360.1960.73861.0872-0.34281.62060.76560.7443-0.9972-0.20210.5275-0.73250.50551.89750.1440.40620.167-0.10621.0215-0.07810.7687-32.3231-14.07996.3196
140.80650.18960.59950.6391-0.30541.856-0.1769-0.0275-0.6270.20740.73861.2974-0.3754-1.08750.0940.6342-0.167-0.05820.58470.07440.6017-47.0581-12.2752-22.659
150.4170.11390.06350.89570.60370.3158-0.00920.1979-0.409-0.6478-0.0528-0.11750.0497-0.7672-0.01010.6057-0.09350.08660.5455-0.01080.5958-42.4008-9.8571-27.0663
160.0668-0.1919-0.33360.21930.40210.7129-0.04690.15590.3734-0.3141-0.39340.07090.9453-0.4553-0.08430.4539-0.0185-0.20990.63690.00780.7834-55.0575-30.4391-36.0897
170.11960.16790.4630.63280.42270.7389-0.1625-0.50730.50650.0843-0.1014-0.5021-0.21850.032-0.00060.64460.047-0.1580.5667-0.08990.6294-53.447-39.1645-22.8046
182.33920.8039-0.28870.9270.65830.93870.526-0.2858-0.49760.41210.33161.3828-0.31840.76280.41031.9862-0.2841-0.4902-0.044601.3782-51.7912-21.4361-34.2808
190.2138-0.26620.14330.5843-0.45570.294-0.26150.0050.1872-0.14130.6079-0.0691-0.7824-0.55810.01390.6708-0.0969-0.08230.6383-0.06840.5947-48.8562-28.4864-23.5434
202.04170.7916-0.78461.295-0.37770.40540.1427-0.0494-0.56260.810.11990.5053-0.4654-0.5684-00.55240.11970.08460.61970.04530.5602-54.3239-38.35334.265
212.55921.0081-3.55524.9802-4.64927.2054-1.8063-0.42420.3247-0.8103-1.43250.319-0.3037-0.1973-1.09291.06630.0394-0.450.5567-0.27681.5442-51.6803-52.2606-0.1644
223.9398-0.1346-5.54141.74710.24527.8862-2.81270.64310.26120.1801-0.68370.87990.55471.1643-2.88370.76810.0305-0.16850.79990.26521.0618-52.75110.4482-20.9755
230.5803-0.23390.27440.2494-0.07230.1253-1.01570.1305-0.4057-0.1636-1.1061-0.6127-1.6341-0.6223-1.10290.6619-0.0805-0.0880.9204-0.27851.359-48.255-51.0087-28.855
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 258 through 265 )A258 - 265
2X-RAY DIFFRACTION2chain 'A' and (resid 266 through 280 )A266 - 280
3X-RAY DIFFRACTION3chain 'A' and (resid 281 through 287 )A281 - 287
4X-RAY DIFFRACTION4chain 'A' and (resid 288 through 302 )A288 - 302
5X-RAY DIFFRACTION5chain 'A' and (resid 303 through 319 )A303 - 319
6X-RAY DIFFRACTION6chain 'A' and (resid 320 through 335 )A320 - 335
7X-RAY DIFFRACTION7chain 'B' and (resid 255 through 260 )B255 - 260
8X-RAY DIFFRACTION8chain 'B' and (resid 261 through 287 )B261 - 287
9X-RAY DIFFRACTION9chain 'B' and (resid 288 through 302 )B288 - 302
10X-RAY DIFFRACTION10chain 'B' and (resid 303 through 319 )B303 - 319
11X-RAY DIFFRACTION11chain 'B' and (resid 320 through 335 )B320 - 335
12X-RAY DIFFRACTION12chain 'C' and (resid 259 through 280 )C259 - 280
13X-RAY DIFFRACTION13chain 'C' and (resid 281 through 302 )C281 - 302
14X-RAY DIFFRACTION14chain 'C' and (resid 303 through 319 )C303 - 319
15X-RAY DIFFRACTION15chain 'C' and (resid 320 through 335 )C320 - 335
16X-RAY DIFFRACTION16chain 'D' and (resid 257 through 265 )D257 - 265
17X-RAY DIFFRACTION17chain 'D' and (resid 266 through 280 )D266 - 280
18X-RAY DIFFRACTION18chain 'D' and (resid 281 through 287 )D281 - 287
19X-RAY DIFFRACTION19chain 'D' and (resid 288 through 302 )D288 - 302
20X-RAY DIFFRACTION20chain 'D' and (resid 303 through 335 )D303 - 335
21X-RAY DIFFRACTION21chain 'E' and (resid 0 through 5 )E0 - 5
22X-RAY DIFFRACTION22chain 'F' and (resid 0 through 5 )F0 - 5
23X-RAY DIFFRACTION23chain 'G' and (resid 0 through 5 )G0 - 5

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