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- PDB-5ioi: X-RAY STRUCTURE OF THE N-TERMINAL DOMAIN OF HUMAN DOUBLECORTIN -

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Basic information

Entry
Database: PDB / ID: 5ioi
TitleX-RAY STRUCTURE OF THE N-TERMINAL DOMAIN OF HUMAN DOUBLECORTIN
ComponentsNeuronal migration protein doublecortinDevelopment of the nervous system
KeywordsTRANSFERASE / DCX DOMAIN / UBIQUITIN-LIKE FOLD / MICROTUBULE ASSOCIATED / SIGNALING PROTEIN
Function / homology
Function and homology information


axoneme assembly / Neurofascin interactions / microtubule associated complex / central nervous system development / neuron migration / retina development in camera-type eye / nervous system development / microtubule binding / microtubule / cytoskeleton ...axoneme assembly / Neurofascin interactions / microtubule associated complex / central nervous system development / neuron migration / retina development in camera-type eye / nervous system development / microtubule binding / microtubule / cytoskeleton / neuron projection / intracellular signal transduction / protein kinase binding / cytosol
Similarity search - Function
Doublecortin domain / Neuronal migration protein doublecortin, chordata / : / Doublecortin / Doublecortin domain profile. / Domain in the Doublecortin (DCX) gene product / Doublecortin domain / Doublecortin domain superfamily / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
Neuronal migration protein doublecortin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsRuf, A. / Benz, J. / Burger, D. / D'Arcy, B. / Debulpaep, M. / Di Lello, P. / Fry, D. / Huber, W. / Kremer, T. / Laeremans, T. ...Ruf, A. / Benz, J. / Burger, D. / D'Arcy, B. / Debulpaep, M. / Di Lello, P. / Fry, D. / Huber, W. / Kremer, T. / Laeremans, T. / Matile, H. / Ross, A. / Rudolph, M.G. / Rufer, A.C. / Sharma, A. / Steinmetz, M.O. / Steyaert, J. / Schoch, G. / Stihle, M. / Thoma, R.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Crystal Structures of the Human Doublecortin C- and N-terminal Domains in Complex with Specific Antibodies.
Authors: Burger, D. / Stihle, M. / Sharma, A. / Di Lello, P. / Benz, J. / D'Arcy, B. / Debulpaep, M. / Fry, D. / Huber, W. / Kremer, T. / Laeremans, T. / Matile, H. / Ross, A. / Rufer, A.C. / Schoch, ...Authors: Burger, D. / Stihle, M. / Sharma, A. / Di Lello, P. / Benz, J. / D'Arcy, B. / Debulpaep, M. / Fry, D. / Huber, W. / Kremer, T. / Laeremans, T. / Matile, H. / Ross, A. / Rufer, A.C. / Schoch, G. / Steinmetz, M.O. / Steyaert, J. / Rudolph, M.G. / Thoma, R. / Ruf, A.
History
DepositionMar 8, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1May 18, 2016Group: Database references
Revision 1.2Jun 8, 2016Group: Database references
Revision 1.3Aug 10, 2016Group: Database references
Revision 1.4Dec 14, 2016Group: Structure summary
Revision 1.5Jan 10, 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: Neuronal migration protein doublecortin
F: Neuronal migration protein doublecortin


Theoretical massNumber of molelcules
Total (without water)73,8226
Polymers73,8226
Non-polymers00
Water6,359353
1
A: Neuronal migration protein doublecortin


Theoretical massNumber of molelcules
Total (without water)12,3041
Polymers12,3041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Neuronal migration protein doublecortin


Theoretical massNumber of molelcules
Total (without water)12,3041
Polymers12,3041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Neuronal migration protein doublecortin


Theoretical massNumber of molelcules
Total (without water)12,3041
Polymers12,3041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Neuronal migration protein doublecortin


Theoretical massNumber of molelcules
Total (without water)12,3041
Polymers12,3041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Neuronal migration protein doublecortin


Theoretical massNumber of molelcules
Total (without water)12,3041
Polymers12,3041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Neuronal migration protein doublecortin


Theoretical massNumber of molelcules
Total (without water)12,3041
Polymers12,3041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.719, 97.719, 377.089
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein
Neuronal migration protein doublecortin / Development of the nervous system / Doublin / Lissencephalin-X / Lis-X


Mass: 12303.672 Da / Num. of mol.: 6 / Fragment: N-TERMINAL DOMAIN, RESIDUES 133-231 / Mutation: K215D, K216D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DCX, DBCN, LISX / Production host: Escherichia coli (E. coli) / References: UniProt: O43602
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 353 / 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: 3.87 Å3/Da / Density % sol: 68.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: N-DCXDD crystals were either obtained out of 20mM CAPS pH 10.5, 100 mM NaCl, 5 mM TCEP or 20 mM HEPES pH 7.5, 100 mM NaCl, 5 mM DTT
PH range: 7.5-10.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 19, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.4→35.14 Å / Num. obs: 43037 / % possible obs: 99.9 % / Redundancy: 21.1 % / Biso Wilson estimate: 55.14 Å2 / CC1/2: 1 / Rsym value: 0.124 / Net I/σ(I): 15.6
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 20.5 % / Mean I/σ(I) obs: 3.5 / Rsym value: 0.645 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.9.2refinement
XDSJanuary 30 2009data reduction
SADABS2008/2data scaling
PHASER2.1.4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BQQ

2bqq


Resolution: 2.4→35.14 Å / Cor.coef. Fo:Fc: 0.9368 / Cor.coef. Fo:Fc free: 0.9146 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2336 2200 5.13 %RANDOM
Rwork0.196 ---
obs0.1979 42903 99.9 %-
Displacement parametersBiso mean: 49.04 Å2
Baniso -1Baniso -2Baniso -3
1--0.5205 Å20 Å20 Å2
2---0.5205 Å20 Å2
3---1.041 Å2
Refine analyzeLuzzati coordinate error obs: 0.307 Å
Refinement stepCycle: LAST / Resolution: 2.4→35.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4733 0 0 353 5086
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014827HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.146503HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1709SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes134HARMONIC2
X-RAY DIFFRACTIONt_gen_planes710HARMONIC5
X-RAY DIFFRACTIONt_it4827HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.21
X-RAY DIFFRACTIONt_other_torsion21.44
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion591SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5419SEMIHARMONIC4
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2595 150 4.83 %
Rwork0.2494 2956 -
all0.2499 3106 -

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