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- PDB-5io9: X-RAY STRUCTURE OF THE N-TERMINAL DOMAIN OF HUMAN DOUBLECORTIN -

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Basic information

Entry
Database: PDB / ID: 5io9
TitleX-RAY STRUCTURE OF THE N-TERMINAL DOMAIN OF HUMAN DOUBLECORTIN
ComponentsNeuronal migration protein doublecortin
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 / intracellular signal transduction / neuron projection / 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: 1.3 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


Theoretical massNumber of molelcules
Total (without water)24,4092
Polymers24,4092
Non-polymers00
Water4,738263
1
A: Neuronal migration protein doublecortin


Theoretical massNumber of molelcules
Total (without water)12,2051
Polymers12,2051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Neuronal migration protein doublecortin


Theoretical massNumber of molelcules
Total (without water)12,2051
Polymers12,2051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)27.026, 37.783, 47.752
Angle α, β, γ (deg.)88.65, 105.78, 96.55
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 12204.541 Da / Num. of mol.: 2 / Fragment: N-TERMINAL DOMAIN, UNP 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


Mass: 18.015 Da / Num. of mol.: 263 / 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: 2.09 Å3/Da / Density % sol: 41.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 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: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 14, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→26 Å / Num. obs: 39956 / % possible obs: 85.7 % / Redundancy: 2.2 % / Biso Wilson estimate: 13.8 Å2 / CC1/2: 1 / Rsym value: 0.042 / Net I/σ(I): 13.3
Reflection shellResolution: 1.3→1.33 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.35 / % possible all: 46.3

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Processing

Software
NameVersionClassification
BUSTER2.9.3refinement
XDSJanuary 30 2009data reduction
SADABS2008/1data scaling
MOLREP10.2.31phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IOI

5ioi


Resolution: 1.3→26 Å / Cor.coef. Fo:Fc: 0.9537 / Cor.coef. Fo:Fc free: 0.949 / SU R Cruickshank DPI: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.062 / SU Rfree Blow DPI: 0.063 / SU Rfree Cruickshank DPI: 0.061
RfactorNum. reflection% reflectionSelection details
Rfree0.2099 2023 5.06 %RANDOM
Rwork0.1864 ---
obs0.1876 39956 89.94 %-
Displacement parametersBiso mean: 19.09 Å2
Baniso -1Baniso -2Baniso -3
1-1.2748 Å2-0.9083 Å2-0.3194 Å2
2---1.646 Å22.1124 Å2
3---0.3712 Å2
Refine analyzeLuzzati coordinate error obs: 0.161 Å
Refinement stepCycle: LAST / Resolution: 1.3→26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1600 0 0 263 1863
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0131638HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.152217HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d586SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes46HARMONIC2
X-RAY DIFFRACTIONt_gen_planes247HARMONIC5
X-RAY DIFFRACTIONt_it1638HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.14
X-RAY DIFFRACTIONt_other_torsion16.71
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion202SEMIHARMONIC5
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_contact2112SEMIHARMONIC4
LS refinement shellResolution: 1.3→1.33 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2618 97 5.53 %
Rwork0.2603 1656 -
all0.2604 1753 -
obs--89.94 %

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