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- PDB-5ip4: X-RAY STRUCTURE OF THE C-TERMINAL DOMAIN OF HUMAN DOUBLECORTIN -

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Basic information

Entry
Database: PDB / ID: 5ip4
TitleX-RAY STRUCTURE OF THE C-TERMINAL DOMAIN OF HUMAN DOUBLECORTIN
Components
  • Neuronal migration protein doublecortin
  • XA4551 NANOBODY AGAINST C-DCX
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 / 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
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 / Immunoglobulins ...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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Neuronal migration protein doublecortin
Similarity search - Component
Biological speciesLama glama (llama)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 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 9, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references
Revision 1.2Aug 10, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: XA4551 NANOBODY AGAINST C-DCX
B: XA4551 NANOBODY AGAINST C-DCX
D: Neuronal migration protein doublecortin
E: Neuronal migration protein doublecortin


Theoretical massNumber of molelcules
Total (without water)47,5544
Polymers47,5544
Non-polymers00
Water6,972387
1
A: XA4551 NANOBODY AGAINST C-DCX
E: Neuronal migration protein doublecortin


Theoretical massNumber of molelcules
Total (without water)23,7772
Polymers23,7772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: XA4551 NANOBODY AGAINST C-DCX
D: Neuronal migration protein doublecortin


Theoretical massNumber of molelcules
Total (without water)23,7772
Polymers23,7772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.840, 86.191, 73.267
Angle α, β, γ (deg.)90.00, 123.00, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12D
22E

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A1 - 300
2115B1 - 300
1125D1 - 500
2125E1 - 500

NCS ensembles :
ID
1
2

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Components

#1: Protein XA4551 NANOBODY AGAINST C-DCX


Mass: 13419.717 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#2: Protein Neuronal migration protein doublecortin / Doublin / Lissencephalin-X / Lis-X


Mass: 10357.084 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN, UNP RESIDUES 251-341
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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 387 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.8 Å3/Da / Density % sol: 56.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5 / Details: 20% PEGMME, 100 mM Bis-Tris pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 14, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.81→44.77 Å / Num. obs: 42622 / % possible obs: 99.8 % / Redundancy: 3.42 % / Rrim(I) all: 0.077 / Rsym value: 0.067 / Net I/σ(I): 10.33
Reflection shellResolution: 1.81→1.9 Å / Redundancy: 3.28 % / Mean I/σ(I) obs: 1.27 / Rrim(I) all: 1.1 / % possible all: 99.7

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Processing

Software
NameVersionClassification
XDS(VERSION December 6 2010)data reduction
SADABS2008/1data scaling
REFMAC5.6.0112refinement
PHASER2.1.4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ENSEMBLE OF 2X1O, 2X1P, 2X6M, 3DWT, 3EAK, 3G9A, AND 3P0G

2x1o

2x1p

2x6m

3dwt

3eak

3g9a

3p0g


Resolution: 1.81→44.77 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.445 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.135
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT MTRIX1 1 1.000000 0.000000 0.000000 0.00000 1 MTRIX2 1 0.000000 1.000000 0.000000 0.00000 1 MTRIX3 1 0.000000 0.000000 1.000000 0.00000 1 ...Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT MTRIX1 1 1.000000 0.000000 0.000000 0.00000 1 MTRIX2 1 0.000000 1.000000 0.000000 0.00000 1 MTRIX3 1 0.000000 0.000000 1.000000 0.00000 1 MTRIX1 2 -0.953542 0.007739 -0.301161 0.89565 1 MTRIX2 2 -0.006502 -0.999966 -0.005108 126.50698 1 MTRIX3 2 -0.301190 -0.002913 0.953560 -7.08845 1
RfactorNum. reflection% reflectionSelection details
Rfree0.24635 2063 5 %RANDOM
Rwork0.19398 ---
obs0.1967 38934 95.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 31.575 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å20 Å20.46 Å2
2---0.37 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.81→44.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2986 0 0 387 3373
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.023042
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1211.9444113
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5285379
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.23623.986138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.08315522
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.6871520
X-RAY DIFFRACTIONr_chiral_restr0.1520.2461
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022281
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A436medium positional0.150.5
22D320medium positional0.540.5
11A405loose positional0.525
22D311loose positional0.95
11A436medium thermal1.822
22D320medium thermal5.412
11A405loose thermal2.6810
22D311loose thermal5.6110
LS refinement shellResolution: 1.81→1.857 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.448 153 -
Rwork0.418 2566 -
obs--87.12 %

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