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- PDB-2bqq: X-ray Structure of the N-terminal Domain of Human Doublecortin -

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Basic information

Entry
Database: PDB / ID: 2bqq
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: 2.2 Å
AuthorsKim, M.H. / Cooper, D.R. / Derewenda, U. / Derewenda, Z.S.
CitationJournal: Proteins / Year: 2006
Title: The Dc-Module of Doublecortin: Dynamics, Domain Boundaries, and Functional Implications.
Authors: Cierpicki, T. / Kim, M.H. / Cooper, D.R. / Derewenda, U. / Bushweller, J.H. / Derewenda, Z.S.
History
DepositionApr 27, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 19, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 2, 2013Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Revision 1.3Apr 1, 2015Group: Structure summary
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NEURONAL MIGRATION PROTEIN DOUBLECORTIN


Theoretical massNumber of molelcules
Total (without water)12,9441
Polymers12,9441
Non-polymers00
Water1,820101
1
A: NEURONAL MIGRATION PROTEIN DOUBLECORTIN

A: NEURONAL MIGRATION PROTEIN DOUBLECORTIN


Theoretical massNumber of molelcules
Total (without water)25,8892
Polymers25,8892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_566x,-y+1,-z+11
Buried area1830 Å2
ΔGint-6.3 kcal/mol
Surface area10470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.655, 61.655, 116.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein NEURONAL MIGRATION PROTEIN DOUBLECORTIN / Development of the nervous system / DOUBLECORTIN / LISSENCEPHALIN-X / LIS-X / DOUBLIN


Mass: 12944.309 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN RESIDUES 45-150 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGSTUNI1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O43602
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, LYS 134 TO ASP ENGINEERED RESIDUE IN CHAIN A, LYS 135 TO ASP
Sequence detailsK134D, K135D MUTATIONS WERE TO AID CRYSTALLIZATION, INITIAL GAMDPEFA ARE CLONING ARTIFACT

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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: 2.1 Å3/Da / Density % sol: 41.9 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 4.4
Details: 1.4 M NAH2PO4, 0.35 M K2HPO4, 0.6% PEG 150, SITTING DROP, pH 4.40

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.9793
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 16, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 6002 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 8.8 % / Biso Wilson estimate: 36.9 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 28.3
Reflection shellResolution: 2→2.28 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 4.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MG4
Resolution: 2.2→40 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.926 / SU B: 9.956 / SU ML: 0.137 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.269 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.237 581 9.7 %RANDOM
Rwork0.173 ---
obs0.179 5996 99.9 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 46.52 Å2
Baniso -1Baniso -2Baniso -3
1--0.247 Å20 Å20 Å2
2---0.247 Å20 Å2
3---0.495 Å2
Refinement stepCycle: LAST / Resolution: 2.2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms781 0 0 101 882
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022797
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.5251.9421075
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.438595
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.40323.33345
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.57515132
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.199158
X-RAY DIFFRACTIONr_chiral_restr0.1210.2111
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02628
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1870.2328
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.2543
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.271
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2140.268
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2480.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6161.5486
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.1182764
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.8893357
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9684.5311
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
LS refinement shellResolution: 9.57→40 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.304 9
Rwork0.238 85
Refinement TLS params.Method: refined / Origin x: 11.987 Å / Origin y: 36.321 Å / Origin z: 44.075 Å
111213212223313233
T-0.2674 Å20.0324 Å2-0.0196 Å2--0.1349 Å2-0.0077 Å2---0.1855 Å2
L3.5966 °2-0.3224 °2-0.6415 °2-3.8869 °20.3138 °2--3.3573 °2
S0.1299 Å °0.1174 Å °0.1306 Å °-0.0173 Å °-0.1787 Å °0.2593 Å °-0.185 Å °-0.6208 Å °0.0488 Å °

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