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- PDB-4cqi: Crystal structure of recombinant tubulin-binding cofactor A (TBCA... -

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Basic information

Entry
Database: PDB / ID: 4cqi
TitleCrystal structure of recombinant tubulin-binding cofactor A (TBCA) from Leishmania major
ComponentsTUBULIN-BINDING COFACTOR A
KeywordsSTRUCTURAL PROTEIN / TUBULIN-BINDING COFACTOR A
Function / homology
Function and homology information


post-chaperonin tubulin folding pathway / tubulin complex assembly / beta-tubulin binding / tubulin binding / protein folding / microtubule cytoskeleton / microtubule / cytoplasm
Similarity search - Function
Tubulin binding cofactor A / Tubulin binding cofactor A superfamily / Tubulin binding cofactor A / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #90 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Tubulin-specific chaperone A
Similarity search - Component
Biological speciesLEISHMANIA MAJOR (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.9 Å
AuthorsBarrack, K.L. / Fyfe, P.K. / Hunter, W.N.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2015
Title: The Structure of Tubulin-Binding Cofactor a from Leishmania Major Infers a Mode of Association During the Early Stages of Microtubule Assembly
Authors: Barrack, K.L. / Fyfe, P.K. / Hunter, W.N.
History
DepositionFeb 17, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1May 13, 2015Group: Database references / Structure summary
Revision 1.2May 20, 2015Group: Database references
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TUBULIN-BINDING COFACTOR A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4133
Polymers14,2251
Non-polymers1882
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.757, 76.757, 39.433
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein TUBULIN-BINDING COFACTOR A


Mass: 14224.944 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LEISHMANIA MAJOR (eukaryote) / Strain: FRIEDLIN / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9U1D9
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTWO RESIDUES AT N-TERMINUS (GH) REMAIN FROM CLEAVED EXPRESSION TAG.

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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: 2.36 Å3/Da / Density % sol: 47.82 % / Description: NONE
Crystal growDetails: RESERVOIR CONTAINED 0.2M (NH4)2HPO4 AND 1.6M (NH4)2SO4.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 17, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.9→39.4 Å / Num. obs: 10821 / % possible obs: 100 % / Redundancy: 12.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 24.9
Reflection shellResolution: 1.9→2 Å / Redundancy: 12.4 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 6.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.9→39.43 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.931 / SU B: 2.975 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES WITH INSUFFICIENT ELECTRON DENSITY WERE NOT MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2276 521 4.8 %RANDOM
Rwork0.18506 ---
obs0.18713 10286 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.981 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å2-0.18 Å20 Å2
2---0.35 Å20 Å2
3---0.53 Å2
Refinement stepCycle: LAST / Resolution: 1.9→39.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms839 0 11 90 940
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.019872
X-RAY DIFFRACTIONr_bond_other_d0.0010.02613
X-RAY DIFFRACTIONr_angle_refined_deg1.5862.0051176
X-RAY DIFFRACTIONr_angle_other_deg0.96131506
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7135110
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.2132542
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.96115176
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.491159
X-RAY DIFFRACTIONr_chiral_restr0.0750.2140
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021950
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02151
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
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 34 -
Rwork0.211 702 -
obs--100 %

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