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- PDB-4b6w: Architecture of Trypanosoma brucei Tubulin-Binding cofactor B -

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Basic information

Entry
Database: PDB / ID: 4b6w
TitleArchitecture of Trypanosoma brucei Tubulin-Binding cofactor B
ComponentsTUBULIN-SPECIFIC CHAPERONE
KeywordsCHAPERONE / CAP-GLY / UBIQUITIN-LIKE
Function / homology
Function and homology information


post-chaperonin tubulin folding pathway / tubulin complex assembly / microtubule plus-end / microtubule plus-end binding / alpha-tubulin binding / cytoplasmic microtubule organization / nucleus / cytoplasm
Similarity search - Function
Tubulin-folding cofactor B, N-terminal ubiquitin-like domain / Ubiquitin-like domain / CAP Gly-rich domain / CAP Gly-rich domain superfamily / CAP-Gly domain / CAP-Gly domain profile. / CAP_GLY / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin-like domain ...Tubulin-folding cofactor B, N-terminal ubiquitin-like domain / Ubiquitin-like domain / CAP Gly-rich domain / CAP Gly-rich domain superfamily / CAP-Gly domain / CAP-Gly domain profile. / CAP_GLY / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Tubulin-specific chaperone, putative
Similarity search - Component
Biological speciesTRYPANOSOMA BRUCEI BRUCEI STRAIN 927/4 GUTAT10.1 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 Å
AuthorsFleming, J.R. / Morgan, R.E. / Fyfe, P.K. / Kelly, S.M. / Hunter, W.N.
CitationJournal: FEBS J. / Year: 2013
Title: The Architecture of Trypanosoma Brucei Tubulin-Binding Cofactor B and Implications for Function.
Authors: Fleming, J.R. / Morgan, R.E. / Fyfe, P.K. / Kelly, S.M. / Hunter, W.N.
History
DepositionAug 15, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Refinement description
Revision 1.2May 15, 2013Group: Database references
Revision 1.3Jul 17, 2013Group: Database references
Revision 1.4Oct 23, 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_conn / 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_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: TUBULIN-SPECIFIC CHAPERONE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,1422
Polymers10,0801
Non-polymers621
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.920, 50.920, 77.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein TUBULIN-SPECIFIC CHAPERONE


Mass: 10080.010 Da / Num. of mol.: 1 / Fragment: TBC-B UBL DOMAIN, RESIDUES 2-87
Source method: isolated from a genetically manipulated source
Details: DOMAIN OBTAINED VIA CHYMOTRYPSIN PROTEOLYIS OF FULL LENGTH TBC-B PROTEIN
Source: (gene. exp.) TRYPANOSOMA BRUCEI BRUCEI STRAIN 927/4 GUTAT10.1 (eukaryote)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS / References: UniProt: Q388K4
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsPOLYPEPTIDE FOR CRYSTALLISATION GENERATED BY PROTEOLYSIS

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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: 2.16 Å3/Da / Density % sol: 43 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.98
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.35→38.6 Å / Num. obs: 4631 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 12.7 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 15.4
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 3.3 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.6.0119refinement
XDSdata reduction
SCALAdata scaling
CRANKphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.35→36.01 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.946 / SU B: 10.8 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.317 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20972 230 5 %RANDOM
Rwork0.16434 ---
obs0.16664 4365 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.28 Å2
Baniso -1Baniso -2Baniso -3
1-1.21 Å20 Å20 Å2
2--1.21 Å20 Å2
3----2.43 Å2
Refinement stepCycle: LAST / Resolution: 2.35→36.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms696 0 4 60 760
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.022742
X-RAY DIFFRACTIONr_bond_other_d0.0010.02515
X-RAY DIFFRACTIONr_angle_refined_deg1.5331.961002
X-RAY DIFFRACTIONr_angle_other_deg0.95931256
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.355590
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.85724.05437
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.79515138
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.977156
X-RAY DIFFRACTIONr_chiral_restr0.0890.2111
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021819
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02147
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: 2.351→2.412 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 14 -
Rwork0.196 266 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 17.667 Å / Origin y: 2.881 Å / Origin z: -9.428 Å
111213212223313233
T0.0447 Å20.0134 Å20.0087 Å2-0.1322 Å2-0.0133 Å2--0.173 Å2
L2.2292 °2-0.4076 °2-0.0948 °2-2.3101 °2-0.6818 °2--7.0179 °2
S0.0039 Å °0.0043 Å °-0.1002 Å °-0.104 Å °0.0263 Å °0.0339 Å °0.1244 Å °-0.1447 Å °-0.0302 Å °

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