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- PDB-5aj8: Tubulin Binding Cofactor C from Leishmania major -

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Basic information

Entry
Database: PDB / ID: 5aj8
TitleTubulin Binding Cofactor C from Leishmania major
ComponentsTUBULIN BINDING COFACTOR C
KeywordsSTRUCTURAL PROTEIN
Function / homology
Function and homology information


post-chaperonin tubulin folding pathway / tubulin complex assembly / protein folding / cytoplasm
Similarity search - Function
Tubulin-specific chaperone C / Tubulin binding cofactor C-like domain / Tubulin binding cofactor C / CARP motif / Domain in CAPs (cyclase-associated proteins) and X-linked retinitis pigmentosa 2 gene product. / C-CAP/cofactor C-like domain / C-CAP/cofactor C-like domain profile. / Cyclase-associated protein CAP/septum formation inhibitor MinC, C-terminal
Similarity search - Domain/homology
C-CAP/cofactor C-like domain-containing protein
Similarity search - Component
Biological speciesLEISHMANIA MAJOR (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsBarrack, K.L. / Fyfe, P.K. / Finney, A.J. / Hunter, W.N.
CitationJournal: Mol.Biochem.Parasitol. / Year: 2015
Title: Crystal Structure of the C-Terminal Domain of Tubulin-Binding Cofactor C from Leishmania Major.
Authors: Barrack, K.L. / Fyfe, P.K. / Finney, A.J. / Hunter, W.N.
History
DepositionFeb 20, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2015Group: Database references
Revision 1.2Aug 26, 2015Group: Database references
Revision 1.3Nov 6, 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
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_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TUBULIN BINDING COFACTOR C
B: TUBULIN BINDING COFACTOR C


Theoretical massNumber of molelcules
Total (without water)41,3132
Polymers41,3132
Non-polymers00
Water5,405300
1
A: TUBULIN BINDING COFACTOR C


Theoretical massNumber of molelcules
Total (without water)20,6571
Polymers20,6571
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TUBULIN BINDING COFACTOR C


Theoretical massNumber of molelcules
Total (without water)20,6571
Polymers20,6571
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.644, 93.236, 48.277
Angle α, β, γ (deg.)90.00, 108.38, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.6089, -0.01911, 0.793), (0.01711, -0.9998, -0.01095), (0.793, 0.006893, 0.6091)
Vector: 20.1, 96.07, -38.21)

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Components

#1: Protein TUBULIN BINDING COFACTOR C


Mass: 20656.740 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LEISHMANIA MAJOR (eukaryote) / Strain: FRIEDLIN / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q4Q1A3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTRUNCATED FORM COMPRISING RESIDUES 152-355

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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: 1.91 Å3/Da / Density % sol: 36 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97911
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Sep 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2.2→46.62 Å / Num. obs: 15839 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 11.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 17.5
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 6.8 / % possible all: 86.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
Aimlessdata scaling
PHENIXAUTOSOLphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.2→46.62 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.934 / SU B: 8.81 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.348 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.19738 792 5 %RANDOM
Rwork0.1555 ---
obs0.15758 15026 98.29 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.539 Å2
Baniso -1Baniso -2Baniso -3
1-1.41 Å20 Å2-1.2 Å2
2---0.48 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 2.2→46.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2586 0 0 300 2886
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192777
X-RAY DIFFRACTIONr_bond_other_d0.0040.022490
X-RAY DIFFRACTIONr_angle_refined_deg1.3261.9323799
X-RAY DIFFRACTIONr_angle_other_deg0.94435748
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0665358
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.41222.927123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.78115418
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5851521
X-RAY DIFFRACTIONr_chiral_restr0.080.2413
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213240
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02677
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_it1.8371.1121399
X-RAY DIFFRACTIONr_mcbond_other1.8281.111398
X-RAY DIFFRACTIONr_mcangle_it3.0151.6511768
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.8291.4081378
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: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.212 48 -
Rwork0.168 965 -
obs--85.99 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.40710.03880.721.854-0.36161.37930.04440.02310.0169-0.0322-0.05750.03290.09940.06190.01310.07290.00420.00460.0261-0.01110.022420.75342.120.831
20.40060.20410.72311.40810.5011.3201-0.0178-0.01750.0380.0557-0.0476-0.0292-0.0127-0.03540.06550.0814-0.00190.01850.0128-0.0060.014629.80254.21624.753
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A158 - 325
2X-RAY DIFFRACTION2B158 - 323

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