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- PDB-4b6m: Trypansoma brucei tubulin binding cofactor B CAP-Gly domain -

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Basic information

Entry
Database: PDB / ID: 4b6m
TitleTrypansoma brucei tubulin binding cofactor B CAP-Gly domain
ComponentsTUBULIN-SPECIFIC CHAPERONE, PUTATIVE
KeywordsSTRUCTURAL PROTEIN
Function / homology
Function and homology information


Ubiquitin-like domain / CAP Gly-rich-like domain / CAP Gly-rich domain / CAP Gly-rich domain superfamily / CAP-Gly domain / CAP-Gly domain profile. / CAP_GLY / SH3 type barrels. / Ubiquitin-like domain / Ubiquitin-like domain superfamily ...Ubiquitin-like domain / CAP Gly-rich-like domain / CAP Gly-rich domain / CAP Gly-rich domain superfamily / CAP-Gly domain / CAP-Gly domain profile. / CAP_GLY / SH3 type barrels. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
FORMIC ACID / Tubulin-specific chaperone, putative
Similarity search - Component
Biological speciesTRYPANOSOMA BRUCEI (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsFleming, J.R. / Morgan, R.E. / 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 14, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1May 15, 2013Group: Data collection / Database references
Revision 1.2Jul 17, 2013Group: Database references
Revision 1.3Oct 16, 2019Group: Data collection / Other / Category: pdbx_database_status / reflns_shell
Item: _pdbx_database_status.status_code_sf / _reflns_shell.Rmerge_I_obs
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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, PUTATIVE
B: TUBULIN-SPECIFIC CHAPERONE, PUTATIVE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7939
Polymers18,4712
Non-polymers3227
Water4,125229
1
A: TUBULIN-SPECIFIC CHAPERONE, PUTATIVE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,4205
Polymers9,2351
Non-polymers1844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TUBULIN-SPECIFIC CHAPERONE, PUTATIVE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3744
Polymers9,2351
Non-polymers1383
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.660, 55.730, 80.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TUBULIN-SPECIFIC CHAPERONE, PUTATIVE / TUBULIN BINDING COFACTOR B


Mass: 9235.447 Da / Num. of mol.: 2 / Fragment: CAP-GLY DOMAIN, RESIDUES 152-232
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRYPANOSOMA BRUCEI (eukaryote) / Strain: 947 / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS / References: UniProt: D0A053
#2: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: CH2O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 229 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE M231V DIFFERENCE IS OWING TO STRAIN VARIATION

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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: 41.45 % / Description: NONE
Crystal growDetails: 0.2 M POTASSIUM FORMATE, 30% PEG 3350 AND A PROTEIN SOLUTION CONSISTING OF 50 MM TRIS-HCL PH 7.5, 250 MM NABR WITH THE PROTEIN AT 7.5 MG ML-1.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9199
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 17, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9199 Å / Relative weight: 1
ReflectionResolution: 1.59→40.18 Å / Num. obs: 20384 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 13.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 28.2
Reflection shellResolution: 1.59→1.68 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 9.6 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WHG

1whg


Resolution: 1.59→45.79 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.921 / SU B: 1.93 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 149 TO 152 AND TWO RESIDUES LEFT OVER FROM THE TAG DISORDERED IN BOTH CHAINS. FINAL RESIDUE 232 OF CHAIN B DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.24034 1042 5.1 %RANDOM
Rwork0.20094 ---
obs0.20286 19291 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: 14.84 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å20 Å20 Å2
2--0.56 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.59→45.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1224 0 21 229 1474
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191359
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4441.9691853
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.135182
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.19622.89969
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.16215208
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3891515
X-RAY DIFFRACTIONr_chiral_restr0.0880.2190
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0221108
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
LS refinement shellResolution: 1.592→1.633 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 75 -
Rwork0.231 1281 -
obs--99.93 %

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