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- PDB-1qsd: RBL2P, BETA-TUBULIN BINDING POST-CHAPERONIN COFACTOR -

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Basic information

Entry
Database: PDB / ID: 1qsd
TitleRBL2P, BETA-TUBULIN BINDING POST-CHAPERONIN COFACTOR
ComponentsPROTEIN (BETA-TUBULIN BINDING POST-CHAPERONIN COFACTOR)
KeywordsCHAPERONE / FOUR-HELIX-BUNDLE
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 speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsSteinbacher, S.
CitationJournal: Nat.Struct.Biol. / Year: 1999
Title: Crystal structure of the post-chaperonin beta-tubulin binding cofactor Rbl2p
Authors: Steinbacher, S.
History
DepositionJun 21, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (BETA-TUBULIN BINDING POST-CHAPERONIN COFACTOR)
B: PROTEIN (BETA-TUBULIN BINDING POST-CHAPERONIN COFACTOR)


Theoretical massNumber of molelcules
Total (without water)24,7982
Polymers24,7982
Non-polymers00
Water2,792155
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.4, 110.1, 49.4
Angle α, β, γ (deg.)90, 106.2, 90
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PROTEIN (BETA-TUBULIN BINDING POST-CHAPERONIN COFACTOR)


Mass: 12398.963 Da / Num. of mol.: 2 / Fragment: RBL2P / Source method: isolated from a natural source / Details: ORIGINAL SEQUENCE / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P48606
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O

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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: 2.39 Å3/Da / Density % sol: 48.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.6 M NA-CITRATE/CITRIC ACID, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
Conc.: 1.6 M / Common name: trisodium citrate/citric acid

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Data collection

DiffractionMean temperature: 289 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Jan 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→15 Å / Num. all: 11128 / Num. obs: 11128 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 25.3 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 12.8
Reflection shellResolution: 2.2→2.25 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.152 / % possible all: 96.1
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 96.1 %

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Processing

Software
NameVersionClassification
SHELXSphasing
MLPHAREphasing
CCP4model building
RAVEmodel building
X-PLOR3.851refinement
MOSFLMdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
CCP4phasing
RAVEphasing
RefinementResolution: 2.2→8 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflectionSelection details
Rfree0.297 537 RANDOM
Rwork0.208 --
all0.211 10958 -
obs0.211 10958 -
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1682 0 0 155 1837
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.668
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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