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- PDB-1ffx: TUBULIN:STATHMIN-LIKE DOMAIN COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1ffx
TitleTUBULIN:STATHMIN-LIKE DOMAIN COMPLEX
Components
  • (PROTEIN (TUBULIN)) x 2
  • PROTEIN (STATHMIN-LIKE DOMAIN OF RB3)
KeywordsSTRUCTURAL PROTEIN / ALPHA-TUBULIN / BETA-TUBULIN / STATHMIN / MICROTUBULE / TUBULIN
Function / homology
Function and homology information


Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / microtubule cytoskeleton organization / mitotic cell cycle / microtubule / hydrolase activity / GTPase activity / GTP binding / metal ion binding / cytoplasm
Similarity search - Function
Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / 60s Ribosomal Protein L30; Chain: A; / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal ...Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / 60s Ribosomal Protein L30; Chain: A; / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / Helix Hairpins / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Tubulin alpha-1A chain / Tubulin beta chain
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.95 Å
AuthorsGigant, B. / Martin-Barbey, C. / Knossow, M.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2000
Title: The 4 A X-ray structure of a tubulin:stathmin-like domain complex.
Authors: Gigant, B. / Curmi, P.A. / Martin-Barbey, C. / Charbaut, E. / Lachkar, S. / Lebeau, L. / Siavoshian, S. / Sobel, A. / Knossow, M.
History
DepositionJul 26, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 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: PROTEIN (TUBULIN)
B: PROTEIN (TUBULIN)
C: PROTEIN (TUBULIN)
D: PROTEIN (TUBULIN)
E: PROTEIN (STATHMIN-LIKE DOMAIN OF RB3)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,7539
Polymers207,8215
Non-polymers1,9334
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12100 Å2
ΔGint-83 kcal/mol
Surface area70590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)328.500, 328.500, 54.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

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Components

#1: Protein PROTEIN (TUBULIN)


Mass: 50121.266 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: BRAIN / References: UniProt: P02550
#2: Protein PROTEIN (TUBULIN)


Mass: 49907.770 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: BRAIN / References: UniProt: P02554
#3: Protein PROTEIN (STATHMIN-LIKE DOMAIN OF RB3) / RB3


Mass: 7762.560 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Organ: BRAIN / Production host: Escherichia coli (E. coli)
#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#5: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM

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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: 3.9 Å3/Da / Density % sol: 68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 293.K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
2PEG1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 22, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 3.95→50 Å / Num. obs: 29784 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 130.2 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 18.9
Reflection shellResolution: 3.95→4.02 Å / Redundancy: 3 % / Rmerge(I) obs: 0.333 / Mean I/σ(I) obs: 2.9 / Rsym value: 0.333 / % possible all: 98.7
Reflection shell
*PLUS
% possible obs: 98.7 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TUB

1tub


Resolution: 3.95→7 Å / Rfactor Rfree error: 0.011 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.367 1144 4.6 %RANDOM
Rwork0.267 ---
obs0.267 23280 94.3 %-
Displacement parametersBiso mean: 78.8 Å2
Baniso -1Baniso -2Baniso -3
1--3.47 Å222.77 Å20 Å2
2---3.47 Å20 Å2
3---6.95 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.71 Å0.48 Å
Luzzati d res low-5 Å
Luzzati sigma a1.1 Å0.77 Å
Refinement stepCycle: LAST / Resolution: 3.95→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13448 0 120 0 13568
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.12
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCS
Ens-IDDom-IDRefine-IDRms dev position (Å)Weight position
11X-RAY DIFFRACTION0.073180
22X-RAY DIFFRACTION0.069180
LS refinement shellResolution: 3.95→4.15 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.422 188 5.5 %
Rwork0.319 3238 -
obs--83.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.12

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