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- PDB-2btq: Structure of BtubAB heterodimer from Prosthecobacter dejongeii -

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Basic information

Entry
Database: PDB / ID: 2btq
TitleStructure of BtubAB heterodimer from Prosthecobacter dejongeii
Components
  • TUBULIN BTUBA
  • TUBULIN BTUBB
KeywordsSTRUCTURAL PROTEIN / CYTOSKELETAL PROTEIN-COMPLEX / BACTERIAL TUBULIN / CYTOSKELETON / POLYMERIZATION / VERRUCOMICROBIA / PROTEIN COMPLEX / CYTOSKELETAL PROTEIN
Function / homology
Function and homology information


microtubule-based process / structural constituent of cytoskeleton / microtubule / hydrolase activity / GTPase activity / GTP binding
Similarity search - Function
Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / 60s Ribosomal Protein L30; Chain: A; / Alpha tubulin / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site ...Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / 60s Ribosomal Protein L30; Chain: A; / Alpha tubulin / 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 / Tubulin BtubB / Tubulin
Similarity search - Component
Biological speciesPROSTHECOBACTER DEJONGEII (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsSchlieper, D. / Lowe, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: Structure of Bacterial Tubulin Btuba/B: Evidence for Horizontal Gene Transfer.
Authors: Schlieper, D. / Oliva, M.A. / Andreu, J.M. / Lowe, J.
History
DepositionJun 6, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TUBULIN BTUBA
B: TUBULIN BTUBB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,5927
Polymers97,7652
Non-polymers8275
Water00
1
A: TUBULIN BTUBA
B: TUBULIN BTUBB
hetero molecules

A: TUBULIN BTUBA
B: TUBULIN BTUBB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,18514
Polymers195,5304
Non-polymers1,65510
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_544x,x-y-1,-z-1/61
MethodPQS
Unit cell
Length a, b, c (Å)154.398, 154.398, 256.330
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein TUBULIN BTUBA


Mass: 51299.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PROSTHECOBACTER DEJONGEII (bacteria)
Description: GERMAN COLLECTION OF MICROORGANISMS (DSM 12251)
Plasmid: PHIS17 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q8GCC5
#2: Protein TUBULIN BTUBB


Mass: 46465.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PROSTHECOBACTER DEJONGEII (bacteria)
Description: GERMAN COLLECTION OF MICROORGANISMS (DSM 12251)
Plasmid: PHIS17 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q8GCC1
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
Sequence detailsTHE SEQADV RECORDS BELOW FOR THE BTUBA SEQUENCE APPEARS TO BE FROM A NATURAL VARIATION IN THE GENE.

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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: 4.51 Å3/Da / Density % sol: 72.73 %
Crystal growpH: 7.5 / Details: 1.5M LI2SO4, 0.4M TRIS/HCL, PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 8, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 3.2→53.52 Å / Num. obs: 29998 / % possible obs: 99 % / Observed criterion σ(I): 2.6 / Redundancy: 3.6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.8
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.6 / % possible all: 99.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BTO

2bto


Resolution: 3.2→53.52 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: MAXIMUM LIKELIHOOD TARGET USING AMPLITUDES
RfactorNum. reflection% reflectionSelection details
Rfree0.2466 1509 4.9 %RANDOM
Rwork0.2147 ---
obs0.2147 29998 98.3 %-
Solvent computationBsol: 90.9632 Å2 / ksol: 0.339518 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--10.911 Å2-4.063 Å20 Å2
2---10.911 Å20 Å2
3---21.823 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.35 Å
Luzzati sigma a0.57 Å0.53 Å
Refinement stepCycle: LAST / Resolution: 3.2→53.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6354 0 48 0 6402
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007352
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_deg1.37569
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.80424
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8158
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
LS refinement shellResolution: 3.2→3.24 Å / Total num. of bins used: 30 /
RfactorNum. reflection
Rfree0.3334 51
Rwork0.3538 939
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2GDP.PAR
X-RAY DIFFRACTION3SO4.PAR

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