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- PDB-2bto: Structure of BtubA from Prosthecobacter dejongeii -

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Basic information

Entry
Database: PDB / ID: 2bto
TitleStructure of BtubA from Prosthecobacter dejongeii
Components
  • THIOREDOXIN 1
  • TUBULIN BTUBA
KeywordsCYTOSKELETAL PROTEIN / BACTERIAL TUBULIN / POLYMERIZATION / CYTOSKELETON / PROTEIN COMPLEX
Function / homology
Function and homology information


positive regulation of DNA-directed DNA polymerase activity / DNA polymerase processivity factor activity / protein-disulfide reductase activity / microtubule-based process / cell redox homeostasis / structural constituent of cytoskeleton / microtubule / oxidoreductase activity / hydrolase activity / GTP binding ...positive regulation of DNA-directed DNA polymerase activity / DNA polymerase processivity factor activity / protein-disulfide reductase activity / microtubule-based process / cell redox homeostasis / structural constituent of cytoskeleton / microtubule / oxidoreductase activity / hydrolase activity / GTP binding / cytosol / cytoplasm
Similarity search - Function
Thioredoxin / Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / 60s Ribosomal Protein L30; Chain: A; / Alpha tubulin / Tubulin ...Thioredoxin / Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / 60s Ribosomal Protein L30; Chain: A; / Alpha tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Thioredoxin domain profile. / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Thioredoxin 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 / Glutaredoxin / Glutaredoxin / Helix Hairpins / Thioredoxin-like superfamily / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Thioredoxin 1 / Thioredoxin 1 / Tubulin
Similarity search - Component
Biological speciesPROSTHECOBACTER DEJONGEII (bacteria)
ESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 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 4, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 23, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description / 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_ncs_dom_lim
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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TUBULIN BTUBA
B: TUBULIN BTUBA
T: THIOREDOXIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,3325
Polymers114,2863
Non-polymers1,0462
Water3,891216
1
A: TUBULIN BTUBA
B: TUBULIN BTUBA
T: THIOREDOXIN 1
hetero molecules

A: TUBULIN BTUBA
B: TUBULIN BTUBA
T: THIOREDOXIN 1
hetero molecules

A: TUBULIN BTUBA
B: TUBULIN BTUBA
T: THIOREDOXIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)345,99715
Polymers342,8589
Non-polymers3,1396
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+y+1,-x,z1
crystal symmetry operation2_545-y,x-y-1,z1
MethodPQS
Unit cell
Length a, b, c (Å)180.539, 180.539, 84.229
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 6 / Auth seq-ID: 3 - 432 / Label seq-ID: 3 - 432

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein TUBULIN BTUBA


Mass: 51299.371 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PROSTHECOBACTER DEJONGEII (bacteria)
Description: GERMAN COLLECTION OF MICROORGANISMS (DSM 12251)
Plasmid: PET32(APDA10) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): C41(DE3) / References: UniProt: Q8GCC5
#2: Protein THIOREDOXIN 1 / TRX1 / TRX


Mass: 11687.388 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P00274, UniProt: P0AA25*PLUS
#3: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE PROTEIN WAS CRYSTALLIZED AS A THIOREDOXIN-BTUBA-HIS6 FUSION PROTEIN. THE SEQUENCE OF THIS ...THE PROTEIN WAS CRYSTALLIZED AS A THIOREDOXIN-BTUBA-HIS6 FUSION PROTEIN. THE SEQUENCE OF THIS FUSION PROTEIN IS SDKIIHLTDDSFDTDVLKADGAILVDFWAEWCGPCKMIAPILDEIADEYQGKLTVA KLNIDQNPGTAPKYGIRGIPTLLLFKNGEVAATKVGALSKGQLKEFLDANLAGSGS GHKVNNTIVVSIGQAGNQIAASFWKTVCLEHGIDPLTGQTAPGVAPRGNWSSFFSK LGESSSGSYVPRAIMVDLEPSVIDNVKATSGSLFNPANLISRTEGAGGNFAVGYLG AGREVLPEVMSRLDYEIDKCDNVGGIIVLHAIGGGTGSGFGALLIESLKEKYGEIP VLSCAVLPSPQVSSVVTEPYNTVFALNTLRRSADACLIFDNEALFDLAHRKWNIES PTVDDLNLLITEALAGITASMRFSGFLTVEISLRELLTNLVPQPSLHFLMCAFAPLA TPPDRSKFEELGIEEMIKSLFDNGSVFACSPMEGRFLSTAVLYRGIMEDKPLADAAL AAMREKLPLTYWIPTAFKIGYVEQPGISHRKSMVLLANNTEIARVLDRICHNFDKLW QRKAFANWYLNEGMSEEQINVLRASAQELVQSYQVAEESGAKAKVQDSAGDTGMRAA AAGVSDDARGSMSLRDLVDRRRLEHHHHHH

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.8 Å3/Da / Density % sol: 67.37 %
Crystal growDetails: 1.6M NA K PHOSPHATE, PH 6.0

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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: Apr 28, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.5→31.6 Å / Num. obs: 54524 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 4.9 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.5
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 5 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.922 / SU B: 16.873 / SU ML: 0.187 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.294 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SOLVE AND SHARP WERE ALSO USED TO THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.235 2732 5 %RANDOM
Rwork0.2 ---
obs0.202 52031 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 54.62 Å2
Baniso -1Baniso -2Baniso -3
1-2.23 Å21.12 Å20 Å2
2--2.23 Å20 Å2
3----3.35 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7171 0 64 216 7451
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0227382
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3521.98110039
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6755930
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.28924.625307
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.607151209
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2211538
X-RAY DIFFRACTIONr_chiral_restr0.0930.21150
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025516
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2070.23336
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.25031
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2346
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.250.250
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0790.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5923.54773
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.97247490
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.94552963
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.4726.52549
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
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3095 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
loose positional0.55
loose thermal2.910
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.279 206
Rwork0.27 3804
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)
11.3136-0.43020.12584.1966-0.57511.64550.22520.1399-0.0567-1.0491-0.2288-0.08930.53480.16730.00360.33860.1303-0.0066-0.34450.0047-0.285396.643-21.166-13.832
20.9782-0.80810.44676.1839-1.39581.741-0.1192-0.03440.08371.3669-0.1865-0.8265-0.54540.1510.30570.2096-0.1006-0.2149-0.30180.0716-0.1775104.906-25.27928.058
39.047-4.838-2.166613.85864.12828.8924-1.6288-0.6664-1.01621.87710.50543.45271.0148-0.29821.12350.01050.11320.4411-0.32080.18870.70967.596-19.8648.399
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 432
2X-RAY DIFFRACTION2B3 - 432
3X-RAY DIFFRACTION3T23 - 125

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