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- PDB-2xka: Crystal structure of a GTPyS-form protofilament of Bacillus thuri... -

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Basic information

Entry
Database: PDB / ID: 2xka
TitleCrystal structure of a GTPyS-form protofilament of Bacillus thuringiensis serovar israelensis TubZ
ComponentsFTSZ/TUBULIN-RELATED PROTEIN
KeywordsSTRUCTURAL PROTEIN / MOTOR PROTEIN / CYTOSKELETON / CYTOMOTIVE / DNA SEGREGATION / MICROTUBULE / PBTOXIS / PBT156 / REPX / TUBR
Function / homology
Function and homology information


plasmid partitioning / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / GTPase activity / GTP binding / identical protein binding / metal ion binding / cytoplasm
Similarity search - Function
Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / Tubulin-like protein TubZ
Similarity search - Component
Biological speciesBACILLUS THURINGIENSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsAylett, C.H.S. / Lowe, J.
CitationJournal: Proc Natl Acad Sci U S A / Year: 2010
Title: Filament structure of bacterial tubulin homologue TubZ.
Authors: Christopher H S Aylett / Qing Wang / Katharine A Michie / Linda A Amos / Jan Löwe /
Abstract: Low copy number plasmids often depend on accurate partitioning systems for their continued survival. Generally, such systems consist of a centromere-like region of DNA, a DNA-binding adaptor, and a ...Low copy number plasmids often depend on accurate partitioning systems for their continued survival. Generally, such systems consist of a centromere-like region of DNA, a DNA-binding adaptor, and a polymerizing cytomotive filament. Together these components drive newly replicated plasmids to opposite ends of the dividing cell. The Bacillus thuringiensis plasmid pBToxis relies on a filament of the tubulin/FtsZ-like protein TubZ for its segregation. By combining crystallography and electron microscopy, we have determined the structure of this filament. We explain how GTP hydrolysis weakens the subunit-subunit contact and also shed light on the partitioning of the plasmid-adaptor complex. The double helical superstructure of TubZ filaments is unusual for tubulin-like proteins. Filaments of ParM, the actin-like partitioning protein, are also double helical. We suggest that convergent evolution shapes these different types of cytomotive filaments toward a general mechanism for plasmid separation.
History
DepositionJul 7, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 10, 2010Provider: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FTSZ/TUBULIN-RELATED PROTEIN
B: FTSZ/TUBULIN-RELATED PROTEIN
C: FTSZ/TUBULIN-RELATED PROTEIN
D: FTSZ/TUBULIN-RELATED PROTEIN
E: FTSZ/TUBULIN-RELATED PROTEIN
F: FTSZ/TUBULIN-RELATED PROTEIN
G: FTSZ/TUBULIN-RELATED PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)335,25521
Polymers331,3107
Non-polymers3,94514
Water0
1
A: FTSZ/TUBULIN-RELATED PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8943
Polymers47,3301
Non-polymers5642
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: FTSZ/TUBULIN-RELATED PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8943
Polymers47,3301
Non-polymers5642
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: FTSZ/TUBULIN-RELATED PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8943
Polymers47,3301
Non-polymers5642
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: FTSZ/TUBULIN-RELATED PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8943
Polymers47,3301
Non-polymers5642
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: FTSZ/TUBULIN-RELATED PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8943
Polymers47,3301
Non-polymers5642
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: FTSZ/TUBULIN-RELATED PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8943
Polymers47,3301
Non-polymers5642
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: FTSZ/TUBULIN-RELATED PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8943
Polymers47,3301
Non-polymers5642
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.060, 85.150, 632.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1113A4 - 15
2113B4 - 15
3113C4 - 15
4113D4 - 15
5113E4 - 15
6113F4 - 15
7113G4 - 15
1213A18 - 31
2213B18 - 31
3213C18 - 31
4213D18 - 31
5213E18 - 31
6213F18 - 31
7213G18 - 31
1313A33 - 58
2313B33 - 58
3313C33 - 58
4313D33 - 58
5313E33 - 58
6313F33 - 58
7313G33 - 58
1413A66 - 77
2413B66 - 77
3413C66 - 77
4413D66 - 77
5413E66 - 77
6413F66 - 77
7413G66 - 77
1513A127 - 144
2513B127 - 144
3513C127 - 144
4513D127 - 144
5513E127 - 144
6513F127 - 144
7513G127 - 144
1613A146 - 153
2613B146 - 153
3613C146 - 153
4613D146 - 153
5613E146 - 153
6613F146 - 153
7613G146 - 153
1713A156 - 175
2713B156 - 175
3713C156 - 175
4713D156 - 175
5713E156 - 175
6713F156 - 175
7713G156 - 175
1813A178 - 222
2813B178 - 222
3813C178 - 222
4813D178 - 222
5813E178 - 222
6813F178 - 222
7813G178 - 222
1913A236 - 255
2913B236 - 255
3913C236 - 255
4913D236 - 255
5913E236 - 255
6913F236 - 255
7913G236 - 255
11013A267 - 288
21013B267 - 288
31013C267 - 288
41013D267 - 288
51013E267 - 288
61013F267 - 288
71013G267 - 288
11113A300 - 329
21113B300 - 329
31113C300 - 329
41113D300 - 329
51113E300 - 329
61113F300 - 329
71113G300 - 329
11213A344 - 350
21213B344 - 350
31213C344 - 350
41213D344 - 350
51213E344 - 350
61213F344 - 350
71213G344 - 350
11313A359 - 363
21313B359 - 363
31313C359 - 363
41313D359 - 363
51313E359 - 363
61313F359 - 363
71313G359 - 363
11413A371 - 389
21413B371 - 389
31413C371 - 389
41413D371 - 389
51413E371 - 389
61413F371 - 389
71413G371 - 389

NCS oper:
IDCodeMatrixVector
1given(0.26475, 0.95429, -0.13871), (-0.95798, 0.27675, 0.07546), (0.1104, 0.11291, 0.98745)88.2923, -2.9732, -132.61496
2given(0.65757, 0.74534, -0.1099), (-0.75126, 0.65967, -0.02119), (0.0567, 0.0965, 0.99372)54.93379, 20.43809, -87.99482
3given(0.90991, 0.38724, 0.1487), (-0.38073, 0.92194, -0.07118), (-0.16466, 0.00816, 0.98632)-4.94514, 23.07034, -36.36363
4given(0.91676, -0.3935, -0.06865), (0.3923, 0.91932, -0.03076), (0.07521, 0.00127, 0.99717)-5.32271, -15.02204, 42.63932
5given(0.6764, -0.73578, -0.03337), (0.73287, 0.67686, -0.06902), (0.07337, 0.02223, 0.99706)-18.15366, -35.0983, 88.28479
6given(0.2767, -0.95845, 0.06936), (0.95273, 0.28304, 0.11047), (-0.12551, 0.03551, 0.99146)-27.8295, -84.21684, 142.40529

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Components

#1: Protein
FTSZ/TUBULIN-RELATED PROTEIN / TUBZ


Mass: 47330.051 Da / Num. of mol.: 7 / Fragment: RESIDUES 1-421 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: GSP, MG / Source: (gene. exp.) BACILLUS THURINGIENSIS (bacteria) / Strain: SEROVAR ISRAELENSIS / Description: J. POGLIANO LABORATORY UCSD / Plasmid: PET28A / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q8KNP3
#2: Chemical
ChemComp-GSP / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE


Mass: 539.246 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C10H16N5O13P3S
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
Compound detailsENGINEERED RESIDUE IN CHAIN A, LEU 2 TO VAL ENGINEERED RESIDUE IN CHAIN B, LEU 2 TO VAL ENGINEERED ...ENGINEERED RESIDUE IN CHAIN A, LEU 2 TO VAL ENGINEERED RESIDUE IN CHAIN B, LEU 2 TO VAL ENGINEERED RESIDUE IN CHAIN C, LEU 2 TO VAL ENGINEERED RESIDUE IN CHAIN D, LEU 2 TO VAL ENGINEERED RESIDUE IN CHAIN E, LEU 2 TO VAL ENGINEERED RESIDUE IN CHAIN F, LEU 2 TO VAL ENGINEERED RESIDUE IN CHAIN G, LEU 2 TO VAL
Nonpolymer detailsMG: C999 IS ALSO BOUND TO OD2 ATOM OF ASP C64.
Sequence detailsL2V, DELTA422-484

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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: 2.08 Å3/Da / Density % sol: 40.85 % / Description: 52 SE SITES FOR SE SAD
Crystal growpH: 8.5 / Details: TRISCL PH 8.5 200 MM MGCL2 30% PEG 400 WV

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9395 Å / Relative weight: 1
ReflectionResolution: 3→52.69 Å / Num. obs: 52941 / % possible obs: 93.2 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 47.86 Å2 / Rmerge(I) obs: 0.12 / Rsym value: 0.122 / Net I/σ(I): 7.4
Reflection shellResolution: 3→3.16 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 3.6 / Rsym value: 0.339 / % possible all: 71

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing
SOLVERESOLVEphasing
REFMAC5.5.0109refinement
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 3→50 Å / Cor.coef. Fo:Fc: 0.884 / Cor.coef. Fo:Fc free: 0.834 / SU B: 24.492 / SU ML: 0.45 / Cross valid method: THROUGHOUT / ESU R Free: 0.598 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.28438 2649 5 %RANDOM
Rwork0.23198 ---
obs0.23459 50190 92.5 %-
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: 24.013 Å2
Baniso -1Baniso -2Baniso -3
1-6.12 Å20 Å20 Å2
2---2.64 Å20 Å2
3----3.48 Å2
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22407 0 231 0 22638
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02223073
X-RAY DIFFRACTIONr_bond_other_d0.0020.0215500
X-RAY DIFFRACTIONr_angle_refined_deg1.3331.96531256
X-RAY DIFFRACTIONr_angle_other_deg0.972337798
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.67752819
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.37525.0721181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.522153951
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.43315136
X-RAY DIFFRACTIONr_chiral_restr0.0760.23405
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0225817
X-RAY DIFFRACTIONr_gen_planes_other0.0020.024563
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_refined0.1550.2465
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.030.23
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2130.278
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2590.2180
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1940.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5683.514044
X-RAY DIFFRACTIONr_mcbond_other0.0593.55772
X-RAY DIFFRACTIONr_mcangle_it1.054422624
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.80159029
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.4526.58632
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

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1513tight positional0.030.05
2B1513tight positional0.030.05
3C1513tight positional0.030.05
4D1513tight positional0.030.05
5E1513tight positional0.030.05
6F1513tight positional0.030.05
7G1513tight positional0.030.05
1A1874loose positional0.035
2B1874loose positional0.035
3C1874loose positional0.035
4D1874loose positional0.035
5E1874loose positional0.035
6F1874loose positional0.035
7G1874loose positional0.035
1A1513tight thermal0.050.5
2B1513tight thermal0.060.5
3C1513tight thermal0.060.5
4D1513tight thermal0.050.5
5E1513tight thermal0.060.5
6F1513tight thermal0.060.5
7G1513tight thermal0.050.5
1A1874loose thermal0.0410
2B1874loose thermal0.0410
3C1874loose thermal0.0510
4D1874loose thermal0.0410
5E1874loose thermal0.0410
6F1874loose thermal0.0510
7G1874loose thermal0.0410
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 141 -
Rwork0.321 2602 -
obs--67.66 %

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