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- PDB-3zbq: Protofilament of TubZ from Bacteriophage PhiKZ -

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Basic information

Entry
Database: PDB / ID: 3zbq
TitleProtofilament of TubZ from Bacteriophage PhiKZ
ComponentsPHIKZ039
KeywordsVIRAL PROTEIN / FTSZ / TUBULIN / TUBZ / CYTOSKELETON
Function / homology
Function and homology information


Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / host cell cytoplasm / GTPase activity / GTP binding
Similarity search - Function
Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Phage tubulin-like protein
Similarity search - Component
Biological speciesPSEUDOMONAS PHAGE PHIKZ (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsAylett, C.H.S. / Lowe, J.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Structure of the Tubulin/Ftsz-Like Protein Tubz from Pseudomonas Bacteriophage Phikz
Authors: Aylett, C.H.S. / Izore, T. / Amos, L.A. / Lowe, J.
History
DepositionNov 12, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2013Group: Database references
Revision 1.2Jun 12, 2013Group: Database references
Revision 2.0Jan 24, 2018Group: Atomic model / Source and taxonomy / Category: atom_site / 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 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
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 / _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

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Assembly

Deposited unit
A: PHIKZ039
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7442
Polymers37,3011
Non-polymers4431
Water5,621312
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.494, 66.243, 52.581
Angle α, β, γ (deg.)90.00, 112.69, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PHIKZ039 / PHUZ


Mass: 37300.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS PHAGE PHIKZ (virus) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q8SDC3
#2: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 1.92 Å3/Da / Density % sol: 35.92 % / Description: NONE
Crystal growpH: 5.5 / Details: 20% PEG3K, 0.1 M NA-CITRATE PH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 27, 2012
RadiationMonochromator: GRAPHITE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.7→48.51 Å / Num. obs: 40924 / % possible obs: 99.2 % / Observed criterion σ(I): 1.5 / Redundancy: 3.7 % / Biso Wilson estimate: 17.393 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.2
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 1.7 / % possible all: 95.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3R4V

3r4v


Resolution: 1.7→48.51 Å / SU ML: 0.21 / σ(F): 1.13 / Phase error: 22.68 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2032 2957 5.1 %
Rwork0.168 --
obs0.1698 30081 98.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→48.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2466 0 28 312 2806
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072541
X-RAY DIFFRACTIONf_angle_d1.013445
X-RAY DIFFRACTIONf_dihedral_angle_d15.01933
X-RAY DIFFRACTIONf_chiral_restr0.069389
X-RAY DIFFRACTIONf_plane_restr0.004447
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.72790.30261070.31592259X-RAY DIFFRACTION84
1.7279-1.75770.3541260.31092432X-RAY DIFFRACTION89
1.7577-1.78960.34071330.28682562X-RAY DIFFRACTION96
1.7896-1.82410.31051530.26432664X-RAY DIFFRACTION100
1.8241-1.86130.30651510.25032689X-RAY DIFFRACTION100
1.8613-1.90180.24151800.22432647X-RAY DIFFRACTION100
1.9018-1.9460.24341640.21782654X-RAY DIFFRACTION99
1.946-1.99470.28351290.1982695X-RAY DIFFRACTION100
1.9947-2.04860.26461210.19122684X-RAY DIFFRACTION100
2.0486-2.10890.22871350.16982735X-RAY DIFFRACTION100
2.1089-2.1770.21471320.16942704X-RAY DIFFRACTION100
2.177-2.25480.20961420.16122681X-RAY DIFFRACTION100
2.2548-2.3450.20911450.1482691X-RAY DIFFRACTION100
2.345-2.45180.19341360.15682708X-RAY DIFFRACTION100
2.4518-2.5810.20481280.15022683X-RAY DIFFRACTION100
2.581-2.74270.21251450.1512719X-RAY DIFFRACTION100
2.7427-2.95440.19141360.15422650X-RAY DIFFRACTION100
2.9544-3.25170.16151670.15072665X-RAY DIFFRACTION100
3.2517-3.72210.15091440.132690X-RAY DIFFRACTION100
3.7221-4.68880.15951350.12592700X-RAY DIFFRACTION100
4.6888-48.52950.17051480.16242680X-RAY DIFFRACTION99

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