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- PDB-3zbp: Monomeric subunit of TubZ from Bacteriophage PhiKZ -

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Basic information

Entry
Database: PDB / ID: 3zbp
TitleMonomeric subunit 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
Phage tubulin-like protein, C-terminal domain / 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: 2 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 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 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

Downloads & links

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Assembly

Deposited unit
A: PHIKZ039
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7442
Polymers37,3011
Non-polymers4431
Water4,828268
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.453, 76.275, 54.065
Angle α, β, γ (deg.)90.00, 90.13, 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.: 268 / 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: 2.35 Å3/Da / Density % sol: 47.57 % / Description: NONE
Crystal growpH: 8
Details: 8% ETHYLENE GLYCOL, 20% PEG5KMME, 0.15 M TRIS-CL PH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9787
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 4, 2012
RadiationMonochromator: GRAPHITE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2→44.11 Å / Num. obs: 26417 / % possible obs: 99.8 % / Observed criterion σ(I): 2.5 / Redundancy: 3.4 % / Biso Wilson estimate: 17.869 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.9
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.6 / % possible all: 99.5

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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: 2→44.108 Å / SU ML: 0.18 / σ(F): 1.1 / Phase error: 19.4 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2103 2166 5 %
Rwork0.1723 --
obs0.1742 22755 96.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→44.108 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2361 0 28 268 2657
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072435
X-RAY DIFFRACTIONf_angle_d1.1263300
X-RAY DIFFRACTIONf_dihedral_angle_d15.06896
X-RAY DIFFRACTIONf_chiral_restr0.074372
X-RAY DIFFRACTIONf_plane_restr0.004426
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.04650.23881320.23932677X-RAY DIFFRACTION95
2.0465-2.09770.28971890.23622590X-RAY DIFFRACTION94
2.0977-2.15440.26561410.22572697X-RAY DIFFRACTION95
2.1544-2.21780.24011160.20382766X-RAY DIFFRACTION96
2.2178-2.28940.23991250.19062728X-RAY DIFFRACTION95
2.2894-2.37120.20561440.19122661X-RAY DIFFRACTION95
2.3712-2.46620.26141630.1892720X-RAY DIFFRACTION95
2.4662-2.57840.22791410.18882707X-RAY DIFFRACTION96
2.5784-2.71430.18041280.17142805X-RAY DIFFRACTION97
2.7143-2.88430.24031370.1772746X-RAY DIFFRACTION97
2.8843-3.1070.18651250.172760X-RAY DIFFRACTION96
3.107-3.41950.1941710.15762748X-RAY DIFFRACTION98
3.4195-3.91410.16291310.13332764X-RAY DIFFRACTION98
3.9141-4.93030.18091630.13592722X-RAY DIFFRACTION97
4.9303-44.11890.20931600.16272726X-RAY DIFFRACTION97

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