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- PDB-4xcq: Clostridium botulinum phage c-st TubZ (C-terminal tail truncated ... -

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Basic information

Entry
Database: PDB / ID: 4xcq
TitleClostridium botulinum phage c-st TubZ (C-terminal tail truncated protein)
ComponentsTubZL-lysine cyclodeaminase
KeywordsHYDROLASE / tubulin-like / GTPase
Function / homology
Function and homology information


plasmid partitioning / microtubule-based process / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / host cell cytoplasm / microtubule / GTPase activity / GTP binding
Similarity search - Function
60s Ribosomal Protein L30; Chain: A; - #150 / Tubulin/FtsZ, GTPase domain / 60s Ribosomal Protein L30; Chain: A; / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / Rossmann fold ...60s Ribosomal Protein L30; Chain: A; - #150 / Tubulin/FtsZ, GTPase domain / 60s Ribosomal Protein L30; Chain: A; / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Tubulin-like protein TubZ
Similarity search - Component
Biological speciesClostridium botulinum C phage (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsOliva, M.A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBFU2013-47014-P Spain
CitationJournal: To Be Published
Title: Structure of phage c-st truncated TubZ at 2.4 Angstroms resolution
Authors: Oliva, M.A.
History
DepositionDec 18, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2016Group: Data collection
Revision 1.2Dec 14, 2016Group: Other
Revision 2.0Sep 13, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Derived calculations
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_validate_close_contact / struct_conn / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.ptnr2_auth_seq_id / _struct_site_gen.auth_seq_id
Revision 2.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TubZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1133
Polymers35,6471
Non-polymers4662
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-14 kcal/mol
Surface area13230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.970, 86.342, 44.734
Angle α, β, γ (deg.)90.000, 92.490, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein TubZ / L-lysine cyclodeaminase


Mass: 35646.840 Da / Num. of mol.: 1 / Fragment: UNP residues 1-316 / Mutation: C-terminal tail truncation (42 residues)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum C phage (virus) / Gene: CST189 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q331T7
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine 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: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.94 Å3/Da / Density % sol: 58.23 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: sodium citrate, sodium cloride, PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.39→44.69 Å / Num. obs: 15849 / % possible obs: 99.4 % / Redundancy: 6.6 % / CC1/2: 0.989 / Net I/σ(I): 7.7
Reflection shellResolution: 2.39→2.53 Å / Mean I/σ(I) obs: 0.93 / Num. unique all: 2476 / CC1/2: 0.462 / % possible all: 96.7

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3v3t

3v3t


Resolution: 2.39→44.69 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2395 794 5.02 %
Rwork0.1959 15038 -
obs0.1981 15832 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 121.58 Å2 / Biso mean: 50.7662 Å2 / Biso min: 22.29 Å2
Refinement stepCycle: final / Resolution: 2.39→44.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2374 0 29 44 2447
Biso mean--48.5 50.54 -
Num. residues----303
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042451
X-RAY DIFFRACTIONf_angle_d0.83303
X-RAY DIFFRACTIONf_chiral_restr0.031370
X-RAY DIFFRACTIONf_plane_restr0.003417
X-RAY DIFFRACTIONf_dihedral_angle_d14.592926
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3866-2.53610.30851310.28612430256197
2.5361-2.73190.3111350.260624902625100
2.7319-3.00680.26771270.23825192646100
3.0068-3.44170.26381340.200725292663100
3.4417-4.33560.19541330.15824992632100
4.3356-44.69950.23091340.180225712705100
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)
13.728-1.18261.19113.9497-1.20475.0728-0.2222-0.2671-0.42730.08550.18860.30090.4943-0.77180.01750.2936-0.07370.10590.4241-0.01570.341110.6692-3.569110.315
21.28850.1502-0.50482.50780.20533.73520.07840.0577-0.024-0.049-0.02470.01380.12230.1441-0.05010.237-0.00090.03250.3411-0.0010.248520.78093.20922.6164
30.98340.80711.03051.7115-0.48098.2164-0.020.00120.0433-0.1510.0698-0.1836-0.19880.2827-0.01530.3378-0.05370.03590.3866-0.00120.335926.43115.6723-4.0112
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 83 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 84 through 215 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 216 through 306 )A0

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