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- PDB-7c48: Crystal structure of phosphorylated Ser78 form of Rv1045 toxin -

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Basic information

Entry
Database: PDB / ID: 7c48
TitleCrystal structure of phosphorylated Ser78 form of Rv1045 toxin
ComponentsRv1045 toxin
KeywordsTRANSFERASE / Nucleotidyltransferase / Toxin-Antitoxin / TglT Toxin / Rv1045 / guanylyltransferase
Function / homologyNucleotidyl transferase AbiEii toxin, Type IV TA system / Nucleotidyl transferase AbiEii toxin, Type IV TA system / nucleotide binding / metal ion binding / Nucleotidyl transferase AbiEii/AbiGii toxin family protein
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsDeep, A. / Kaur, J. / Thakur, K.G.
Funding support India, 2items
OrganizationGrant numberCountry
Department of Science & Technology (DST, India)EMR/2016/003728 India
Council of Scientific & Industrial Research (CSIR) India
CitationJournal: To Be Published
Title: Crystal structure of Rv1045 toxin in it's Ser78 phosphorylated form
Authors: Deep, A. / Kaur, J. / Thakur, K.G.
History
DepositionMay 15, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rv1045 toxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3664
Polymers32,0781
Non-polymers2883
Water5,134285
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, A Monomeric protein, gel filtration, A Monomeric protein
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-9 kcal/mol
Surface area14010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.420, 94.420, 61.910
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-637-

HOH

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Components

#1: Protein Rv1045 toxin


Mass: 32077.586 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Gene: Rv1045 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: P96356
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.48 Å3/Da / Density % sol: 50.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 2.4M ammonium phosphate dibasic, 0.1M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.9779 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9779 Å / Relative weight: 1
ReflectionResolution: 1.6→81.77 Å / Num. obs: 42300 / % possible obs: 100 % / Redundancy: 19.1 % / Biso Wilson estimate: 18.55 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.029 / Rrim(I) all: 0.092 / Net I/σ(I): 24.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) all% possible allRpim(I) all
1.6-1.6317.91.38920880.7861.43100
8.76-49.3614.60.02729210.02898.90.007

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Processing

Software
NameVersionClassification
REFMAC5.8.0218refinement
Aimless0.6.3data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7C46

7c46


Resolution: 1.6→81.77 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.948 / SU B: 5.748 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22718 2088 4.9 %RANDOM
Rwork0.18519 ---
obs0.18727 40210 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.181 Å2
Baniso -1Baniso -2Baniso -3
1-1.78 Å20.89 Å20 Å2
2--1.78 Å2-0 Å2
3----5.76 Å2
Refinement stepCycle: 1 / Resolution: 1.6→81.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2222 0 15 285 2522
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192281
X-RAY DIFFRACTIONr_bond_other_d0.0010.022166
X-RAY DIFFRACTIONr_angle_refined_deg1.2331.9753114
X-RAY DIFFRACTIONr_angle_other_deg0.74734991
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2595288
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.21822.85798
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.91615360
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8931523
X-RAY DIFFRACTIONr_chiral_restr0.0670.2365
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212526
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02461
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_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.9652.6191155
X-RAY DIFFRACTIONr_mcbond_other2.9552.6171154
X-RAY DIFFRACTIONr_mcangle_it3.8483.9341442
X-RAY DIFFRACTIONr_mcangle_other3.853.9361443
X-RAY DIFFRACTIONr_scbond_it3.1323.0691126
X-RAY DIFFRACTIONr_scbond_other3.0393.0311115
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6994.4011655
X-RAY DIFFRACTIONr_long_range_B_refined5.80834.0852620
X-RAY DIFFRACTIONr_long_range_B_other5.20132.9992538
X-RAY DIFFRACTIONr_rigid_bond_restr1.80134447
X-RAY DIFFRACTIONr_sphericity_free41.8585153
X-RAY DIFFRACTIONr_sphericity_bonded26.91554536
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 158 -
Rwork0.303 2945 -
obs--99.94 %

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