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- PDB-7c46: Crystal Structure of Rv1045 toxin point variant K189A -

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Basic information

Entry
Database: PDB / ID: 7c46
TitleCrystal Structure of Rv1045 toxin point variant K189A
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 / SAD / Resolution: 1.93 Å
AuthorsDeep, A. / Kaur, J. / Thakur, K.G.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Science & Technology (DST, India)EMR/2016/003728 India
CitationJournal: To Be Published
Title: Crystal Structure of Rv1045 toxin point variant K189A
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 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)32,7037
Polymers32,1271
Non-polymers5766
Water4,035224
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-18 kcal/mol
Surface area13730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.010, 94.010, 61.771
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-475-

HOH

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Components

#1: Protein Rv1045 toxin


Mass: 32127.082 Da / Num. of mol.: 1 / Mutation: K189A
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.: 6 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.47 Å3/Da / Density % sol: 50.14 %
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: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97947 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 1.93→81.41 Å / Num. obs: 23924 / % possible obs: 100 % / Redundancy: 11.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.04 / Rrim(I) all: 0.138 / Net I/σ(I): 16.2
Reflection shellResolution: 1.93→2 Å / Redundancy: 11.2 % / Rmerge(I) obs: 1.029 / Num. unique obs: 2386 / CC1/2: 0.768 / Rpim(I) all: 0.318 / Rrim(I) all: 1.078 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0218refinement
Aimless0.6.3data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 1.93→81.41 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.935 / SU B: 8.724 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.657 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21698 1184 5 %RANDOM
Rwork0.15928 ---
obs0.16219 22717 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.74 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å2-0.27 Å20 Å2
2---0.55 Å20 Å2
3---1.78 Å2
Refinement stepCycle: 1 / Resolution: 1.93→81.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2205 0 30 224 2459
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192276
X-RAY DIFFRACTIONr_bond_other_d0.0010.022145
X-RAY DIFFRACTIONr_angle_refined_deg1.2161.9823110
X-RAY DIFFRACTIONr_angle_other_deg0.75334940
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2855287
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.67422.85798
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.43915341
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4551523
X-RAY DIFFRACTIONr_chiral_restr0.0710.2367
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212519
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02460
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_it2.8912.2781151
X-RAY DIFFRACTIONr_mcbond_other2.8812.2761150
X-RAY DIFFRACTIONr_mcangle_it3.7553.391437
X-RAY DIFFRACTIONr_mcangle_other3.7613.3911438
X-RAY DIFFRACTIONr_scbond_it3.312.8561124
X-RAY DIFFRACTIONr_scbond_other3.1922.7521101
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8093.9531638
X-RAY DIFFRACTIONr_long_range_B_refined5.85829.0442559
X-RAY DIFFRACTIONr_long_range_B_other5.24728.3092504
X-RAY DIFFRACTIONr_rigid_bond_restr6.73334420
X-RAY DIFFRACTIONr_sphericity_free47.885115
X-RAY DIFFRACTIONr_sphericity_bonded16.21654492
LS refinement shellResolution: 1.933→1.983 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 78 -
Rwork0.241 1668 -
obs--99.66 %
Refinement TLS params.Method: refined / Origin x: 4.615 Å / Origin y: 41.546 Å / Origin z: 17.887 Å
111213212223313233
T0.0641 Å2-0.0004 Å20.001 Å2-0.0687 Å2-0.0015 Å2--0.0002 Å2
L0.1819 °20.0652 °2-0.0039 °2-0.031 °2-0.0174 °2--0.0349 °2
S0.0053 Å °-0.0114 Å °-0.0026 Å °0.0046 Å °-0.0038 Å °-0.0001 Å °0.003 Å °0.0014 Å °-0.0015 Å °

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