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- PDB-6jqy: Crystal structure of N-terminal domain of VapB46 antitoxin from M... -

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Basic information

Entry
Database: PDB / ID: 6jqy
TitleCrystal structure of N-terminal domain of VapB46 antitoxin from Mycobacterium tuberculosis
ComponentsAntitoxin VapB46
KeywordsDNA BINDING PROTEIN / Phd/YefM fold / DNA binding / Virulence associated protein / antitoxin
Function / homology
Function and homology information


: / YefM-like domain / Type II toxin-antitoxin system, antitoxin Phd/YefM / Antitoxin Phd_YefM, type II toxin-antitoxin system / YefM-like superfamily / YefM-like fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Antitoxin VapB46
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.643 Å
AuthorsRoy, M. / Singh, B.K. / Bhattacharyya, S. / Das, A.K.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (India)BT/PR12404/BRB/10/1362/ 2014 India
CitationJournal: To Be Published
Title: Crystal structure of N-terminal domain of VapB46 antitoxin from Mycobacterium tuberculosis
Authors: Roy, M. / Singh, B.K. / Bhattacharyya, S. / Das, A.k.
History
DepositionApr 2, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Antitoxin VapB46
B: Antitoxin VapB46
C: Antitoxin VapB46
D: Antitoxin VapB46
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4086
Polymers19,2904
Non-polymers1182
Water1,856103
1
A: Antitoxin VapB46
B: Antitoxin VapB46
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,7043
Polymers9,6452
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-13 kcal/mol
Surface area5300 Å2
MethodPISA
2
C: Antitoxin VapB46
D: Antitoxin VapB46
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,7043
Polymers9,6452
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-13 kcal/mol
Surface area5390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.043, 50.548, 42.623
Angle α, β, γ (deg.)90.00, 116.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide
Antitoxin VapB46


Mass: 4822.547 Da / Num. of mol.: 4 / Mutation: R23Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh) (bacteria)
Strain: CDC 1551 / Oshkosh / Gene: vapB46, MT3493 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15(pREP4) / References: UniProt: P9WF12
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 1.91 Å3/Da / Density % sol: 35.5 % / Description: Dagger shaped
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1M Sodium acetate trihydrate pH 4.6, 2M NaCl, 0.1M NaBr

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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: 0.97949 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.643→38.267 Å / Num. obs: 17661 / % possible obs: 99.2 % / Redundancy: 4.1 % / Rpim(I) all: 0.025 / Rrim(I) all: 0.052 / Rsym value: 0.045 / Net I/av σ(I): 13.6 / Net I/σ(I): 18.1
Reflection shellResolution: 1.64→1.73 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.608 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 9093 / CC1/2: 0.849 / Rpim(I) all: 0.353 / % possible all: 95.1

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZLX

4zlx


Resolution: 1.643→21.253 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.39
RfactorNum. reflection% reflection
Rfree0.2321 901 5.11 %
Rwork0.1952 --
obs0.197 17617 99.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.643→21.253 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1285 0 8 103 1396
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091305
X-RAY DIFFRACTIONf_angle_d1.2251770
X-RAY DIFFRACTIONf_dihedral_angle_d10.754906
X-RAY DIFFRACTIONf_chiral_restr0.065225
X-RAY DIFFRACTIONf_plane_restr0.008233
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6427-1.74560.29731520.27392644X-RAY DIFFRACTION95
1.7456-1.88030.32571420.23192792X-RAY DIFFRACTION100
1.8803-2.06940.23621560.18912812X-RAY DIFFRACTION100
2.0694-2.36850.22161710.18622796X-RAY DIFFRACTION100
2.3685-2.98270.22431210.2072829X-RAY DIFFRACTION100
2.9827-21.25470.21851590.17972843X-RAY DIFFRACTION99
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)
12.2776-0.90240.08334.5957-0.28555.15950.101-0.1772-0.20170.3808-0.08330.02820.062-0.00640.01870.229-0.0158-0.03970.129-0.01390.1716-9.4974-1.848815.5443
21.7830.52580.14132.86950.58335.1029-0.06370.0828-0.10770.11990.1551-0.3557-0.37010.7383-0.03250.2148-0.016-0.05960.2278-0.02840.1654-2.13496.472115.4475
33.03170.37431.62153.51610.08192.0138-0.02960.6057-0.03-0.40560.1581-0.1195-0.07040.51640.02660.2169-0.0471-0.00410.25290.00620.1416-11.64396.3178-3.7265
43.4099-0.78421.00913.5232-1.47493.3883-0.0128-0.0231-0.00460.0602-0.01190.1966-0.2769-0.0290.06060.17840.0008-0.03770.1053-0.02320.1464-16.76314.62661.825
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 11:54)
2X-RAY DIFFRACTION2(chain B and resseq 12:54)
3X-RAY DIFFRACTION3(chain C and resseq 11:54)
4X-RAY DIFFRACTION4(chain D and resseq 11:53)

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