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- PDB-4nnk: Structural basis for targeting the ribosomal protein S1 of Mycoba... -

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Basic information

Entry
Database: PDB / ID: 4nnk
TitleStructural basis for targeting the ribosomal protein S1 of Mycobacterium tuberculosis by pyrazinamide
Components30S ribosomal protein S1
KeywordsRIBOSOMAL PROTEIN / beta barrel
Function / homology
Function and homology information


peptidoglycan-based cell wall / cytosolic small ribosomal subunit / structural constituent of ribosome / translation / mRNA binding / plasma membrane / cytosol
Similarity search - Function
: / Ribosomal protein S1-like / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Small ribosomal subunit protein bS1
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.31 Å
AuthorsYang, J. / Liu, Y. / Cai, Q. / Lin, D.
CitationJournal: Mol.Microbiol. / Year: 2015
Title: Structural basis for targeting the ribosomal protein S1 of Mycobacterium tuberculosis by pyrazinamide.
Authors: Yang, J. / Liu, Y. / Bi, J. / Cai, Q. / Liao, X. / Li, W. / Guo, C. / Zhang, Q. / Lin, T. / Zhao, Y. / Wang, H. / Liu, J. / Zhang, X. / Lin, D.
History
DepositionNov 18, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 30S ribosomal protein S1


Theoretical massNumber of molelcules
Total (without water)18,4101
Polymers18,4101
Non-polymers00
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.445, 55.689, 65.043
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 30S ribosomal protein S1


Mass: 18409.506 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 285-434 / Mutation: Y418F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: MTCY01B2.22, rpsA, Rv1630 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P9WH43
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.75 Å3/Da / Density % sol: 55.22 %
Crystal growTemperature: 295 K / Method: hanging drop / pH: 8.5
Details: magnesium formate, pH 8.5, hanging drop, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Type: OTHER / Wavelength: 0.979 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Apr 25, 2013 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.31→50 Å

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
SOLVEphasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
DENZOdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.31→40.83 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.886 / Occupancy max: 1 / Occupancy min: 1 / SU B: 6.268 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.397 / ESU R Free: 0.272 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27073 868 10 %RANDOM
Rwork0.2166 ---
obs0.22205 7800 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.221 Å2
Baniso -1Baniso -2Baniso -3
1-2.12 Å20 Å2-0 Å2
2---1.11 Å2-0 Å2
3----1 Å2
Refinement stepCycle: LAST / Resolution: 2.31→40.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1296 0 0 70 1366
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0191324
X-RAY DIFFRACTIONr_bond_other_d0.0010.021225
X-RAY DIFFRACTIONr_angle_refined_deg1.8141.9311784
X-RAY DIFFRACTIONr_angle_other_deg0.92732815
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1445158
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.08624.15677
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.89815229
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7791511
X-RAY DIFFRACTIONr_chiral_restr0.1210.2182
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021525
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02324
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.314→2.374 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 59 -
Rwork0.244 520 -
obs--93.69 %

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