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- PDB-6jmk: Ribosomal protein S7 from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 6jmk
TitleRibosomal protein S7 from Mycobacterium tuberculosis
Components30S ribosomal protein S7
KeywordsRIBOSOMAL PROTEIN / S7 / Mycobacterium tuberculosis
Function / homology
Function and homology information


peptidoglycan-based cell wall / ribosomal small subunit assembly / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome / ribosome / translation / mRNA binding / plasma membrane / cytosol
Similarity search - Function
Ribosomal Protein S7 / Ribosomal protein S7/S5 / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S7, conserved site / Ribosomal protein S7 signature. / Ribosomal protein S5/S7 / Ribosomal protein S7 domain / Ribosomal protein S7 domain superfamily / Ribosomal protein S7p/S5e / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Small ribosomal subunit protein uS7
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLi, Z. / Li, J.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2016YFA0500600 China
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2019
Title: Structural insights into the complex of trigger factor chaperone and ribosomal protein S7 from Mycobacterium tuberculosis.
Authors: Li, Z. / Wu, D. / Zhan, B. / Hu, X. / Gan, J. / Ji, C. / Li, J.
History
DepositionMar 11, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 1, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 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: 30S ribosomal protein S7
B: 30S ribosomal protein S7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7796
Polymers35,4412
Non-polymers3384
Water4,053225
1
A: 30S ribosomal protein S7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8132
Polymers17,7201
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8370 Å2
MethodPISA
2
B: 30S ribosomal protein S7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9674
Polymers17,7201
Non-polymers2463
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint1 kcal/mol
Surface area7810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.712, 58.428, 126.025
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 S7


Mass: 17720.496 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: rpsG, rps7, Rv0683, MTV040.11
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P9WH29
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 2.84 Å3/Da / Density % sol: 56.72 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 0.2M potassium tartrate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97928 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 19, 2017
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97928 Å / Relative weight: 1
ReflectionResolution: 1.8→41.31 Å / Num. obs: 38244 / % possible obs: 99.95 % / Redundancy: 2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.033 / Rrim(I) all: 0.047 / Net I/σ(I): 11.88
Reflection shellResolution: 1.8→1.864 Å / Rmerge(I) obs: 0.1508 / Mean I/σ(I) obs: 4.09 / Num. unique obs: 3755 / CC1/2: 0.885 / Rrim(I) all: 0.2133 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HUS

1hus


Resolution: 1.8→41.31 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.165 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.101 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21248 1981 5.2 %RANDOM
Rwork0.18478 ---
obs0.18628 36273 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.337 Å2
Baniso -1Baniso -2Baniso -3
1-1.31 Å20 Å20 Å2
2---0.58 Å20 Å2
3----0.73 Å2
Refinement stepCycle: 1 / Resolution: 1.8→41.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2161 0 22 225 2408
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0192222
X-RAY DIFFRACTIONr_bond_other_d0.0030.022194
X-RAY DIFFRACTIONr_angle_refined_deg2.2571.9823001
X-RAY DIFFRACTIONr_angle_other_deg1.22535043
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9435283
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.74422.62699
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.37915397
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2131530
X-RAY DIFFRACTIONr_chiral_restr0.160.2354
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022468
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02446
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_it2.652.1661132
X-RAY DIFFRACTIONr_mcbond_other2.6222.1631131
X-RAY DIFFRACTIONr_mcangle_it3.783.2271415
X-RAY DIFFRACTIONr_mcangle_other3.7783.231416
X-RAY DIFFRACTIONr_scbond_it4.2032.651090
X-RAY DIFFRACTIONr_scbond_other4.1992.651090
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.223.7611587
X-RAY DIFFRACTIONr_long_range_B_refined7.80927.1982554
X-RAY DIFFRACTIONr_long_range_B_other7.80927.2242555
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 121 -
Rwork0.241 2650 -
obs--100 %

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