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- PDB-7cq1: Solution structure of the C-terminal domain of Mycobacterium Tube... -

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Basic information

Entry
Database: PDB / ID: 7cq1
TitleSolution structure of the C-terminal domain of Mycobacterium Tuberculosis ribosome maturation factor protein RimM
ComponentsRibosome maturation factor RimM
KeywordsPROTEIN BINDING / Ribosome maturation / 30S subunit
Function / homology
Function and homology information


ribosomal small subunit biogenesis / rRNA processing / ribosome binding / ribosome / cytoplasm
Similarity search - Function
RimM, N-terminal / 16S rRNA processing protein RimM / RimM, N-terminal domain superfamily / RimM N-terminal domain / PRC-barrel domain / PRC-barrel domain / PRC-barrel-like superfamily / Translation protein, beta-barrel domain superfamily
Similarity search - Domain/homology
Ribosome maturation factor RimM
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsZhang, H. / Lin, D.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2016YFA0500600 China
CitationJournal: Biomolecules / Year: 2021
Title: Structural Basis for the C-Terminal Domain of Mycobacterium tuberculosis Ribosome Maturation Factor RimM to Bind Ribosomal Protein S19.
Authors: Zhang, H. / Zhou, Q. / Guo, C. / Feng, L. / Wang, H. / Liao, X. / Lin, D.
History
DepositionAug 8, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2May 19, 2021Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribosome maturation factor RimM


Theoretical massNumber of molelcules
Total (without water)9,2931
Polymers9,2931
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4660 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Ribosome maturation factor RimM


Mass: 9293.420 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: rimM, Rv2907c, MTCY274.38c / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WH19

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic12D 1H-15N HSQC
122isotropic12D 1H-13C HSQC
133isotropic13D HN(CA)CB
143isotropic13D CBCA(CO)NH
153isotropic13D HNCA
163isotropic13D HN(CO)CA
173isotropic13D HNCO
183isotropic13D HN(CA)CO
193isotropic13D (H)CCH-COSY
1103isotropic13D H(CCO)NH
1113isotropic13D HBHA(CO)NH
1123isotropic13D (H)CCH-TOCSY
1133isotropic13D C(CO)NH
1142isotropic13D 15N-edited NOESY-HSQC
1153isotropic13D 13C-edited NOESY-HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.6 mM C-terminal domain of ribosome maturation factor RimM, 20 mM potassium phosphate, 100 mM potassium chloride, 0.02 % w/v sodium azide, 90% H2O/10% D2Onon-labelled_sample90% H2O/10% D2O
solution20.6 mM [U-99% 15N] C-terminal domain of ribosome maturation factor RimM, 20 mM potassium phosphate, 100 mM potassium chloride, 0.02 % w/v sodium azide, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
solution30.6 mM [U-99% 13C; U-99% 15N] C-terminal domain of ribosome maturation factor RimM, 20 mM potassium phosphate, 100 mM potassium chloride, 0.02 % w/v sodium azide, 90% H2O/10% D2O13C/15N_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMC-terminal domain of ribosome maturation factor RimMnatural abundance1
20 mMpotassium phosphatenatural abundance1
100 mMpotassium chloridenatural abundance1
0.02 % w/vsodium azidenatural abundance1
0.6 mMC-terminal domain of ribosome maturation factor RimM[U-99% 15N]2
20 mMpotassium phosphatenatural abundance2
100 mMpotassium chloridenatural abundance2
0.02 % w/vsodium azidenatural abundance2
0.6 mMC-terminal domain of ribosome maturation factor RimM[U-99% 13C; U-99% 15N]3
20 mMpotassium phosphatenatural abundance3
100 mMpotassium chloridenatural abundance3
0.02 % w/vsodium azidenatural abundance3
Sample conditionsIonic strength: 120 mM / Label: conditions_1 / pH: 7.2 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 850 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNSAria2Brunger, Adams, Clore, Gros, Nilges and Readstructure calculation
NMRFAM-SPARKY1.4.7Lee W., Tonelli M., Markley J. L.chemical shift assignment
CNSAria2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
Refinement
MethodSoftware ordinal
simulated annealing2
simulated annealing1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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