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- PDB-2k4x: Solution structure of 30S ribosomal protein S27A from Thermoplasm... -

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Basic information

Entry
Database: PDB / ID: 2k4x
TitleSolution structure of 30S ribosomal protein S27A from Thermoplasma acidophilum
Components30S ribosomal protein S27ae
KeywordsRIBOSOMAL PROTEIN / 30S ribosomal protein S27A / Metal-binding / Ribonucleoprotein / Zinc-finger / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / Ontario Centre for Structural Proteomics / OCSP
Function / homology
Function and homology information


ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / zinc ion binding
Similarity search - Function
N-terminal domain of TfIIb - #180 / Ribosomal protein S27ae / N-terminal domain of TfIIb / Other non-globular / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Special / Zinc-binding ribosomal protein
Similarity search - Domain/homology
Small ribosomal subunit protein eS31
Similarity search - Component
Biological speciesThermoplasma acidophilum (acidophilic)
MethodSOLUTION NMR / simulated annealing
AuthorsWu, B. / Yee, A. / Fares, C. / Lemak, A. / Semest, A. / Arrowsmith, C. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG) / Ontario Centre for Structural Proteomics (OCSP)
Citation
Journal: To be Published
Title: Solution structure of 30S ribosomal protein S27A from Thermoplasma acidophilum/Northeast Structural Genomics Consortium Target TaT88/Ontario Center for Structural Proteomics target ta1093
Authors: Wu, B. / Yee, A. / Fares, C. / Lemak, A. / Semest, A. / Arrowsmith, C.
#1: Journal: J.Biomol.Nmr / Year: 2011
Title: A novel strategy for NMR resonance assignment and protein structure determination.
Authors: Lemak, A. / Gutmanas, A. / Chitayat, S. / Karra, M. / Fares, C. / Sunnerhagen, M. / Arrowsmith, C.H.
History
DepositionJun 20, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 23, 2012Group: Database references
Revision 1.3Feb 19, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4Jun 14, 2023Group: Database references / Derived calculations / Other / Category: database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5May 8, 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: 30S ribosomal protein S27ae
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,4632
Polymers6,3981
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein 30S ribosomal protein S27ae


Mass: 6397.507 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Species: acidophilum / Gene: rps27ae, Ta1093 / Plasmid: p11 / Species (production host): coli / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HJ78
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCO
1213D CBCA(CO)NH
1313D HN(CA)CB
1413D HN(CO)CA
1513D HNCA
1613D C(CO)NH
1713D H(CCO)NH
1813D HBHA(CO)NH
1913D (H)CCH-TOCSY
11013D CCH-TOCSY
11113D 1H-15N NOESY
11213D 1H-13C NOESY
11323D 1H-13C NOESY
11413D 1H-13C NOESY aromatic

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-100% 13C; U-100% 15N] 30S ribosomal protein S27A, 10 mM [U-100% 2H] TRIS, 300 mM sodium chloride, 10 uM ZnSO4, 10 mM [U-100% 2H] DTT, 0.01 % sodium azide, 10 mM benzamidine, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-100% 13C; U-100% 15N] 30S ribosomal protein S27A, 10 mM [U-100% 2H] TRIS, 300 mM sodium chloride, 10 uM ZnSO4, 10 mM [U-100% 2H] DTT, 0.01 % sodium azide, 10 mM benzamidine, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mM30S ribosomal protein S27A[U-100% 13C; U-100% 15N]1
10 mMTRIS[U-100% 2H]1
300 mMsodium chloride1
10 uMZnSO41
10 mMDTT[U-100% 2H]1
0.01 %sodium azide1
10 mMbenzamidine1
0.5 mM30S ribosomal protein S27A[U-100% 13C; U-100% 15N]2
10 mMTRIS[U-100% 2H]2
300 mMsodium chloride2
10 uMZnSO42
10 mMDTT[U-100% 2H]2
0.01 %sodium azide2
10 mMbenzamidine2
Sample conditionsIonic strength: 300 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky3.95Goddarddata analysis
Sparky3.95Goddardpeak picking
AutoAssignZimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CNS1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
AutoStructureHuang, Tejero, Powers and Montelionenmr structure quality assessment
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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