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- PDB-5d8h: CRYSTAL STRUCTURE OF THE BASE OF THE RIBOSOMAL P STALK FROM METHA... -

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Basic information

Entry
Database: PDB / ID: 5d8h
TitleCRYSTAL STRUCTURE OF THE BASE OF THE RIBOSOMAL P STALK FROM METHANOCOCCUS JANNASCHII WITH ANTIBIOTIC THIOSTREPTON
Components
  • (50S ribosomal protein ...) x 2
  • 23S ribosomal RNA
  • THIOSTREPTON
KeywordsRIBOSOMAL PROTEIN / ribosome / P-stalk / archaea / ANTIBIOTIC / THIOSTREPTON
Function / homology
Function and homology information


large ribosomal subunit rRNA binding / large ribosomal subunit / cytoplasmic translation / cytosolic large ribosomal subunit / structural constituent of ribosome / defense response to bacterium / translation / extracellular region
Similarity search - Function
Ribosomal protein L10, N-terminal fragment, domain II / Thiazolylpeptide-type bacteriocin precursor / Ribosomal protein L10, N-terminal RNA-binding domain / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12, N-terminal domain / Molybdopterin biosynthesis moea protein, domain 2 / 50S ribosomal protein L10, archaea / 50S ribosomal protein L10, insertion domain superfamily / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P ...Ribosomal protein L10, N-terminal fragment, domain II / Thiazolylpeptide-type bacteriocin precursor / Ribosomal protein L10, N-terminal RNA-binding domain / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12, N-terminal domain / Molybdopterin biosynthesis moea protein, domain 2 / 50S ribosomal protein L10, archaea / 50S ribosomal protein L10, insertion domain superfamily / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / Ribosomal protein L11, conserved site / Ribosomal protein L10-like domain superfamily / Ribosomal protein L11 signature. / Ribosomal protein L10P / Ribosomal protein L10 / Ribosomal protein L11, N-terminal / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11, RNA binding domain / Alpha-Beta Plaits / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
THIOSTREPTON / RNA / RNA (> 10) / : / Thiostrepton / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL10
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
Streptomyces azureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsGabdulkhakov, A.G. / Mitroshin, I.V. / Garber, M.B.
CitationJournal: To Be Published
Title: CRYSTAL STRUCTURE OF THE BASE OF THE RIBOSOMAL P STALK FROM METHANOCOCCUS JANNASCHII WITH ANTIBIOTIC THIOSTREPTON
Authors: Gabdulkhakov, A.G. / Mitroshin, I.V. / Garber, M.B.
History
DepositionAug 17, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Structure summary
Revision 1.2Dec 21, 2016Group: Non-polymer description
Revision 1.3Apr 10, 2019Group: Advisory / Data collection / Database references
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_validate_polymer_linkage / struct_ref
Item: _struct_ref.db_code
Revision 2.0Apr 24, 2019Group: Data collection / Polymer sequence
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / entity_poly / pdbx_seq_map_depositor_info
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_seq_map_depositor_info.one_letter_code

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 23S ribosomal RNA
B: 50S ribosomal protein L10
C: 50S ribosomal protein L11
D: THIOSTREPTON
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,89022
Polymers67,1644
Non-polymers72618
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8810 Å2
ΔGint-170 kcal/mol
Surface area27490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.070, 127.160, 132.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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50S ribosomal protein ... , 2 types, 2 molecules BC

#2: Protein 50S ribosomal protein L10 / / Acidic ribosomal protein P0 homolog / MjaL10


Mass: 23635.162 Da / Num. of mol.: 1 / Fragment: UNP residues 9-221 / Mutation: Met changed to SeMet
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: rpl10, rplP0, MJ0509 / Plasmid: pET-11c/MjaP0NTF / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pUBS520 / References: UniProt: P54049
#3: Protein 50S ribosomal protein L11 /


Mass: 17794.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: rpl11, MJ0373 / Plasmid: pET-11c/MjaL11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pUBS520 / References: UniProt: P54030

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RNA chain / Protein/peptide , 2 types, 2 molecules AD

#1: RNA chain 23S ribosomal RNA /


Mass: 23928.295 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Plasmid: pMja23S-74.UC18 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): XL1(Blue) / References: REF: 470491724
#4: Protein/peptide THIOSTREPTON / /


Type: Thiopeptide / Class: Antibiotic / Mass: 1805.985 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Thiostrepton is a hetrocyclic thiopeptide belonging to the thiocillin family, consisting of four thiazole, one thiozoline and one piperideine rings. A modified quinoline linked to main-chain ...Details: Thiostrepton is a hetrocyclic thiopeptide belonging to the thiocillin family, consisting of four thiazole, one thiozoline and one piperideine rings. A modified quinoline linked to main-chain residue 1 and side-chain of residue 12. Post translational maturation of thiazole and oxazole containing antibiotics involves the enzymic condensation of a Cys or Ser with the alpha-carbonyl of the preceding amino acid to form a thioether or ether bond, then dehydration to form a double bond with the alpha-amino nitrogen. Thiazoline or oxazoline ring are dehydrogenated to form thiazole or oxazole rings. the pyridinyl involves the cross-linking of a Ser and a Cys-Ser pair usually separated by 7 or 8 residues along the peptide chain. The Ser residues are dehydrated to didehydroalanines, then bonded between their beta carbons. The alpha carbonyl of the Cys condenses with alpha carbon of the first Ser to form a pyridinyl ring. The ring may be mutiply dehydrogenated to form a pyridine ring with loss of the amino nitrogen of the first Ser. The amidation of Ser-17 probably does not occur by the same mechanism, oxidative cleavage of glycine, as in eukaryotes.
Source: (natural) Streptomyces azureus (bacteria) / References: UniProt: P0C8P8, THIOSTREPTON

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Non-polymers , 4 types, 83 molecules

#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsTHIOSTREPTON IS A MEMBER OF A SULPHUR-RICH HETEROCYCLIC PEPTIDES CLASS. ALL SHARE A MACROCYLIC ...THIOSTREPTON IS A MEMBER OF A SULPHUR-RICH HETEROCYCLIC PEPTIDES CLASS. ALL SHARE A MACROCYLIC CORE, CONSISTING OF A NITROGEN CONTAINING, SIX-MEMBERED RING CENTRAL TO DEHYDROAMINO ACIDS AND A SUBSET OF FIVE MEMBER RING STRUCTURES INCLUDING THIAZOLES, THIAZOLINES AND OXAZOLES. HERE, THIOSTREPTON IS REPRESENTED BY THE SEQUENCE (SEQRES)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.97 Å3/Da / Density % sol: 69 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 mM Tris-HCl, pH 7.5, 10% PEG 8000, 20% glycerol, 1 mM TCEP (tris(2-carboxyethyl)phosphine), 0.125 mM CTAB

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97953 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97953 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 50260 / Num. obs: 50260 / % possible obs: 99.3 % / Redundancy: 3.47 % / Rsym value: 0.061 / Net I/σ(I): 14.96
Reflection shellResolution: 2.8→2.97 Å / Redundancy: 3.49 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 1.32 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→45.545 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.26 / Phase error: 30.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.245 2495 4.98 %
Rwork0.2081 --
obs0.2099 50053 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→45.545 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2900 1588 39 65 4592
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0164737
X-RAY DIFFRACTIONf_angle_d1.9296754
X-RAY DIFFRACTIONf_dihedral_angle_d16.0042035
X-RAY DIFFRACTIONf_chiral_restr0.066840
X-RAY DIFFRACTIONf_plane_restr0.01577
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8001-2.85390.46921320.40382647X-RAY DIFFRACTION98
2.8539-2.91220.36011360.35912623X-RAY DIFFRACTION100
2.9122-2.97550.31411350.32122648X-RAY DIFFRACTION99
2.9755-3.04470.31151380.29472644X-RAY DIFFRACTION99
3.0447-3.12080.25371370.2722640X-RAY DIFFRACTION99
3.1208-3.20520.35351390.23832625X-RAY DIFFRACTION99
3.2052-3.29950.25791430.22042636X-RAY DIFFRACTION99
3.2995-3.40590.37371410.22612633X-RAY DIFFRACTION99
3.4059-3.52760.24431360.22862643X-RAY DIFFRACTION100
3.5276-3.66880.24661420.21212642X-RAY DIFFRACTION100
3.6688-3.83570.25481440.20462677X-RAY DIFFRACTION99
3.8357-4.03780.22761390.18872626X-RAY DIFFRACTION100
4.0378-4.29060.22531410.18742666X-RAY DIFFRACTION100
4.2906-4.62160.23141390.19172635X-RAY DIFFRACTION99
4.6216-5.08620.21641410.1722672X-RAY DIFFRACTION100
5.0862-5.82080.21861350.17082649X-RAY DIFFRACTION100
5.8208-7.32870.19191400.1992654X-RAY DIFFRACTION100
7.3287-45.55090.24021370.20022598X-RAY DIFFRACTION98

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