50S ribosomal protein ... , 2 types, 2 molecules BC
#2: Protein
50SribosomalproteinL10 / 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
50SribosomalproteinL11
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
23SribosomalRNA
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
Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O
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Details
Compound details
THIOSTREPTON 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
Experiment
Method: X-RAY DIFFRACTION
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Sample preparation
Crystal
Density Matthews: 3.97 Å3/Da / Density % sol: 69 %
Crystal grow
Temperature: 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
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97953 Å / Relative weight: 1
Reflection
Resolution: 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 shell
Resolution: 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
Name
Version
Classification
PHENIX
1.9_1692
refinement
XDS
datareduction
XSCALE
datascaling
PHENIX
phasing
Refinement
Method 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
Rfactor
Num. reflection
% reflection
Rfree
0.245
2495
4.98 %
Rwork
0.2081
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-
obs
0.2099
50053
99.22 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement step
Cycle: LAST / Resolution: 2.8→45.545 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2900
1588
39
65
4592
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.016
4737
X-RAY DIFFRACTION
f_angle_d
1.929
6754
X-RAY DIFFRACTION
f_dihedral_angle_d
16.004
2035
X-RAY DIFFRACTION
f_chiral_restr
0.066
840
X-RAY DIFFRACTION
f_plane_restr
0.01
577
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.8001-2.8539
0.4692
132
0.4038
2647
X-RAY DIFFRACTION
98
2.8539-2.9122
0.3601
136
0.3591
2623
X-RAY DIFFRACTION
100
2.9122-2.9755
0.3141
135
0.3212
2648
X-RAY DIFFRACTION
99
2.9755-3.0447
0.3115
138
0.2947
2644
X-RAY DIFFRACTION
99
3.0447-3.1208
0.2537
137
0.272
2640
X-RAY DIFFRACTION
99
3.1208-3.2052
0.3535
139
0.2383
2625
X-RAY DIFFRACTION
99
3.2052-3.2995
0.2579
143
0.2204
2636
X-RAY DIFFRACTION
99
3.2995-3.4059
0.3737
141
0.2261
2633
X-RAY DIFFRACTION
99
3.4059-3.5276
0.2443
136
0.2286
2643
X-RAY DIFFRACTION
100
3.5276-3.6688
0.2466
142
0.2121
2642
X-RAY DIFFRACTION
100
3.6688-3.8357
0.2548
144
0.2046
2677
X-RAY DIFFRACTION
99
3.8357-4.0378
0.2276
139
0.1887
2626
X-RAY DIFFRACTION
100
4.0378-4.2906
0.2253
141
0.1874
2666
X-RAY DIFFRACTION
100
4.2906-4.6216
0.2314
139
0.1917
2635
X-RAY DIFFRACTION
99
4.6216-5.0862
0.2164
141
0.172
2672
X-RAY DIFFRACTION
100
5.0862-5.8208
0.2186
135
0.1708
2649
X-RAY DIFFRACTION
100
5.8208-7.3287
0.1919
140
0.199
2654
X-RAY DIFFRACTION
100
7.3287-45.5509
0.2402
137
0.2002
2598
X-RAY DIFFRACTION
98
+
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