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- PDB-5ndk: Crystal structure of aminoglycoside TC007 co-crystallized with 70... -

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Basic information

Entry
Database: PDB / ID: 5ndk
TitleCrystal structure of aminoglycoside TC007 co-crystallized with 70S ribosome from Thermus thermophilus, three tRNAs and mRNA
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 27
  • 16S ribosomal RNA
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • mRNAMessenger RNA
  • tRNA-Phe
KeywordsRIBOSOME / translation / 3S / 50S / 70S / tRNA / mRNA / bacteria / RNA-protein complex / inhibitor / antibiotic / aminoglycoside
Function / homology
Function and homology information


large ribosomal subunit / 5S rRNA binding / small ribosomal subunit / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex ...large ribosomal subunit / 5S rRNA binding / small ribosomal subunit / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / zinc ion binding / metal ion binding / cytoplasm
Similarity search - Function
30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein S14, type Z / Ribosomal protein L31 type A / Ribosomal protein L31 signature. ...30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein S14, type Z / Ribosomal protein L31 type A / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein S14/S29 / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L32p, bacterial type / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L28 / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L20 signature. / Ribosomal protein S3, bacterial-type / Ribosomal protein L27, conserved site / Ribosomal protein S6, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S6 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L14P, bacterial-type / Ribosomal protein S4, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal L28 family / Ribosomal protein L28/L24 / : / Ribosomal protein L30, bacterial-type / Ribosomal protein L16 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / L28p-like / Ribosomal protein L20 / Ribosomal protein S16 / Ribosomal protein S16 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein S16 domain superfamily / Ribosomal protein L21 / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L19 / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein S15, bacterial-type / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal L32p protein family / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein L24
Similarity search - Domain/homology
TC007 / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL6 ...TC007 / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL34 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL29 / 30S ribosomal protein S17 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL5 / 30S ribosomal protein S14 type Z / 30S ribosomal protein S8 / 50S ribosomal protein L6 / Large ribosomal subunit protein uL18 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL25 / Small ribosomal subunit protein bTHX / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein bL31 / Small ribosomal subunit protein bS16 / Large ribosomal subunit protein bL35 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS18 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein bL17
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsProkhorova, I. / Djumagulov, M. / Urzhumtsev, A. / Yusupov, M. / Yusupova, G.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Aminoglycoside interactions and impacts on the eukaryotic ribosome.
Authors: Prokhorova, I. / Altman, R.B. / Djumagulov, M. / Shrestha, J.P. / Urzhumtsev, A. / Ferguson, A. / Chang, C.T. / Yusupov, M. / Blanchard, S.C. / Yusupova, G.
History
DepositionMar 8, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
13: 16S ribosomal RNA
A8: 50S ribosomal protein L18
B5: 50S ribosomal protein L23
11: 50S ribosomal protein L2
L5: 50S ribosomal protein L34
2A: 30S ribosomal protein S11
8I: 30S ribosomal protein S17
22: 30S ribosomal protein S3
8E: 30S ribosomal protein S9
1G: 16S ribosomal RNA
58: 50S ribosomal protein L13
65: 50S ribosomal protein L18
G8: 50S ribosomal protein L24
19: 50S ribosomal protein L2
Q8: 50S ribosomal protein L35
3I: 30S ribosomal protein S12
8A: 30S ribosomal protein S17
3E: 30S ribosomal protein S4
82: 30S ribosomal protein S9
1H: 23S ribosomal RNA
15: 50S ribosomal protein L13
B8: 50S ribosomal protein L19
C5: 50S ribosomal protein L24
L8: 50S ribosomal protein L30
M5: 50S ribosomal protein L35
61: 50S ribosomal protein L9
3A: 30S ribosomal protein S12
9I: 30S ribosomal protein S18
32: 30S ribosomal protein S4
1F: 30S ribosomal protein Thx
14: 23S ribosomal RNA
68: 50S ribosomal protein L14
75: 50S ribosomal protein L19
H8: 50S ribosomal protein L25
H5: 50S ribosomal protein L30
21: 50S ribosomal protein L3
69: 50S ribosomal protein L9
4I: 30S ribosomal protein S13
9A: 30S ribosomal protein S18
4E: 30S ribosomal protein S5
1B: 30S ribosomal protein Thx
16: 5S ribosomal RNA
25: 50S ribosomal protein L14
C8: 50S ribosomal protein L20
D5: 50S ribosomal protein L25
M8: 50S ribosomal protein L31
29: 50S ribosomal protein L3
4A: 30S ribosomal protein S13
AI: 30S ribosomal protein S19
42: 30S ribosomal protein S5
1J: 5S ribosomal RNA
78: 50S ribosomal protein L15
85: 50S ribosomal protein L20
I8: 50S ribosomal protein L27
I5: 50S ribosomal protein L31
31: 50S ribosomal protein L4
5I: 30S ribosomal protein S14 type Z
AA: 30S ribosomal protein S19
5E: 30S ribosomal protein S6
35: 50S ribosomal protein L15
D8: 50S ribosomal protein L21
E5: 50S ribosomal protein L27
N8: 50S ribosomal protein L32
39: 50S ribosomal protein L4
5A: 30S ribosomal protein S14 type Z
BI: 30S ribosomal protein S20
52: 30S ribosomal protein S6
88: 50S ribosomal protein L16
95: 50S ribosomal protein L21
J8: 50S ribosomal protein L28
J5: 50S ribosomal protein L32
41: 50S ribosomal protein L5
6I: 30S ribosomal protein S15
BA: 30S ribosomal protein S20
6E: 30S ribosomal protein S7
45: 50S ribosomal protein L16
E8: 50S ribosomal protein L22
F5: 50S ribosomal protein L28
49: 50S ribosomal protein L5
6A: 30S ribosomal protein S15
1E: 30S ribosomal protein S2
62: 30S ribosomal protein S7
98: 50S ribosomal protein L17
A5: 50S ribosomal protein L22
K8: 50S ribosomal protein L29
51: 50S ribosomal protein L6
1A: 30S ribosomal protein S10
1I: 30S ribosomal protein S10
7I: 30S ribosomal protein S16
12: 30S ribosomal protein S2
7E: 30S ribosomal protein S8
55: 50S ribosomal protein L17
F8: 50S ribosomal protein L23
G5: 50S ribosomal protein L29
P8: 50S ribosomal protein L34
59: 50S ribosomal protein L6
2I: 30S ribosomal protein S11
7A: 30S ribosomal protein S16
2E: 30S ribosomal protein S3
72: 30S ribosomal protein S8
Y1: mRNA
W1: tRNA-Phe
X1: tRNA-Phe
V1: tRNA-Phe
Y4: mRNA
W4: tRNA-Phe
X4: tRNA-Phe
V4: tRNA-Phe
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,521,8071764
Polymers4,479,475108
Non-polymers42,3331656
Water22,5551252
1
13: 16S ribosomal RNA
A8: 50S ribosomal protein L18
11: 50S ribosomal protein L2
8I: 30S ribosomal protein S17
8E: 30S ribosomal protein S9
58: 50S ribosomal protein L13
G8: 50S ribosomal protein L24
Q8: 50S ribosomal protein L35
3I: 30S ribosomal protein S12
3E: 30S ribosomal protein S4
1H: 23S ribosomal RNA
B8: 50S ribosomal protein L19
L8: 50S ribosomal protein L30
61: 50S ribosomal protein L9
9I: 30S ribosomal protein S18
1F: 30S ribosomal protein Thx
68: 50S ribosomal protein L14
H8: 50S ribosomal protein L25
21: 50S ribosomal protein L3
4I: 30S ribosomal protein S13
4E: 30S ribosomal protein S5
16: 5S ribosomal RNA
C8: 50S ribosomal protein L20
M8: 50S ribosomal protein L31
AI: 30S ribosomal protein S19
78: 50S ribosomal protein L15
I8: 50S ribosomal protein L27
31: 50S ribosomal protein L4
5I: 30S ribosomal protein S14 type Z
5E: 30S ribosomal protein S6
D8: 50S ribosomal protein L21
N8: 50S ribosomal protein L32
BI: 30S ribosomal protein S20
88: 50S ribosomal protein L16
J8: 50S ribosomal protein L28
41: 50S ribosomal protein L5
6I: 30S ribosomal protein S15
6E: 30S ribosomal protein S7
E8: 50S ribosomal protein L22
1E: 30S ribosomal protein S2
98: 50S ribosomal protein L17
K8: 50S ribosomal protein L29
51: 50S ribosomal protein L6
1I: 30S ribosomal protein S10
7I: 30S ribosomal protein S16
7E: 30S ribosomal protein S8
F8: 50S ribosomal protein L23
P8: 50S ribosomal protein L34
2I: 30S ribosomal protein S11
2E: 30S ribosomal protein S3
Y1: mRNA
W1: tRNA-Phe
X1: tRNA-Phe
V1: tRNA-Phe
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,261,463905
Polymers2,239,73754
Non-polymers21,725851
Water27015
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B5: 50S ribosomal protein L23
L5: 50S ribosomal protein L34
2A: 30S ribosomal protein S11
22: 30S ribosomal protein S3
1G: 16S ribosomal RNA
65: 50S ribosomal protein L18
19: 50S ribosomal protein L2
8A: 30S ribosomal protein S17
82: 30S ribosomal protein S9
15: 50S ribosomal protein L13
C5: 50S ribosomal protein L24
M5: 50S ribosomal protein L35
3A: 30S ribosomal protein S12
32: 30S ribosomal protein S4
14: 23S ribosomal RNA
75: 50S ribosomal protein L19
H5: 50S ribosomal protein L30
69: 50S ribosomal protein L9
9A: 30S ribosomal protein S18
1B: 30S ribosomal protein Thx
25: 50S ribosomal protein L14
D5: 50S ribosomal protein L25
29: 50S ribosomal protein L3
4A: 30S ribosomal protein S13
42: 30S ribosomal protein S5
1J: 5S ribosomal RNA
85: 50S ribosomal protein L20
I5: 50S ribosomal protein L31
AA: 30S ribosomal protein S19
35: 50S ribosomal protein L15
E5: 50S ribosomal protein L27
39: 50S ribosomal protein L4
5A: 30S ribosomal protein S14 type Z
52: 30S ribosomal protein S6
95: 50S ribosomal protein L21
J5: 50S ribosomal protein L32
BA: 30S ribosomal protein S20
45: 50S ribosomal protein L16
F5: 50S ribosomal protein L28
49: 50S ribosomal protein L5
6A: 30S ribosomal protein S15
62: 30S ribosomal protein S7
A5: 50S ribosomal protein L22
1A: 30S ribosomal protein S10
12: 30S ribosomal protein S2
55: 50S ribosomal protein L17
G5: 50S ribosomal protein L29
59: 50S ribosomal protein L6
7A: 30S ribosomal protein S16
72: 30S ribosomal protein S8
Y4: mRNA
W4: tRNA-Phe
X4: tRNA-Phe
V4: tRNA-Phe
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,260,345859
Polymers2,239,73754
Non-polymers20,607805
Water27015
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)209.070, 447.360, 619.490
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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RNA chain , 5 types, 14 molecules 131G1H14161JY1Y4W1X1V1W4X4V4

#1: RNA chain 16S ribosomal RNA /


Mass: 493997.312 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: GenBank: 55771382
#15: RNA chain 23S ribosomal RNA /


Mass: 948539.875 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: GenBank: 55771382
#26: RNA chain 5S ribosomal RNA /


Mass: 39540.617 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: GenBank: 55771382
#51: RNA chain mRNA / Messenger RNA


Mass: 7911.565 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#52: RNA chain
tRNA-Phe


Mass: 24485.539 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 1134491115

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50S ribosomal protein ... , 27 types, 54 molecules A865B5F81119L5P85815G8C5Q8M5B875L8H561696825H8D52129C885M8I5...

#2: Protein 50S ribosomal protein L18 / / TL24


Mass: 12639.845 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHQ4
#3: Protein 50S ribosomal protein L23 /


Mass: 10759.808 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHP0
#4: Protein 50S ribosomal protein L2 /


Mass: 30532.551 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P60405
#5: Protein/peptide 50S ribosomal protein L34 /


Mass: 6132.449 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P80340
#10: Protein 50S ribosomal protein L13 /


Mass: 15927.903 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P60488
#11: Protein 50S ribosomal protein L24 /


Mass: 12085.611 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHP9
#12: Protein 50S ribosomal protein L35 /


Mass: 7506.178 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SKU1
#16: Protein 50S ribosomal protein L19 /


Mass: 17188.830 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P60490
#17: Protein 50S ribosomal protein L30 /


Mass: 6799.126 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHQ6
#18: Protein 50S ribosomal protein L9 /


Mass: 16422.180 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SLQ1
#21: Protein 50S ribosomal protein L14 /


Mass: 13323.612 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHP8
#22: Protein 50S ribosomal protein L25 / / TL5


Mass: 23238.572 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHZ1
#23: Protein 50S ribosomal protein L3 /


Mass: 22450.213 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHN8
#27: Protein 50S ribosomal protein L20 /


Mass: 13779.275 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P60491
#28: Protein 50S ribosomal protein L31 /


Mass: 8300.543 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SJE1
#30: Protein 50S ribosomal protein L15 /


Mass: 16319.142 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHQ7
#31: Protein 50S ribosomal protein L27 /


Mass: 9529.074 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P60493
#32: Protein 50S ribosomal protein L4 / / L1e


Mass: 23271.914 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHN9
#35: Protein 50S ribosomal protein L21 /


Mass: 11069.153 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P60492
#36: Protein 50S ribosomal protein L32 /


Mass: 6722.050 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P80339
#38: Protein 50S ribosomal protein L16 /


Mass: 15993.909 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P60489
#39: Protein 50S ribosomal protein L28 /


Mass: 11004.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P60494
#40: Protein 50S ribosomal protein L5 /


Mass: 21061.596 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHQ0
#43: Protein 50S ribosomal protein L22 /


Mass: 12808.055 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHP3
#45: Protein 50S ribosomal protein L17 /


Mass: 13750.148 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q9Z9H5
#46: Protein 50S ribosomal protein L29 /


Mass: 8670.258 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHP6
#47: Protein 50S ribosomal protein L6 /


Mass: 19568.926 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHQ3, UniProt: P0DOY8*PLUS

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30S ribosomal protein ... , 20 types, 40 molecules 2A2I8I8A222E8E823I3A3E329I9A1F1B4I4A4E42AIAA5I5A5E52BIBA6I6A...

#6: Protein 30S ribosomal protein S11 /


Mass: 13737.868 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P80376
#7: Protein 30S ribosomal protein S17 /


Mass: 12325.655 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHP7, UniProt: P0DOY7*PLUS
#8: Protein 30S ribosomal protein S3 /


Mass: 26751.076 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P80372
#9: Protein 30S ribosomal protein S9 /


Mass: 14410.614 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P80374
#13: Protein 30S ribosomal protein S12 /


Mass: 14637.384 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHN3
#14: Protein 30S ribosomal protein S4 /


Mass: 24373.447 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P80373
#19: Protein 30S ribosomal protein S18 /


Mass: 10258.299 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SLQ0
#20: Protein/peptide 30S ribosomal protein Thx / Ribosome / S31


Mass: 3350.030 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SIH3
#24: Protein 30S ribosomal protein S13 /


Mass: 14338.861 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P80377
#25: Protein 30S ribosomal protein S5 /


Mass: 17583.416 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHQ5
#29: Protein 30S ribosomal protein S19 /


Mass: 10605.464 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHP2
#33: Protein 30S ribosomal protein S14 type Z / Ribosome


Mass: 7158.725 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHQ1, UniProt: P0DOY6*PLUS
#34: Protein 30S ribosomal protein S6 / / TS9


Mass: 11988.753 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SLP8
#37: Protein 30S ribosomal protein S20 /


Mass: 11736.143 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P80380
#41: Protein 30S ribosomal protein S15 /


Mass: 10578.407 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SJ76
#42: Protein 30S ribosomal protein S7 /


Mass: 18050.973 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P17291
#44: Protein 30S ribosomal protein S2 /


Mass: 29317.703 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P80371
#48: Protein 30S ribosomal protein S10 /


Mass: 11954.968 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHN7
#49: Protein 30S ribosomal protein S16 /


Mass: 10409.983 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SJH3
#50: Protein 30S ribosomal protein S8 /


Mass: 15868.570 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHQ2, UniProt: P0DOY9*PLUS

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Non-polymers , 4 types, 2908 molecules

#53: Chemical
ChemComp-8UZ / TC007


Mass: 483.514 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H37N5O10
#54: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1646 / Source method: obtained synthetically / Formula: Mg
#55: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#56: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1252 / 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: 3.23 Å3/Da / Density % sol: 61.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 4% PEG20K, 4% PEGMME 550, 100mM Tris/HAc, 200mM KSCN

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.95→152.739 Å / Num. obs: 1204009 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 46.833 % / Biso Wilson estimate: 72.68 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.307 / Rrim(I) all: 0.31 / Χ2: 0.939 / Net I/σ(I): 16.04 / Num. measured all: 56386821 / Scaling rejects: 4433
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.95-3.0521.112.5741.3824027981138661138230.4712.636100
3.05-3.1528.6141.8512.37285811999918998860.7541.883100
3.15-3.2532.3041.413.33284759888163881510.8441.432100
3.25-3.3542.6511.2624.58332013577848778440.9171.277100
3.35-3.4549.0281.1795.43338777069102690980.941.192100
3.45-3.646.1520.9416.58415449290020900180.9540.952100
3.6-455.3830.71610.4799158851790421790410.9850.722100
4-4.2558.3670.51915.2468234280222802220.9930.523100
4.25-4.557.6760.40318.88365780463420634200.9950.407100
4.5-4.7556.6860.3322.18288460150887508870.9970.333100
4.75-555.4150.28424.83228053741154411540.9970.287100
5-654.7010.20931.1557258461046761046760.9980.211100
6-758.7080.17337.37313729253439534390.9990.175100
7-857.7320.13146.72173922730126301260.9990.132100
8-955.8220.11152.34102081818287182870.9990.112100
9-1052.2020.09357.4661258611735117350.9990.094100
10-5054.7460.0679.471748583319423194010.06100
50-20039.6490.07296.3103883102620.9880.07484.5
200-3003
152.739-3002

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Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.95→152.739 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2531 24076 2 %
Rwork0.2127 1179674 -
obs0.2135 1203750 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 242.32 Å2 / Biso mean: 78.5617 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.95→152.739 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms90276 206267 3036 0 299579
Biso mean--56.87 --
Num. residues----20933
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013324188
X-RAY DIFFRACTIONf_angle_d1.915486918
X-RAY DIFFRACTIONf_chiral_restr0.07761501
X-RAY DIFFRACTIONf_plane_restr0.0125460
X-RAY DIFFRACTIONf_dihedral_angle_d18.194172249
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.95-2.98350.39547980.3683911039908100
2.9835-3.01860.36897960.3353902739823100
3.0186-3.05540.35527950.31183902739822100
3.0554-3.09410.33197990.30213911739916100
3.0941-3.13480.32277970.2863909739894100
3.1348-3.17780.31198000.28143912939929100
3.1778-3.22320.31017990.26883920240001100
3.2232-3.27130.30667990.2613916139960100
3.2713-3.32240.29987980.2473911639914100
3.3224-3.37690.28918000.23963915139951100
3.3769-3.43510.28437970.23613908539882100
3.4351-3.49760.27848010.23453923540036100
3.4976-3.56490.26747990.2273912739926100
3.5649-3.63770.27378000.22363919339993100
3.6377-3.71680.24958010.21183925640057100
3.7168-3.80320.25248010.21013926540066100
3.8032-3.89830.23598010.20183920040001100
3.8983-4.00380.24878010.23928740088100
4.0038-4.12160.24138010.19733924740048100
4.1216-4.25460.24968030.19823931640119100
4.2546-4.40670.24998010.19553928440085100
4.4067-4.58310.22988020.19073935240154100
4.5831-4.79170.23428050.18943936440169100
4.7917-5.04440.23148040.1853942840232100
5.0444-5.36040.21918060.17883948540291100
5.3604-5.77430.22268060.17673950540311100
5.7743-6.35550.23758080.18923961740425100
6.3555-7.27510.2328120.19193974140553100
7.2751-9.16570.22988140.19613992240736100
9.1657-152.94390.23198320.2122406284146099

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