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- PDB-6n9f: Crystal structure of the Thermus thermophilus 70S ribosome in com... -

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Basic information

Entry
Database: PDB / ID: 6n9f
TitleCrystal structure of the Thermus thermophilus 70S ribosome in complex with a short substrate mimic ACCA-DPhe and bound to mRNA and P-site tRNA at 3.7A resolution
Components
  • (30S Ribosomal Protein ...) x 20
  • (50S Ribosomal Protein ...) x 29
  • 16S Ribosomal RNA
  • 23S Ribosomal RNA
  • 5S Ribosomal RNA
  • ACCA-DPhe
  • P-site tRNA, Deacylated Initiator Methionyl-tRNA
  • mRNAMessenger RNA
KeywordsRIBOSOME / D-amino acids / ribosome structure / peptidyl transferase center / expanded genetic code / ribosome engineering
Function / homology30S ribosomal protein / 30S ribosomal protein Thx / Ribosomal protein S15 / Ribosomal protein S14p/S29e / Ribosomal protein S12/S23 / Ribosomal protein L33 superfamily / Ribosomal protein L25, C-terminal / Ribosomal protein S11 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein S18 superfamily ...30S ribosomal protein / 30S ribosomal protein Thx / Ribosomal protein S15 / Ribosomal protein S14p/S29e / Ribosomal protein S12/S23 / Ribosomal protein L33 superfamily / Ribosomal protein L25, C-terminal / Ribosomal protein S11 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein S18 superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein L29/L35 superfamily / L28p-like / Ribosomal protein L30 signature. / Ribosomal protein S10p/S20e / Ribosomal protein L25 / Ribosomal protein L31 type A / Ribosomal protein S10 domain / 30s ribosomal protein S13, C-terminal / Ribosomal protein L28/L24 / Ribosomal protein S16 domain superfamily / Ribosomal protein S14, type Z / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L34, conserved site / Ribosomal protein S9, conserved site / Ribosomal protein S5 domain 2-type fold / Ribosomal protein L30p/L7e / Ribosomal protein S17 / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal L32p protein family / Ribosomal protein S14 signature. / Ribosomal protein S15 signature. / Ribosomal protein S10 signature. / Ribosomal protein S9 signature. / Ribosomal protein S18 signature. / Ribosomal protein S17 signature. / Ribosomal protein S12 signature. / Ribosomal protein S11 signature. / Ribosomal proteins 50S L24/mitochondrial 39S L24 / 30S ribosomal protein Thx / Ribosomal protein TL5, C-terminal domain / Ribosomal L25p family / Ribosomal protein S9/S16 / Ribosomal protein L31 / Ribosomal protein S18 / Ribosomal L27 protein / Ribosomal protein S16 / Ribosomal L29 protein / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L34 / KOW motif / Ribosomal protein S13/S18 / Ribosomal protein S11 / Ribosomal protein L25, beta domain / 30S ribosomal protein S17 / Ribosomal protein L33 signature. / Ribosomal protein S14 / Ribosomal protein L32p / Ribosomal protein L31 / Ribosomal protein S11 / Ribosomal protein S13 / Ribosomal protein L29/L35 / Ribosomal protein S10 / Ribosomal protein L33 / Ribosomal protein L27 / Ribosomal protein S18 / Ribosomal protein L28 / Ribosomal protein L25, long-form / Ribosomal protein S15, bacterial-type / Ribosomal protein S9 / Ribosomal protein S15 / Ribosomal protein S16 / Ribosomal protein L34 / Ribosomal protein S17/S11 / Ribosomal protein S13 signature. / Ribosomal protein L34 signature. / Ribosomal protein L27 signature. / Ribosomal protein L24 signature. / Ribosomal protein L31 signature. / Ribosomal protein S13 family profile. / Ribosomal protein S11, bacterial-type / Ribosomal protein L24 / Ribosomal protein S12, bacterial-type / KOW / Ribosomal protein S13, bacterial-type / Ribosomal protein S17, conserved site / Ribosomal protein S18, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S10, conserved site / Ribosomal protein L33, conserved site / Ribosomal protein L27, conserved site / Ribosomal protein L29, conserved site / Ribosomal S11, conserved site / Ribosomal protein L30, conserved site / Ribosomal protein L30, ferredoxin-like fold domain / Ribosomal protein L2, domain 2 / Ribosomal protein S5 domain 2-type fold, subgroup / Nucleic acid-binding, OB-fold
Function and homology information
Specimen sourceEscherichia coli (E. coli)
Thermus thermophilus (bacteria)
Enterobacteria phage T4 (bacteriophage)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 3.7 Å resolution
AuthorsMelnikov, S.V. / Khabibullina, N.F. / Mairhofer, E. / Vargas-Rodriguez, O. / Reynolds, N.M. / Micura, R. / Soll, D. / Polikanov, Y.S.
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Mechanistic insights into the slow peptide bond formation with D-amino acids in the ribosomal active site.
Authors: Melnikov, S.V. / Khabibullina, N.F. / Mairhofer, E. / Vargas-Rodriguez, O. / Reynolds, N.M. / Micura, R. / Soll, D. / Polikanov, Y.S.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 3, 2018 / Release: Dec 12, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Dec 12, 2018Structure modelrepositoryInitial release
1.1Dec 19, 2018Structure modelData collection / Database referencescitation / citation_author_citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1A: 23S Ribosomal RNA
1B: 5S Ribosomal RNA
1D: 50S Ribosomal Protein L2
1E: 50S Ribosomal Protein L3
1F: 50S Ribosomal Protein L4
1G: 50S Ribosomal Protein L5
1H: 50S Ribosomal Protein L6
1I: 50S Ribosomal Protein L9
1N: 50S Ribosomal Protein L13
1O: 50S Ribosomal Protein L14
1P: 50S Ribosomal Protein L15
1Q: 50S Ribosomal Protein L16
1R: 50S Ribosomal Protein L17
1S: 50S Ribosomal Protein L18
1T: 50S Ribosomal Protein L19
1U: 50S Ribosomal Protein L20
1V: 50S Ribosomal Protein L21
1W: 50S Ribosomal Protein L22
1X: 50S Ribosomal Protein L23
1Y: 50S ribosomal protein L24
1Z: 50S ribosomal protein L25
10: 50S ribosomal protein L27
11: 50S ribosomal protein L28
12: 50S ribosomal protein L29
13: 50S ribosomal protein L30
14: 50S ribosomal protein L31
15: 50S ribosomal protein L32
16: 50S ribosomal protein L33
17: 50S ribosomal protein L34
18: 50S Ribosomal Protein L35
19: 50S Ribosomal Protein L36
1a: 16S Ribosomal RNA
1b: 30S Ribosomal Protein S2
1c: 30S Ribosomal Protein S3
1d: 30S Ribosomal Protein S4
1e: 30S Ribosomal Protein S5
1f: 30S Ribosomal Protein S6
1g: 30S Ribosomal Protein S7
1h: 30S Ribosomal Protein S8
1i: 30S ribosomal protein S9
1j: 30S ribosomal protein S10
1k: 30S ribosomal protein S11
1l: 30S ribosomal protein S12
1m: 30S ribosomal protein S13
1n: 30S ribosomal protein S14 type Z
1o: 30S ribosomal protein S15
1p: 30S ribosomal protein S16
1q: 30S ribosomal protein S17
1r: 30S ribosomal protein S18
1s: 30S Ribosomal Protein S19
1t: 30S Ribosomal Protein S20
1u: 30S ribosomal protein Thx
1v: mRNA
1w: ACCA-DPhe
1x: P-site tRNA, Deacylated Initiator Methionyl-tRNA
2A: 23S Ribosomal RNA
2B: 5S Ribosomal RNA
2D: 50S Ribosomal Protein L2
2E: 50S Ribosomal Protein L3
2F: 50S Ribosomal Protein L4
2G: 50S Ribosomal Protein L5
2H: 50S Ribosomal Protein L6
2I: 50S Ribosomal Protein L9
2N: 50S Ribosomal Protein L13
2O: 50S Ribosomal Protein L14
2P: 50S Ribosomal Protein L15
2Q: 50S Ribosomal Protein L16
2R: 50S Ribosomal Protein L17
2S: 50S Ribosomal Protein L18
2T: 50S Ribosomal Protein L19
2U: 50S Ribosomal Protein L20
2V: 50S Ribosomal Protein L21
2W: 50S Ribosomal Protein L22
2X: 50S Ribosomal Protein L23
2Y: 50S ribosomal protein L24
2Z: 50S ribosomal protein L25
20: 50S ribosomal protein L27
21: 50S ribosomal protein L28
22: 50S ribosomal protein L29
23: 50S ribosomal protein L30
24: 50S ribosomal protein L31
25: 50S ribosomal protein L32
26: 50S ribosomal protein L33
27: 50S ribosomal protein L34
28: 50S Ribosomal Protein L35
29: 50S Ribosomal Protein L36
2a: 16S Ribosomal RNA
2b: 30S Ribosomal Protein S2
2c: 30S Ribosomal Protein S3
2d: 30S Ribosomal Protein S4
2e: 30S Ribosomal Protein S5
2f: 30S Ribosomal Protein S6
2g: 30S Ribosomal Protein S7
2h: 30S Ribosomal Protein S8
2i: 30S ribosomal protein S9
2j: 30S ribosomal protein S10
2k: 30S ribosomal protein S11
2l: 30S ribosomal protein S12
2m: 30S ribosomal protein S13
2n: 30S ribosomal protein S14 type Z
2o: 30S ribosomal protein S15
2p: 30S ribosomal protein S16
2q: 30S ribosomal protein S17
2r: 30S ribosomal protein S18
2s: 30S Ribosomal Protein S19
2t: 30S Ribosomal Protein S20
2u: 30S ribosomal protein Thx
2v: mRNA
2w: ACCA-DPhe
2x: P-site tRNA, Deacylated Initiator Methionyl-tRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,439,0651463
Polyers4,405,032110
Non-polymers34,0331353
Water4,450247
1
1A: 23S Ribosomal RNA
1B: 5S Ribosomal RNA
1D: 50S Ribosomal Protein L2
1E: 50S Ribosomal Protein L3
1F: 50S Ribosomal Protein L4
1G: 50S Ribosomal Protein L5
1H: 50S Ribosomal Protein L6
1I: 50S Ribosomal Protein L9
1N: 50S Ribosomal Protein L13
1O: 50S Ribosomal Protein L14
1P: 50S Ribosomal Protein L15
1Q: 50S Ribosomal Protein L16
1R: 50S Ribosomal Protein L17
1S: 50S Ribosomal Protein L18
1T: 50S Ribosomal Protein L19
1U: 50S Ribosomal Protein L20
1V: 50S Ribosomal Protein L21
1W: 50S Ribosomal Protein L22
1X: 50S Ribosomal Protein L23
1Y: 50S ribosomal protein L24
1Z: 50S ribosomal protein L25
10: 50S ribosomal protein L27
11: 50S ribosomal protein L28
12: 50S ribosomal protein L29
13: 50S ribosomal protein L30
14: 50S ribosomal protein L31
15: 50S ribosomal protein L32
16: 50S ribosomal protein L33
17: 50S ribosomal protein L34
18: 50S Ribosomal Protein L35
19: 50S Ribosomal Protein L36
1a: 16S Ribosomal RNA
1b: 30S Ribosomal Protein S2
1c: 30S Ribosomal Protein S3
1d: 30S Ribosomal Protein S4
1e: 30S Ribosomal Protein S5
1f: 30S Ribosomal Protein S6
1g: 30S Ribosomal Protein S7
1h: 30S Ribosomal Protein S8
1i: 30S ribosomal protein S9
1j: 30S ribosomal protein S10
1k: 30S ribosomal protein S11
1l: 30S ribosomal protein S12
1m: 30S ribosomal protein S13
1n: 30S ribosomal protein S14 type Z
1o: 30S ribosomal protein S15
1p: 30S ribosomal protein S16
1q: 30S ribosomal protein S17
1r: 30S ribosomal protein S18
1s: 30S Ribosomal Protein S19
1t: 30S Ribosomal Protein S20
1u: 30S ribosomal protein Thx
1v: mRNA
1w: ACCA-DPhe
1x: P-site tRNA, Deacylated Initiator Methionyl-tRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,220,517772
Polyers2,202,51655
Non-polymers18,001717
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
2A: 23S Ribosomal RNA
2B: 5S Ribosomal RNA
2D: 50S Ribosomal Protein L2
2E: 50S Ribosomal Protein L3
2F: 50S Ribosomal Protein L4
2G: 50S Ribosomal Protein L5
2H: 50S Ribosomal Protein L6
2I: 50S Ribosomal Protein L9
2N: 50S Ribosomal Protein L13
2O: 50S Ribosomal Protein L14
2P: 50S Ribosomal Protein L15
2Q: 50S Ribosomal Protein L16
2R: 50S Ribosomal Protein L17
2S: 50S Ribosomal Protein L18
2T: 50S Ribosomal Protein L19
2U: 50S Ribosomal Protein L20
2V: 50S Ribosomal Protein L21
2W: 50S Ribosomal Protein L22
2X: 50S Ribosomal Protein L23
2Y: 50S ribosomal protein L24
2Z: 50S ribosomal protein L25
20: 50S ribosomal protein L27
21: 50S ribosomal protein L28
22: 50S ribosomal protein L29
23: 50S ribosomal protein L30
24: 50S ribosomal protein L31
25: 50S ribosomal protein L32
26: 50S ribosomal protein L33
27: 50S ribosomal protein L34
28: 50S Ribosomal Protein L35
29: 50S Ribosomal Protein L36
2a: 16S Ribosomal RNA
2b: 30S Ribosomal Protein S2
2c: 30S Ribosomal Protein S3
2d: 30S Ribosomal Protein S4
2e: 30S Ribosomal Protein S5
2f: 30S Ribosomal Protein S6
2g: 30S Ribosomal Protein S7
2h: 30S Ribosomal Protein S8
2i: 30S ribosomal protein S9
2j: 30S ribosomal protein S10
2k: 30S ribosomal protein S11
2l: 30S ribosomal protein S12
2m: 30S ribosomal protein S13
2n: 30S ribosomal protein S14 type Z
2o: 30S ribosomal protein S15
2p: 30S ribosomal protein S16
2q: 30S ribosomal protein S17
2r: 30S ribosomal protein S18
2s: 30S Ribosomal Protein S19
2t: 30S Ribosomal Protein S20
2u: 30S ribosomal protein Thx
2v: mRNA
2w: ACCA-DPhe
2x: P-site tRNA, Deacylated Initiator Methionyl-tRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,218,548691
Polyers2,202,51655
Non-polymers16,032636
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)211.390, 452.150, 617.640
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP 21 21 21

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Components

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RNA chain , 6 types, 12 molecules 1A2A1B2B1a2a1v2v1w2w1x2x

#1: RNA chain 23S Ribosomal RNA /


Mass: 948035.625 Da / Num. of mol.: 2 / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#2: RNA chain 5S Ribosomal RNA /


Mass: 39188.371 Da / Num. of mol.: 2 / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#32: RNA chain 16S Ribosomal RNA /


Mass: 493864.625 Da / Num. of mol.: 2 / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#53: RNA chain mRNA / Messenger RNA


Mass: 7804.735 Da / Num. of mol.: 2 / Source: (synth.) Enterobacteria phage T4 (bacteriophage) / Details: Synthetic 24-nt M-F-Stop mRNA
#54: RNA chain ACCA-DPhe


Mass: 1370.007 Da / Num. of mol.: 2 / Source: (synth.) Escherichia coli (E. coli) / Details: Synthetic tRNA-mimic ACCA-DPhe
#55: RNA chain P-site tRNA, Deacylated Initiator Methionyl-tRNA


Mass: 24846.902 Da / Num. of mol.: 2 / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE-600 / Production host: Escherichia coli (E. coli) / Strain (production host): MRE-600

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50S Ribosomal Protein ... , 29 types, 58 molecules 1D2D1E2E1F2F1G2G1H2H1I2I1N2N1O2O1P2P1Q2Q1R2R1S2S1T2T1U2U1V2V...

#3: Protein/peptide 50S Ribosomal Protein L2 /


Mass: 30532.551 Da / Num. of mol.: 2 / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#4: Protein/peptide 50S Ribosomal Protein L3 /


Mass: 22450.213 Da / Num. of mol.: 2 / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#5: Protein/peptide 50S Ribosomal Protein L4 /


Mass: 23271.914 Da / Num. of mol.: 2 / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#6: Protein/peptide 50S Ribosomal Protein L5 /


Mass: 21061.596 Da / Num. of mol.: 2 / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#7: Protein/peptide 50S Ribosomal Protein L6 /


Mass: 19568.926 Da / Num. of mol.: 2 / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#8: Protein/peptide 50S Ribosomal Protein L9 /


Mass: 16422.180 Da / Num. of mol.: 2 / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#9: Protein/peptide 50S Ribosomal Protein L13 /


Mass: 15927.903 Da / Num. of mol.: 2 / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#10: Protein/peptide 50S Ribosomal Protein L14 /


Mass: 13323.612 Da / Num. of mol.: 2 / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#11: Protein/peptide 50S Ribosomal Protein L15 /


Mass: 16319.142 Da / Num. of mol.: 2 / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#12: Protein/peptide 50S Ribosomal Protein L16 /


Mass: 15993.909 Da / Num. of mol.: 2 / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#13: Protein/peptide 50S Ribosomal Protein L17 /


Mass: 13750.148 Da / Num. of mol.: 2 / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#14: Protein/peptide 50S Ribosomal Protein L18 /


Mass: 12639.845 Da / Num. of mol.: 2 / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#15: Protein/peptide 50S Ribosomal Protein L19 /


Mass: 17188.830 Da / Num. of mol.: 2 / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#16: Protein/peptide 50S Ribosomal Protein L20 /


Mass: 13779.275 Da / Num. of mol.: 2 / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#17: Protein/peptide 50S Ribosomal Protein L21 /


Mass: 11069.153 Da / Num. of mol.: 2 / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#18: Protein/peptide 50S Ribosomal Protein L22 /


Mass: 12808.055 Da / Num. of mol.: 2 / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#19: Protein/peptide 50S Ribosomal Protein L23 /


Mass: 10759.808 Da / Num. of mol.: 2 / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#20: Protein/peptide 50S ribosomal protein L24 /


Mass: 12085.611 Da / Num. of mol.: 2 / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q56435
#21: Protein/peptide 50S ribosomal protein L25 / / General stress protein CTC


Mass: 23238.572 Da / Num. of mol.: 2 / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q72IA7
#22: Protein/peptide 50S ribosomal protein L27 /


Mass: 9529.074 Da / Num. of mol.: 2 / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P60493
#23: Protein/peptide 50S ribosomal protein L28 /


Mass: 11004.160 Da / Num. of mol.: 2 / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P60494
#24: Protein/peptide 50S ribosomal protein L29 /


Mass: 8670.258 Da / Num. of mol.: 2 / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q72I12
#25: Protein/peptide 50S ribosomal protein L30 /


Mass: 6799.126 Da / Num. of mol.: 2 / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P74909
#26: Protein/peptide 50S ribosomal protein L31 /


Mass: 8300.543 Da / Num. of mol.: 2 / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q72JR0
#27: Protein/peptide 50S ribosomal protein L32 /


Mass: 6722.050 Da / Num. of mol.: 2 / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80339
#28: Protein/peptide 50S ribosomal protein L33 /


Mass: 6632.896 Da / Num. of mol.: 2 / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q72GW3
#29: Protein/peptide 50S ribosomal protein L34 /


Mass: 6132.449 Da / Num. of mol.: 2 / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80340
#30: Protein/peptide 50S Ribosomal Protein L35 /


Mass: 7506.178 Da / Num. of mol.: 2 / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#31: Protein/peptide 50S Ribosomal Protein L36 /


Mass: 4435.411 Da / Num. of mol.: 2 / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8

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30S Ribosomal Protein ... , 20 types, 40 molecules 1b2b1c2c1d2d1e2e1f2f1g2g1h2h1i2i1j2j1k2k1l2l1m2m1n2n1o2o1p2p...

#33: Protein/peptide 30S Ribosomal Protein S2 /


Mass: 29317.703 Da / Num. of mol.: 2 / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#34: Protein/peptide 30S Ribosomal Protein S3 /


Mass: 26751.076 Da / Num. of mol.: 2 / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#35: Protein/peptide 30S Ribosomal Protein S4 /


Mass: 24373.447 Da / Num. of mol.: 2 / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#36: Protein/peptide 30S Ribosomal Protein S5 /


Mass: 17583.416 Da / Num. of mol.: 2 / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#37: Protein/peptide 30S Ribosomal Protein S6 /


Mass: 11988.753 Da / Num. of mol.: 2 / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#38: Protein/peptide 30S Ribosomal Protein S7 /


Mass: 18050.973 Da / Num. of mol.: 2 / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#39: Protein/peptide 30S Ribosomal Protein S8 /


Mass: 15868.570 Da / Num. of mol.: 2 / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#40: Protein/peptide 30S ribosomal protein S9 /


Mass: 14410.614 Da / Num. of mol.: 2 / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80374
#41: Protein/peptide 30S ribosomal protein S10 /


Mass: 11954.968 Da / Num. of mol.: 2 / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80375
#42: Protein/peptide 30S ribosomal protein S11 /


Mass: 13737.868 Da / Num. of mol.: 2 / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P62654
#43: Protein/peptide 30S ribosomal protein S12 /


Mass: 14683.476 Da / Num. of mol.: 2 / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P17293
#44: Protein/peptide 30S ribosomal protein S13 /


Mass: 14338.861 Da / Num. of mol.: 2 / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P62655
#45: Protein/peptide 30S ribosomal protein S14 type Z / Ribosome


Mass: 7158.725 Da / Num. of mol.: 2 / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P24320
#46: Protein/peptide 30S ribosomal protein S15 /


Mass: 10578.407 Da / Num. of mol.: 2 / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80378
#47: Protein/peptide 30S ribosomal protein S16 /


Mass: 10409.983 Da / Num. of mol.: 2 / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P62238
#48: Protein/peptide 30S ribosomal protein S17 /


Mass: 12325.655 Da / Num. of mol.: 2 / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P0DOY7
#49: Protein/peptide 30S ribosomal protein S18 /


Mass: 10258.299 Da / Num. of mol.: 2 / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P62659
#50: Protein/peptide 30S Ribosomal Protein S19 /


Mass: 10605.464 Da / Num. of mol.: 2 / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#51: Protein/peptide 30S Ribosomal Protein S20 /


Mass: 11736.143 Da / Num. of mol.: 2 / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#52: Protein/peptide 30S ribosomal protein Thx / Ribosome


Mass: 3350.030 Da / Num. of mol.: 2 / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P62612

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Non-polymers , 4 types, 1600 molecules

#56: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1339 / Formula: Mg / Magnesium
#57: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Formula: Zn / Zinc
#58: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Formula: Fe4S4 / Iron–sulfur cluster
#59: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / Formula: H2O / Water

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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: 3.35 / Density percent sol: 58.36 % / Description: Long needles
Crystal growTemp: 292 K / Method: vapor diffusion / pH: 7.6
Details: 0.1-0.2 M Arginine-HCl, 0.1M Tris-HCl pH 7.6, 2.5% PEG-20K, 7-12% MPD, 0.5 mM BME

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Data collection

DiffractionMean temperature: 100 / Serial crystal experiment: N
SourceSource: SYNCHROTRON / Type: APS BEAMLINE 24-ID-C / Synchrotron site: APS / Beamline: 24-ID-C / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M-F / Details: S/N 60-0112-F / Detector: PIXEL / Collection date: Mar 24, 2018
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 / Relative weight: 1
ReflectionB iso Wilson estimate: 123.64 / D resolution high: 3.7 / D resolution low: 255.015 / Number obs: 615531 / Observed criterion sigma I: -3 / CC half: 0.995 / Rmerge I obs: 0.177 / Rrim I all: 0.209 / Chi squared: 0.881 / NetI over sigmaI: 5.59 / Number measured all: 2154810 / Redundancy: 3.501 % / Scaling rejects: 345 / Percent possible obs: 98.5
Reflection shell

Diffraction ID: 1

Rmerge I obsHighest resolutionLowest resolutionMeanI over sigI obsNumber measured obsNumber possibleNumber unique obsCC halfRrim I allRedundancyPercent possible all
1.4373.7003.8000.86014206445887452040.2491.7273.14398.500
1.1653.8003.9001.14015581044787446030.3731.3723.49399.600
0.9563.9004.0101.42015641743488433450.4601.1213.60999.700
0.7904.0104.1401.72015232142362422100.5640.9263.60999.600
0.6424.1404.2702.08014578340927407150.6570.7543.58199.500
0.5074.2704.4202.56014007739728394670.7490.5963.54999.300
0.4174.4204.5903.08013425538356380250.8130.4903.53199.100
0.3404.5904.7803.62012544736817362690.8630.4023.45998.500
0.2784.7804.9904.15011142035466346360.8910.3323.21797.700
0.2254.9905.2305.32011813233863335040.9360.2653.52698.900
0.1925.2305.5206.28011723032267319620.9550.2243.66899.100
0.1705.5205.8507.00010982430563301850.9640.1993.63898.800
0.1525.8506.2507.65010208128761282200.9700.1783.61798.100
0.1306.2506.7608.5609234926766263080.9760.1533.51098.300
0.0996.7607.40010.3407773624720238800.9840.1183.25596.600
0.0817.4008.27013.0207784522447218770.9900.0953.55897.500
0.0698.2709.55015.6107074319822193060.9920.0813.66497.400
0.0539.55011.70019.4305865616901163220.9950.0633.59496.600
0.04611.70016.55021.5404062513193124240.9940.0553.27094.200
0.04316.550255.01526.60025995751970690.9950.0513.67794.000

-
Processing

Software
NameVersionClassificationContact authorLocationTypeContact author emailLanguageDate
XDSdata reductionWolfgang Kabschhttp://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xscale_program.htmlpackage
XSCALEdata scalingWolfgang Kabschhttp://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xscale_program.htmlpackage
PHASERphasingRandy J. Readhttp://www-structmed.cimr.cam.ac.uk/phaser/programcimr-phaser[at]lists.cam.ac.uk
PHENIX1.8.2refinementPaul D. Adamshttp://www.phenix-online.org/packagepdadams[at]lbl.govC++
Coot0.8.2model buildingPaul Emsleyhttp://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/program
PDB_EXTRACT3.24data extractionPDBhttp://sw-tools.pdb.org/apps/PDB_EXTRACT/packagedeposit[at]deposit.rcsb.orgC++Sept 1, 2017
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Y4P
Overall SU ML: 0.57 / Cross valid method: FREE R-VALUE / Sigma F: 1.33 / Overall phase error: 28.72 / Stereochemistry target values: ML
Solvent computationSolvent shrinkage radii: 0.9 / Solvent vdw probe radii: 1.11 / Solvent model details: FLAT BULK SOLVENT MODEL
Displacement parametersB iso max: 194.88 / B iso mean: 103.7824 / B iso min: 50.23
Least-squares processR factor R free: 0.2794 / R factor R work: 0.2361 / R factor obs: 0.2382 / Highest resolution: 3.7 / Lowest resolution: 255.015 / Number reflection R free: 30948 / Number reflection R work: 584231 / Number reflection obs: 615179 / Percent reflection R free: 5.03 / Percent reflection obs: 98.49
Refine hist #finalHighest resolution: 3.7 / Lowest resolution: 255.015 / B iso mean ligand: 74.23 / B iso mean solvent: 66.46 / Number residues total: 20661
Number of atoms included #finalProtein: 90996 / Nucleic acid: 195565 / Ligand: 1599 / Solvent: 15 / Total: 288175
Refine LS restraints
Refine IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003313004
X-RAY DIFFRACTIONf_angle_d0.635466774
X-RAY DIFFRACTIONf_chiral_restr0.03459086
X-RAY DIFFRACTIONf_plane_restr0.00425181
X-RAY DIFFRACTIONf_dihedral_angle_d13.625166209
Refine LS shell

Refine ID: X-RAY DIFFRACTION / R factor R free error: 0 / Total number of bins used: 30

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workNumber reflection allPercent reflection obs
3.70000.37830.33933.7420963191962015998.0000
3.74200.36650.32863.78611019192812030098.0000
3.78610.35830.32663.83231060194672052799.0000
3.83230.34320.30793.88089901958520575100.0000
3.88080.33460.29543.931810071966520672100.0000
3.93180.35080.29693.985710301957220602100.0000
3.98570.32710.29264.042710101956820578100.0000
4.04270.32290.28624.103010521956120613100.0000
4.10300.32040.28274.167110641954620610100.0000
4.16710.34770.28594.23541063195652062899.0000
4.23540.33480.28224.30851031195872061899.0000
4.30850.32690.27314.38681033195222055599.0000
4.38680.30740.26644.47121011195452055699.0000
4.47120.28320.24904.56251067195092057699.0000
4.56250.29000.24664.66171057193852044299.0000
4.66170.29300.24134.77021029194002042998.0000
4.77020.30780.24684.88951029193252035498.0000
4.88950.29810.24325.02171011193222033398.0000
5.02170.29060.23325.16941066194042047099.0000
5.16940.26930.21975.33631004196232062799.0000
5.33630.26320.21405.52711069195632063299.0000
5.52710.25920.20985.74841027195692059699.0000
5.74840.26480.21406.01001062194392050198.0000
6.01000.27350.21846.32691007194652047298.0000
6.32690.27050.21456.72331027195292055698.0000
6.72330.24540.20787.24251016193602037697.0000
7.24250.24770.20627.97131040192342027497.0000
7.97130.25980.21199.12491085194992058498.0000
9.12490.21420.189311.49641002194992050197.0000
11.49640.22840.2037255.62251017194462046394.0000

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