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- PDB-4v8f: Crystal structure analysis of ribosomal decoding (near-cognate tR... -

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Basic information

Entry
Database: PDB / ID: 4v8f
TitleCrystal structure analysis of ribosomal decoding (near-cognate tRNA-ttyr complex with paromomycin).
Components
  • (30S RIBOSOMAL PROTEIN ...) x 20
  • (50S ribosomal protein ...) x 28
  • 16S ribosomal RNA
  • 5S RIBOSOMAL RNA
  • MRNAMessenger RNA
  • RNA (2912-MER)
  • TRNA-FMET
  • TRNA-TYR
KeywordsRIBOSOME / RNA / tRNA / translation / mRNA
Function / homology
Function and homology information


large ribosomal subunit / small ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation ...large ribosomal subunit / small ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / 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 L33, conserved site / Ribosomal protein L33 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 S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 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 S4, bacterial-type / Ribosomal protein L14P, 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 L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L33 superfamily / : / 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 S16 domain superfamily / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L21 / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L19 / Ribosomal protein S15, bacterial-type / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein
Similarity search - Domain/homology
osmium (III) hexammine / PAROMOMYCIN / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 ...osmium (III) hexammine / PAROMOMYCIN / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein bL33 / 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: 3.3 Å
AuthorsJenner, L. / Demeshkina, N. / Yusupov, M. / Yusupova, G.
CitationJournal: Nature / Year: 2012
Title: A new understanding of the decoding principle on the ribosome.
Authors: Demeshkina, N. / Jenner, L. / Westhof, E. / Yusupov, M. / Yusupova, G.
History
DepositionDec 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 3UZK, 3UZL, 3UZM, 3UZN
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Nov 22, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 2.0Jul 3, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / entity / struct_conn
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AA: RNA (2912-MER)
AB: 5S RIBOSOMAL RNA
AD: 50S ribosomal protein L2
AE: 50S ribosomal protein L3
AF: 50S ribosomal protein L4
AG: 50S ribosomal protein L5
AH: 50S ribosomal protein L6
AK: 50S ribosomal protein L9
AM: 50S ribosomal protein L13
AN: 50S ribosomal protein L14
AO: 50S ribosomal protein L15
AP: 50S ribosomal protein L16
A0: 50S ribosomal protein L17
AQ: 50S ribosomal protein L18
AR: 50S ribosomal protein L19
A1: 50S ribosomal protein L20
A2: 50S ribosomal protein L21
AS: 50S ribosomal protein L22
AT: 50S ribosomal protein L23
AU: 50S ribosomal protein L24
AV: 50S ribosomal protein L25
A3: 50S ribosomal protein L27
AZ: 50S ribosomal protein L28
AW: 50S ribosomal protein L29
AX: 50S ribosomal protein L30
A4: 50S ribosomal protein L31
A5: 50S ribosomal protein L32
A6: 50S ribosomal protein L33
A7: 50S ribosomal protein L34
A8: 50S ribosomal protein L35
BA: 16S ribosomal RNA
BE: 30S RIBOSOMAL PROTEIN S2
BF: 30S RIBOSOMAL PROTEIN S3
BG: 30S RIBOSOMAL PROTEIN S4
BH: 30S RIBOSOMAL PROTEIN S5
BI: 30S RIBOSOMAL PROTEIN S6
BJ: 30S RIBOSOMAL PROTEIN S7
BK: 30S RIBOSOMAL PROTEIN S8
BL: 30S RIBOSOMAL PROTEIN S9
BM: 30S RIBOSOMAL PROTEIN S10
BN: 30S RIBOSOMAL PROTEIN S11
BO: 30S RIBOSOMAL PROTEIN S12
BP: 30S RIBOSOMAL PROTEIN S13
BQ: 30S RIBOSOMAL PROTEIN S14
BR: 30S RIBOSOMAL PROTEIN S15
BS: 30S RIBOSOMAL PROTEIN S16
BT: 30S RIBOSOMAL PROTEIN S17
BU: 30S RIBOSOMAL PROTEIN S18
BV: 30S RIBOSOMAL PROTEIN S19
BW: 30S RIBOSOMAL PROTEIN S20
BX: 30S RIBOSOMAL PROTEIN THX
BB: TRNA-TYR
BC: TRNA-FMET
BD: TRNA-TYR
B1: MRNA
CA: 16S ribosomal RNA
CE: 30S RIBOSOMAL PROTEIN S2
CF: 30S RIBOSOMAL PROTEIN S3
CG: 30S RIBOSOMAL PROTEIN S4
CH: 30S RIBOSOMAL PROTEIN S5
CI: 30S RIBOSOMAL PROTEIN S6
CJ: 30S RIBOSOMAL PROTEIN S7
CK: 30S RIBOSOMAL PROTEIN S8
CL: 30S RIBOSOMAL PROTEIN S9
CM: 30S RIBOSOMAL PROTEIN S10
CN: 30S RIBOSOMAL PROTEIN S11
CO: 30S RIBOSOMAL PROTEIN S12
CP: 30S RIBOSOMAL PROTEIN S13
CQ: 30S RIBOSOMAL PROTEIN S14
CR: 30S RIBOSOMAL PROTEIN S15
CS: 30S RIBOSOMAL PROTEIN S16
CT: 30S RIBOSOMAL PROTEIN S17
CU: 30S RIBOSOMAL PROTEIN S18
CV: 30S RIBOSOMAL PROTEIN S19
CW: 30S RIBOSOMAL PROTEIN S20
CX: 30S RIBOSOMAL PROTEIN THX
CB: TRNA-TYR
CC: TRNA-FMET
CD: TRNA-TYR
C1: MRNA
DA: RNA (2912-MER)
DB: 5S RIBOSOMAL RNA
DD: 50S ribosomal protein L2
DE: 50S ribosomal protein L3
DF: 50S ribosomal protein L4
DG: 50S ribosomal protein L5
DH: 50S ribosomal protein L6
DK: 50S ribosomal protein L9
DM: 50S ribosomal protein L13
DN: 50S ribosomal protein L14
DO: 50S ribosomal protein L15
DP: 50S ribosomal protein L16
D0: 50S ribosomal protein L17
DQ: 50S ribosomal protein L18
DR: 50S ribosomal protein L19
D1: 50S ribosomal protein L20
D2: 50S ribosomal protein L21
DS: 50S ribosomal protein L22
DT: 50S ribosomal protein L23
DU: 50S ribosomal protein L24
DV: 50S ribosomal protein L25
D3: 50S ribosomal protein L27
DZ: 50S ribosomal protein L28
DW: 50S ribosomal protein L29
DX: 50S ribosomal protein L30
D4: 50S ribosomal protein L31
D5: 50S ribosomal protein L32
D6: 50S ribosomal protein L33
D7: 50S ribosomal protein L34
D8: 50S ribosomal protein L35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,713,0261729
Polymers4,486,266110
Non-polymers226,7591619
Water0
1
AA: RNA (2912-MER)
AB: 5S RIBOSOMAL RNA
AD: 50S ribosomal protein L2
AE: 50S ribosomal protein L3
AF: 50S ribosomal protein L4
AG: 50S ribosomal protein L5
AH: 50S ribosomal protein L6
AK: 50S ribosomal protein L9
AM: 50S ribosomal protein L13
AN: 50S ribosomal protein L14
AO: 50S ribosomal protein L15
AP: 50S ribosomal protein L16
A0: 50S ribosomal protein L17
AQ: 50S ribosomal protein L18
AR: 50S ribosomal protein L19
A1: 50S ribosomal protein L20
A2: 50S ribosomal protein L21
AS: 50S ribosomal protein L22
AT: 50S ribosomal protein L23
AU: 50S ribosomal protein L24
AV: 50S ribosomal protein L25
A3: 50S ribosomal protein L27
AZ: 50S ribosomal protein L28
AW: 50S ribosomal protein L29
AX: 50S ribosomal protein L30
A4: 50S ribosomal protein L31
A5: 50S ribosomal protein L32
A6: 50S ribosomal protein L33
A7: 50S ribosomal protein L34
A8: 50S ribosomal protein L35
BA: 16S ribosomal RNA
BE: 30S RIBOSOMAL PROTEIN S2
BF: 30S RIBOSOMAL PROTEIN S3
BG: 30S RIBOSOMAL PROTEIN S4
BH: 30S RIBOSOMAL PROTEIN S5
BI: 30S RIBOSOMAL PROTEIN S6
BJ: 30S RIBOSOMAL PROTEIN S7
BK: 30S RIBOSOMAL PROTEIN S8
BL: 30S RIBOSOMAL PROTEIN S9
BM: 30S RIBOSOMAL PROTEIN S10
BN: 30S RIBOSOMAL PROTEIN S11
BO: 30S RIBOSOMAL PROTEIN S12
BP: 30S RIBOSOMAL PROTEIN S13
BQ: 30S RIBOSOMAL PROTEIN S14
BR: 30S RIBOSOMAL PROTEIN S15
BS: 30S RIBOSOMAL PROTEIN S16
BT: 30S RIBOSOMAL PROTEIN S17
BU: 30S RIBOSOMAL PROTEIN S18
BV: 30S RIBOSOMAL PROTEIN S19
BW: 30S RIBOSOMAL PROTEIN S20
BX: 30S RIBOSOMAL PROTEIN THX
BB: TRNA-TYR
BC: TRNA-FMET
BD: TRNA-TYR
B1: MRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,361,361913
Polymers2,243,13355
Non-polymers118,227858
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
CA: 16S ribosomal RNA
CE: 30S RIBOSOMAL PROTEIN S2
CF: 30S RIBOSOMAL PROTEIN S3
CG: 30S RIBOSOMAL PROTEIN S4
CH: 30S RIBOSOMAL PROTEIN S5
CI: 30S RIBOSOMAL PROTEIN S6
CJ: 30S RIBOSOMAL PROTEIN S7
CK: 30S RIBOSOMAL PROTEIN S8
CL: 30S RIBOSOMAL PROTEIN S9
CM: 30S RIBOSOMAL PROTEIN S10
CN: 30S RIBOSOMAL PROTEIN S11
CO: 30S RIBOSOMAL PROTEIN S12
CP: 30S RIBOSOMAL PROTEIN S13
CQ: 30S RIBOSOMAL PROTEIN S14
CR: 30S RIBOSOMAL PROTEIN S15
CS: 30S RIBOSOMAL PROTEIN S16
CT: 30S RIBOSOMAL PROTEIN S17
CU: 30S RIBOSOMAL PROTEIN S18
CV: 30S RIBOSOMAL PROTEIN S19
CW: 30S RIBOSOMAL PROTEIN S20
CX: 30S RIBOSOMAL PROTEIN THX
CB: TRNA-TYR
CC: TRNA-FMET
CD: TRNA-TYR
C1: MRNA
DA: RNA (2912-MER)
DB: 5S RIBOSOMAL RNA
DD: 50S ribosomal protein L2
DE: 50S ribosomal protein L3
DF: 50S ribosomal protein L4
DG: 50S ribosomal protein L5
DH: 50S ribosomal protein L6
DK: 50S ribosomal protein L9
DM: 50S ribosomal protein L13
DN: 50S ribosomal protein L14
DO: 50S ribosomal protein L15
DP: 50S ribosomal protein L16
D0: 50S ribosomal protein L17
DQ: 50S ribosomal protein L18
DR: 50S ribosomal protein L19
D1: 50S ribosomal protein L20
D2: 50S ribosomal protein L21
DS: 50S ribosomal protein L22
DT: 50S ribosomal protein L23
DU: 50S ribosomal protein L24
DV: 50S ribosomal protein L25
D3: 50S ribosomal protein L27
DZ: 50S ribosomal protein L28
DW: 50S ribosomal protein L29
DX: 50S ribosomal protein L30
D4: 50S ribosomal protein L31
D5: 50S ribosomal protein L32
D6: 50S ribosomal protein L33
D7: 50S ribosomal protein L34
D8: 50S ribosomal protein L35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,351,665816
Polymers2,243,13355
Non-polymers108,532761
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)210.000, 450.330, 622.860
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 , 6 types, 14 molecules AADAABDBBACABBBDCBCDBCCCB1C1

#1: RNA chain RNA (2912-MER)


Mass: 947013.000 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: GenBank: AP008226.1
#2: RNA chain 5S RIBOSOMAL RNA /


Mass: 39540.617 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: GenBank: AP008226.1
#31: RNA chain 16S ribosomal RNA /


Mass: 489002.531 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: GenBank: AP008226.1
#52: RNA chain
TRNA-TYR


Mass: 27402.457 Da / Num. of mol.: 4 / Source method: obtained synthetically / References: GenBank: AP012306.1
#53: RNA chain TRNA-FMET


Mass: 24801.801 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: GenBank: AP012306.1
#54: RNA chain MRNA / Messenger RNA


Mass: 5177.191 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic construct / References: GenBank: AP012306.1

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50S ribosomal protein ... , 28 types, 56 molecules ADDDAEDEAFDFAGDGAHDHAKDKAMDMANDNAODOAPDPA0D0AQDQARDRA1D1A2D2...

#3: Protein 50S ribosomal protein L2 /


Mass: 30532.551 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P60405
#4: Protein 50S ribosomal protein L3 /


Mass: 22450.213 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHN8
#5: Protein 50S ribosomal protein L4 /


Mass: 23271.914 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHN9
#6: Protein 50S ribosomal protein L5 /


Mass: 21061.596 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHQ0
#7: Protein 50S ribosomal protein L6 /


Mass: 19568.926 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHQ3, UniProt: P0DOY8*PLUS
#8: Protein 50S ribosomal protein L9 /


Mass: 16422.180 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SLQ1
#9: Protein 50S ribosomal protein L13 /


Mass: 15927.903 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P60488
#10: Protein 50S ribosomal protein L14 /


Mass: 13323.612 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHP8
#11: Protein 50S ribosomal protein L15 /


Mass: 16319.142 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHQ7
#12: Protein 50S ribosomal protein L16 /


Mass: 15993.909 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P60489
#13: Protein 50S ribosomal protein L17 /


Mass: 13750.148 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q9Z9H5
#14: Protein 50S ribosomal protein L18 /


Mass: 12639.845 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHQ4
#15: Protein 50S ribosomal protein L19 /


Mass: 17188.830 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P60490
#16: Protein 50S ribosomal protein L20 /


Mass: 13779.275 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P60491
#17: Protein 50S ribosomal protein L21 /


Mass: 11069.153 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P60492
#18: Protein 50S ribosomal protein L22 /


Mass: 12808.055 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHP3
#19: Protein 50S ribosomal protein L23 /


Mass: 10759.808 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHP0
#20: Protein 50S ribosomal protein L24 /


Mass: 12085.611 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHP9
#21: Protein 50S ribosomal protein L25 /


Mass: 23238.572 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHZ1
#22: Protein 50S ribosomal protein L27 /


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


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


Mass: 8670.258 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHP6
#25: Protein 50S ribosomal protein L30 /


Mass: 6799.126 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHQ6
#26: Protein 50S ribosomal protein L31 /


Mass: 8300.543 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SJE1
#27: Protein 50S ribosomal protein L32 /


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


Mass: 6632.896 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P35871
#29: 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 (bacteria) / Strain: HB8 / References: UniProt: P80340
#30: Protein 50S ribosomal protein L35 /


Mass: 7506.178 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SKU1

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30S RIBOSOMAL PROTEIN ... , 20 types, 40 molecules BECEBFCFBGCGBHCHBICIBJCJBKCKBLCLBMCMBNCNBOCOBPCPBQCQBRCRBSCS...

#32: Protein 30S RIBOSOMAL PROTEIN S2 /


Mass: 29317.703 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80371
#33: Protein 30S RIBOSOMAL PROTEIN S3 /


Mass: 26751.076 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80372
#34: Protein 30S RIBOSOMAL PROTEIN S4 /


Mass: 24242.254 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80373
#35: Protein 30S RIBOSOMAL PROTEIN S5 /


Mass: 17583.416 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHQ5
#36: Protein 30S RIBOSOMAL PROTEIN S6 /


Mass: 11988.753 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SLP8
#37: Protein 30S RIBOSOMAL PROTEIN S7 /


Mass: 18050.973 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P17291
#38: Protein 30S RIBOSOMAL PROTEIN S8 /


Mass: 15868.570 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHQ2, UniProt: A0A0M9AFS9*PLUS
#39: Protein 30S RIBOSOMAL PROTEIN S9 /


Mass: 14410.614 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80374
#40: Protein 30S RIBOSOMAL PROTEIN S10 /


Mass: 11954.968 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHN7
#41: Protein 30S RIBOSOMAL PROTEIN S11 /


Mass: 13737.868 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80376
#42: Protein 30S RIBOSOMAL PROTEIN S12 /


Mass: 14637.384 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHN3
#43: Protein 30S RIBOSOMAL PROTEIN S13 /


Mass: 14338.861 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80377
#44: Protein 30S RIBOSOMAL PROTEIN S14 /


Mass: 7158.725 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHQ1, UniProt: A0A0N0BLP2*PLUS
#45: Protein 30S RIBOSOMAL PROTEIN S15 /


Mass: 10578.407 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SJ76
#46: Protein 30S RIBOSOMAL PROTEIN S16 /


Mass: 10409.983 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SJH3
#47: Protein 30S RIBOSOMAL PROTEIN S17 /


Mass: 12325.655 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHP7, UniProt: A0A0N0BLS5*PLUS
#48: Protein 30S RIBOSOMAL PROTEIN S18 /


Mass: 10258.299 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SLQ0
#49: Protein 30S RIBOSOMAL PROTEIN S19 /


Mass: 10605.464 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHP2
#50: Protein 30S RIBOSOMAL PROTEIN S20 /


Mass: 11736.143 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80380
#51: Protein/peptide 30S RIBOSOMAL PROTEIN THX / Ribosome


Mass: 3350.030 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: Q5SIH3

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Non-polymers , 4 types, 1619 molecules

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


Mass: 24.305 Da / Num. of mol.: 903 / Source method: obtained synthetically / Formula: Mg
#56: Chemical...
ChemComp-OHX / osmium (III) hexammine / osmium(6+) hexaazanide


Mass: 286.365 Da / Num. of mol.: 710 / Source method: obtained synthetically / Formula: H12N6Os
#57: Chemical ChemComp-PAR / PAROMOMYCIN / PAROMOMYCIN I, AMMINOSIDIN, CATENULIN, CRESTOMYCIN, MONOMYCIN A, NEOMYCIN E / Paromomycin


Mass: 615.628 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H45N5O14 / Comment: Antimicrobial, medication*YM
#58: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

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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: 3.28 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 4% PEG20K, 4% PEGMME 550, 100mM Tris/HAc, 200mM KSCN, pH 7.5, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 11, 2011
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→300 Å / Num. all: 1164159 / Num. obs: 1161006 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 91.121 Å2 / Rmerge(I) obs: 0.412 / Net I/σ(I): 8.31
Reflection shell
Resolution (Å)Mean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
3-3.10.632385905107776199.5
3.1-3.20.92211684594829199.5
3.2-3.31.25184683683683199.5
3.3-3.41.63162948174332199.5
3.4-3.51.98146646566125199.6
3.5-3.62.49138959258964199.8
3.6-3.73.13124572452759199.6
3.7-3.83.79111557647452199.8
3.8-44.9188596881306199.7
4-59.135553533239291199.9
5-819.443588821912331100
8-1032.18903321305141100
10-5041.96902940324741100
50-30031.061541268185.1
1

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.11data extraction
RemDAqdata collection
PHENIXmodel building
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→152.636 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8315 / SU ML: 0.82 / σ(F): 1.34 / Phase error: 24.51 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2471 1507 0.17 %Random
Rwork0.1957 ---
obs0.1958 874628 99.79 %-
all-1164159 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.791 Å2 / ksol: 0.251 e/Å3
Displacement parametersBiso max: 262.18 Å2 / Biso mean: 94.5188 Å2 / Biso min: 16.2 Å2
Baniso -1Baniso -2Baniso -3
1--20.1571 Å20 Å20 Å2
2--8.5987 Å20 Å2
3---11.5584 Å2
Refinement stepCycle: LAST / Resolution: 3.3→152.636 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26679 65324 0 0 92003
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.021340259
X-RAY DIFFRACTIONf_angle_d1.015500511
X-RAY DIFFRACTIONf_chiral_restr0.08162167
X-RAY DIFFRACTIONf_plane_restr0.00626273
X-RAY DIFFRACTIONf_dihedral_angle_d20.02153358
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.3-3.40650.34741360.28757876178897
3.4065-3.52830.35871360.26697873878874
3.5283-3.66960.28031360.23497882478960
3.6696-3.83660.25031360.20417882978965
3.8366-4.03890.22711370.1887915079287
4.0389-4.29190.23821360.18037906579201
4.2919-4.62330.23351370.17347923579372
4.6233-5.08860.21711370.16137943679573
5.0886-5.8250.21241370.15787969279829
5.825-7.33890.24651380.17517997580113
7.3389-152.79920.2491410.22058141681557

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