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- PDB-4wt8: Crystal Structure of bactobolin A bound to 70S ribosome-tRNA complex -

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Basic information

Entry
Database: PDB / ID: 4wt8
TitleCrystal Structure of bactobolin A bound to 70S ribosome-tRNA complex
Components
  • (30S ribosomal protein ...) x 21
  • (50S ribosomal protein ...) x 32
  • (mRNA) x 2
  • 23S rRNA (2899-MER)
  • 5S rRNA (119-MER)
  • A site tNA, E site tNA
  • DNA (55-MER)
  • P site trNA
  • RNA (1504-MER)
  • ribosomal L10 protein
  • tRNA (5'-D(*AP*UP*CP*CP*CP*CP*GP*UP*GP*UP*CP*CP*UP*UP*GP*GP*UP*UP*CP*G)-3')
  • tRNA (76-MER)
KeywordsRIBOSOME
Function / homology
Function and homology information


large ribosomal subunit / regulation of translation / ribosomal small subunit assembly / large ribosomal subunit rRNA binding / small ribosomal subunit / 5S rRNA binding / transferase activity / cytosolic small ribosomal subunit / ribosomal large subunit assembly / cytosolic large ribosomal subunit ...large ribosomal subunit / regulation of translation / ribosomal small subunit assembly / large ribosomal subunit rRNA binding / small ribosomal subunit / 5S rRNA binding / transferase activity / cytosolic small ribosomal subunit / ribosomal large subunit assembly / cytosolic large ribosomal subunit / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / zinc ion binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L1, bacterial-type / 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 L1, bacterial-type / 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 L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1 / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / 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 L36 signature. / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L32p, bacterial type / 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 L18, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein S14/S29 / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein S3, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein L20 signature. / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 superfamily / Ribosomal protein L30, bacterial-type / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein L16 / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / : / L28p-like / Ribosomal protein L20
Similarity search - Domain/homology
Bactobolin A / PAROMOMYCIN / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 ...Bactobolin A / PAROMOMYCIN / : / : / 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 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 / Small ribosomal subunit protein uS9 / 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 bL36 / 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 / Large ribosomal subunit protein uL1 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS18 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL17
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.4 Å
AuthorsAmunts, A. / Fiedorczuk, K. / Ramakrishnan, V.
CitationJournal: J.Mol.Biol. / Year: 2015
Title: Bactobolin A Binds to a Site on the 70S Ribosome Distinct from Previously Seen Antibiotics.
Authors: Amunts, A. / Fiedorczuk, K. / Truong, T.T. / Chandler, J. / Peter Greenberg, E. / Ramakrishnan, V.
History
DepositionOct 29, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 18, 2015Group: Database references
SupersessionAug 19, 2015ID: 4wus, 4wwe, 4wwt
Revision 1.2Aug 19, 2015Group: Other
Revision 1.3Jul 18, 2018Group: Advisory / Data collection / Derived calculations
Category: database_PDB_caveat / diffrn_radiation_wavelength ...database_PDB_caveat / diffrn_radiation_wavelength / pdbx_validate_close_contact / struct_conn / struct_conn_type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A2: mRNA
AA: 30S ribosomal protein S2
AC: 30S ribosomal protein S3
AD: 30S ribosomal protein S4
AE: 30S ribosomal protein S5
AF: 30S ribosomal protein S6
AG: 30S ribosomal protein S7
AH: 30S ribosomal protein S8
AI: 30S ribosomal protein S9
AJ: 30S ribosomal protein S10
AK: 30S ribosomal protein S11
AL: 30S ribosomal protein S12
AM: 30S ribosomal protein S13
AN: 30S ribosomal protein S14 type Z
AO: 30S ribosomal protein S15
AP: 30S ribosomal protein S16
AR: 30S ribosomal protein S17
AS: 30S ribosomal protein S18
AT: 30S ribosomal protein S19
AU: 30S ribosomal protein S20
AW: 30S ribosomal protein Thx
Ab: RNA (1504-MER)
B2: mRNA
Bb: RNA (1504-MER)
BA: 30S ribosomal protein S2
BC: 30S ribosomal protein S3
BD: 30S ribosomal protein S4
BE: 30S ribosomal protein S5
BF: 30S ribosomal protein S6
BG: 30S ribosomal protein S7
BH: 30S ribosomal protein S8
BI: 30S ribosomal protein S9
BJ: 30S ribosomal protein S10
BK: 30S ribosomal protein S11
BL: 30S ribosomal protein S12
BM: 30S ribosomal protein S13
BN: 30S ribosomal protein S14 type Z
BO: 30S ribosomal protein S15
BP: 30S ribosomal protein S16
BR: 30S ribosomal protein S17
BS: 30S ribosomal protein S18
BT: 30S ribosomal protein S19
BU: 30S ribosomal protein S20
BW: 30S ribosomal protein Thx
C2: A site tNA, E site tNA
C3: A site tNA, E site tNA
C4: P site trNA
CA: 50S ribosomal protein L1
CB: 50S ribosomal protein L2
CC: 50S ribosomal protein L3
CD: 50S ribosomal protein L4
CE: 50S ribosomal protein L5
CF: 50S ribosomal protein L6
CI: 50S ribosomal protein L9
CJ: ribosomal L10 protein
CM: 50S ribosomal protein L13
CN: 50S ribosomal protein L14
CO: 50S ribosomal protein L15
CP: 50S ribosomal protein L16
CQ: 50S ribosomal protein L17
CR: 50S ribosomal protein L18
CS: 50S ribosomal protein L19
CT: 50S ribosomal protein L20
CU: 50S ribosomal protein L21
CW: 50S ribosomal protein L22
CX: 50S ribosomal protein L23
CY: 50S ribosomal protein L24
CZ: 50S ribosomal protein L25
Ca: 50S ribosomal protein L27
CH: 50S ribosomal protein L28
CK: 50S ribosomal protein L29
CL: 50S ribosomal protein L30
C5: 50S ribosomal protein L31
C6: 50S ribosomal protein L32
C7: 50S ribosomal protein L33
C8: 50S ribosomal protein L34
C9: 50S ribosomal protein L35
C0: 50S ribosomal protein L36
C1: 23S rRNA (2899-MER)
Cs: 5S rRNA (119-MER)
D2: tRNA (5'-D(*AP*UP*CP*CP*CP*CP*GP*UP*GP*UP*CP*CP*UP*UP*GP*GP*UP*UP*CP*G)-3')
D3: A site tNA, E site tNA
D4: tRNA (76-MER)
DA: 50S ribosomal protein L1
DB: 50S ribosomal protein L2
DC: 50S ribosomal protein L3
DD: 50S ribosomal protein L4
DE: 50S ribosomal protein L5
DF: 50S ribosomal protein L6
DI: 50S ribosomal protein L9
DJ: ribosomal L10 protein
DM: 50S ribosomal protein L13
DN: 50S ribosomal protein L14
DO: 50S ribosomal protein L15
DP: 50S ribosomal protein L16
DQ: 50S ribosomal protein L17
DR: 50S ribosomal protein L18
DS: 50S ribosomal protein L19
DT: 50S ribosomal protein L20
DU: 50S ribosomal protein L21
DW: 50S ribosomal protein L22
DX: 50S ribosomal protein L23
DY: 50S ribosomal protein L24
DZ: 50S ribosomal protein L25
Da: 50S ribosomal protein L27
DH: 50S ribosomal protein L28
DK: 50S ribosomal protein L29
DL: 50S ribosomal protein L30
D5: 50S ribosomal protein L31
D6: 50S ribosomal protein L32
D7: 50S ribosomal protein L33
D8: 50S ribosomal protein L34
D9: 50S ribosomal protein L35
D0: 50S ribosomal protein L36
Ds: 5S rRNA (119-MER)
D1: 23S rRNA (2899-MER)
DV: DNA (55-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,460,697123
Polymers4,458,655117
Non-polymers2,0426
Water00
1
A2: mRNA
AA: 30S ribosomal protein S2
AC: 30S ribosomal protein S3
AE: 30S ribosomal protein S5
AF: 30S ribosomal protein S6
AG: 30S ribosomal protein S7
AH: 30S ribosomal protein S8
AI: 30S ribosomal protein S9
AJ: 30S ribosomal protein S10
AK: 30S ribosomal protein S11
AL: 30S ribosomal protein S12
AM: 30S ribosomal protein S13
AN: 30S ribosomal protein S14 type Z
AO: 30S ribosomal protein S15
AP: 30S ribosomal protein S16
AR: 30S ribosomal protein S17
AS: 30S ribosomal protein S18
AT: 30S ribosomal protein S19
AU: 30S ribosomal protein S20
AW: 30S ribosomal protein Thx
Ab: RNA (1504-MER)
C2: A site tNA, E site tNA
C3: A site tNA, E site tNA
C4: P site trNA
CA: 50S ribosomal protein L1
CB: 50S ribosomal protein L2
CC: 50S ribosomal protein L3
CD: 50S ribosomal protein L4
CE: 50S ribosomal protein L5
CF: 50S ribosomal protein L6
CI: 50S ribosomal protein L9
CJ: ribosomal L10 protein
CM: 50S ribosomal protein L13
CN: 50S ribosomal protein L14
CO: 50S ribosomal protein L15
CP: 50S ribosomal protein L16
CQ: 50S ribosomal protein L17
CR: 50S ribosomal protein L18
CS: 50S ribosomal protein L19
CT: 50S ribosomal protein L20
CU: 50S ribosomal protein L21
CW: 50S ribosomal protein L22
CX: 50S ribosomal protein L23
CY: 50S ribosomal protein L24
CZ: 50S ribosomal protein L25
Ca: 50S ribosomal protein L27
CH: 50S ribosomal protein L28
CK: 50S ribosomal protein L29
CL: 50S ribosomal protein L30
C5: 50S ribosomal protein L31
C6: 50S ribosomal protein L32
C7: 50S ribosomal protein L33
C8: 50S ribosomal protein L34
C9: 50S ribosomal protein L35
C0: 50S ribosomal protein L36
C1: 23S rRNA (2899-MER)
Cs: 5S rRNA (119-MER)
DI: 50S ribosomal protein L9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,224,29161
Polymers2,223,27058
Non-polymers1,0213
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
AD: 30S ribosomal protein S4
B2: mRNA
Bb: RNA (1504-MER)
BA: 30S ribosomal protein S2
BC: 30S ribosomal protein S3
BD: 30S ribosomal protein S4
BE: 30S ribosomal protein S5
BF: 30S ribosomal protein S6
BG: 30S ribosomal protein S7
BH: 30S ribosomal protein S8
BI: 30S ribosomal protein S9
BJ: 30S ribosomal protein S10
BK: 30S ribosomal protein S11
BL: 30S ribosomal protein S12
BM: 30S ribosomal protein S13
BN: 30S ribosomal protein S14 type Z
BO: 30S ribosomal protein S15
BP: 30S ribosomal protein S16
BR: 30S ribosomal protein S17
BS: 30S ribosomal protein S18
BT: 30S ribosomal protein S19
BU: 30S ribosomal protein S20
BW: 30S ribosomal protein Thx
D2: tRNA (5'-D(*AP*UP*CP*CP*CP*CP*GP*UP*GP*UP*CP*CP*UP*UP*GP*GP*UP*UP*CP*G)-3')
D3: A site tNA, E site tNA
D4: tRNA (76-MER)
DA: 50S ribosomal protein L1
DB: 50S ribosomal protein L2
DC: 50S ribosomal protein L3
DD: 50S ribosomal protein L4
DE: 50S ribosomal protein L5
DF: 50S ribosomal protein L6
DJ: ribosomal L10 protein
DM: 50S ribosomal protein L13
DN: 50S ribosomal protein L14
DO: 50S ribosomal protein L15
DP: 50S ribosomal protein L16
DQ: 50S ribosomal protein L17
DR: 50S ribosomal protein L18
DS: 50S ribosomal protein L19
DT: 50S ribosomal protein L20
DU: 50S ribosomal protein L21
DW: 50S ribosomal protein L22
DX: 50S ribosomal protein L23
DY: 50S ribosomal protein L24
DZ: 50S ribosomal protein L25
Da: 50S ribosomal protein L27
DH: 50S ribosomal protein L28
DK: 50S ribosomal protein L29
DL: 50S ribosomal protein L30
D5: 50S ribosomal protein L31
D6: 50S ribosomal protein L32
D7: 50S ribosomal protein L33
D8: 50S ribosomal protein L34
D9: 50S ribosomal protein L35
D0: 50S ribosomal protein L36
Ds: 5S rRNA (119-MER)
D1: 23S rRNA (2899-MER)
DV: DNA (55-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,236,40662
Polymers2,235,38559
Non-polymers1,0213
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)214.210, 457.450, 639.660
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

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Components

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RNA chain , 10 types, 15 molecules A2AbBbB2C2C3D3C4C1D1CsDsD2D4DV

#1: RNA chain mRNA


Mass: 2840.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579
#22: RNA chain RNA (1504-MER)


Mass: 488391.188 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: GenBank: 55771382, GenBank: 155076
#23: RNA chain mRNA


Mass: 3169.956 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579
#25: RNA chain A site tNA, E site tNA


Mass: 24485.539 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579
#26: RNA chain P site trNA


Mass: 24802.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579
#58: RNA chain 23S rRNA (2899-MER)


Mass: 942978.375 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579
#59: RNA chain 5S rRNA (119-MER)


Mass: 38553.000 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: GenBank: 55771382
#60: RNA chain tRNA (5'-D(*AP*UP*CP*CP*CP*CP*GP*UP*GP*UP*CP*CP*UP*UP*GP*GP*UP*UP*CP*G)-3')


Mass: 6289.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579
#61: RNA chain tRNA (76-MER)


Mass: 24497.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579
#64: RNA chain DNA (55-MER)


Mass: 17821.662 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579

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30S ribosomal protein ... , 21 types, 40 molecules AABAACADBDAEBEAFBFAGBGAHBHAIBIAJBJAKBKALBLAMBMANBNAOBOAPBPAR...

#2: Protein 30S ribosomal protein S2


Mass: 26987.271 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80371
#3: Protein 30S ribosomal protein S3


Mass: 26621.963 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80372
#4: 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 / ATCC 27634 / DSM 579 / References: UniProt: P80373
#5: Protein 30S ribosomal protein S5


Mass: 16331.079 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ5
#6: 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 (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SLP8
#7: Protein 30S ribosomal protein S7


Mass: 17919.775 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P17291
#8: 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 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ2, UniProt: P0DOY9*PLUS
#9: Protein 30S ribosomal protein S9


Mass: 14298.466 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80374, UniProt: P62669
#10: Protein 30S ribosomal protein S10


Mass: 11299.176 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHN7
#11: Protein 30S ribosomal protein S11


Mass: 12606.369 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80376
#12: Protein 30S ribosomal protein S12


Mass: 13804.311 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHN3
#13: Protein 30S ribosomal protein S13


Mass: 14078.486 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80377
#14: Protein 30S ribosomal protein S14 type Z


Mass: 7027.529 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ1, UniProt: P0DOY6*PLUS
#15: Protein 30S ribosomal protein S15


Mass: 10447.213 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SJ76
#16: Protein 30S ribosomal protein S16


Mass: 9924.469 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SJH3
#17: Protein 30S ribosomal protein S17


Mass: 11722.904 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP7, UniProt: P0DOY7*PLUS
#18: Protein 30S ribosomal protein S18


Mass: 8155.812 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SLQ0
#19: Protein 30S ribosomal protein S19


Mass: 8949.435 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP2
#20: Protein 30S ribosomal protein S20


Mass: 10921.086 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80380
#21: Protein/peptide 30S ribosomal protein Thx / S31


Mass: 2960.475 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SIH3
#24: Protein 30S ribosomal protein S3


Mass: 22862.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80372

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50S ribosomal protein ... , 32 types, 60 molecules CACBDBCCDCCDDDCEDECFDFCIDICMDMCNDNCODOCPDPCQDQCRDRCSDSCTDTCU...

#27: Protein 50S ribosomal protein L1


Mass: 19880.480 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SLP7
#28: Protein 50S ribosomal protein L2


Mass: 29828.604 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P60405
#29: Protein 50S ribosomal protein L3


Mass: 22249.953 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHN8
#30: Protein 50S ribosomal protein L4 / L1e


Mass: 23014.670 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHN9
#31: Protein 50S ribosomal protein L5


Mass: 20930.400 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ0
#32: Protein 50S ribosomal protein L6


Mass: 17363.119 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ3, UniProt: P0DOY8*PLUS
#33: Protein 50S ribosomal protein L9


Mass: 16093.858 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SLQ1
#35: Protein 50S ribosomal protein L13


Mass: 15699.658 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P60488
#36: 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 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP8
#37: Protein 50S ribosomal protein L15


Mass: 15858.526 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ7
#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 (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P60489
#39: Protein 50S ribosomal protein L17


Mass: 13618.952 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q9Z9H5, UniProt: Q72I33
#40: Protein 50S ribosomal protein L18 / TL24


Mass: 10941.865 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ4
#41: Protein 50S ribosomal protein L19


Mass: 16218.812 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P60490
#42: Protein 50S ribosomal protein L20


Mass: 13571.984 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P60491
#43: 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 / ATCC 27634 / DSM 579 / References: UniProt: P60492
#44: Protein 50S ribosomal protein L22


Mass: 12808.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP3
#45: Protein 50S ribosomal protein L23


Mass: 10273.117 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP0
#46: Protein 50S ribosomal protein L24


Mass: 11078.515 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP9
#47: Protein 50S ribosomal protein L25 / TL5


Mass: 19892.930 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHZ1
#48: Protein 50S ribosomal protein L27


Mass: 9397.878 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P60493
#49: Protein 50S ribosomal protein L28


Mass: 10458.404 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HBB / ATCC 27634 / DSM 579 / References: UniProt: Q72G84, UniProt: P60494
#50: Protein 50S ribosomal protein L29


Mass: 8539.062 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP6
#51: Protein 50S ribosomal protein L30


Mass: 6670.013 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ6
#52: Protein/peptide 50S ribosomal protein L31


Mass: 3278.860 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SJE1
#53: Protein 50S ribosomal protein L32


Mass: 6590.854 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80339
#54: Protein/peptide 50S ribosomal protein L33


Mass: 5473.432 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P35871
#55: Protein/peptide 50S ribosomal protein L34


Mass: 5975.255 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80340
#56: Protein 50S ribosomal protein L35


Mass: 7245.867 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SKU1
#57: Protein/peptide 50S ribosomal protein L36 / Ribosomal protein B


Mass: 4304.215 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHR2
#62: Protein 50S ribosomal protein L1


Mass: 19866.455 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SLP7
#63: Protein 50S ribosomal protein L22


Mass: 12749.952 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP3

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Protein , 1 types, 2 molecules CJDJ

#34: Protein ribosomal L10 protein


Mass: 11081.651 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579

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Non-polymers , 3 types, 6 molecules

#65: Chemical ChemComp-PAR / PAROMOMYCIN / PAROMOMYCIN I, AMMINOSIDIN, CATENULIN, CRESTOMYCIN, MONOMYCIN A, NEOMYCIN E


Mass: 615.628 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H45N5O14 / Comment: Antimicrobial, medication*YM
#66: Chemical ChemComp-3V6 / Bactobolin A


Mass: 381.252 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22Cl2N2O5
#67: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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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: 3.51 Å3/Da / Density % sol: 65 %
Crystal growTemperature: 293 K / Method: evaporation
Details: 0.2M KSCN, 0.1M Tris-HAc pH7, 3.5-4.5%(w/v) PEG20K, 3.5- 4.5%(w/v) PEG550MME

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.4→49.908 Å / Num. all: 841002 / Num. obs: 841002 / % possible obs: 98.8 % / Redundancy: 6.8 % / Rpim(I) all: 0.112 / Rrim(I) all: 0.298 / Rsym value: 0.275 / Net I/av σ(I): 1.87 / Net I/σ(I): 8.6 / Num. measured all: 5690971
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
3.4-3.5851.3020.56102571211520.6081.3021.497.9
3.58-3.85.20.8660.86082611161680.4010.8662.199.2
3.8-4.065.60.5811.26083271087420.2610.5813.398.7
4.06-4.396.30.4191.66468091023340.1760.4194.999.6
4.39-4.816.80.3051.9644077942250.1220.3057.299.6
4.81-5.3880.2312.3672041842890.0850.23110.398.4
5.38-6.218.60.1922.5645304751650.0670.19213.299.3
6.21-7.69.10.1692.5570442630070.0580.16916.298.2
7.6-10.759.10.1282.8446640490670.0440.1282498.3
10.75-49.9088.90.0813.8238813268530.0280.08144.896.3

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Processing

Software
NameVersionClassificationNB
SCALA3.3.21data scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
RefinementResolution: 3.4→49.908 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.883 / SU B: 29.772 / SU ML: 0.449 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.51 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2412 41975 5 %RANDOM
Rwork0.2044 798407 --
obs0.2062 841002 98.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 364.23 Å2 / Biso mean: 80.037 Å2 / Biso min: 24.5 Å2
Baniso -1Baniso -2Baniso -3
1--2.93 Å2-0 Å2-0 Å2
2--0.16 Å2-0 Å2
3---2.77 Å2
Refinement stepCycle: final / Resolution: 3.4→49.908 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19157 32502 42 0 51701
Biso mean--65.7 --
Num. residues----3898
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.014321484
X-RAY DIFFRACTIONr_bond_other_d0.0020.02191481
X-RAY DIFFRACTIONr_angle_refined_deg1.6151.462480795
X-RAY DIFFRACTIONr_angle_other_deg1.283450224
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.382512004
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.22821.2734148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.4991518136
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.948151332
X-RAY DIFFRACTIONr_chiral_restr0.1480.251709
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02221528
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0274196
X-RAY DIFFRACTIONr_mcbond_it7.6059.1948352
X-RAY DIFFRACTIONr_mcbond_other7.6059.1948352
X-RAY DIFFRACTIONr_mcangle_it12.44613.74460244
LS refinement shellResolution: 3.4→3.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 2938 -
Rwork0.334 57594 -
all-60532 -
obs--97.04 %

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