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- PDB-4v9q: Crystal Structure of Blasticidin S Bound to Thermus Thermophilus ... -

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Basic information

Entry
Database: PDB / ID: 4v9q
TitleCrystal Structure of Blasticidin S Bound to Thermus Thermophilus 70S Ribosome.
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 28
  • 16S ribosomal RNA
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • mRNA
  • tRNA
KeywordsRIBOSOME / Translation termination / peptidyl transfer / ribosomal crystal structure / translation inhibitor / blasticidin S
Function / homology
Function and homology information


large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / ribosomal large subunit assembly / 5S rRNA binding / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding ...large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / ribosomal large subunit assembly / 5S rRNA binding / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / zinc ion binding / metal ion binding / cytoplasm / cytosol
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 ...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 L32p, bacterial type / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / : / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L9 / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L28 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L18, bacterial-type / Ribosomal protein S3, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / : / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein L6, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S4, bacterial-type / Ribosomal protein L5, bacterial-type / Ribosomal protein S5, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L20 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L14P, bacterial-type / Ribosomal protein S14/S29 / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 / Ribosomal protein S9, bacterial/plastid / Ribosomal L28 family / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein L33 superfamily / Ribosomal protein L16 / Ribosomal protein L28/L24 / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / Ribosomal protein L30, bacterial-type / Ribosomal protein S15, bacterial-type / L28p-like / : / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein S12, bacterial-type / Ribosomal protein L20 / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal L32p protein family / Ribosomal protein L21 / Ribosomal protein L19
Similarity search - Domain/homology
BLASTICIDIN S / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bTHX / Large ribosomal subunit protein bL32 ...BLASTICIDIN S / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bTHX / Large ribosomal subunit protein bL32 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL31 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL35
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
Escherichia coli (E. coli)
Synthetic DNA (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsSvidritskiy, E. / Ling, C. / Ermolenko, D.N. / Korostelev, A.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Blasticidin S inhibits translation by trapping deformed tRNA on the ribosome.
Authors: Svidritskiy, E. / Ling, C. / Ermolenko, D.N. / Korostelev, A.A.
History
DepositionJun 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2014Group: Structure summary
SupersessionDec 10, 2014ID: 4L6J, 4L6K, 4L6L, 4L6M
Revision 1.2Dec 10, 2014Group: Other
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_PDB_ins_code / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_PDB_ins_code / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_PDB_ins_code / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Revision 1.5Jan 14, 2026Group: Derived calculations / Structure summary
Category: ndb_struct_na_base_pair / ndb_struct_na_base_pair_step ...ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_modification_feature / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / struct_conf / struct_conn / struct_sheet_range
Item: _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id ..._pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_id / _struct_conf.pdbx_PDB_helix_length / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AA: 23S ribosomal RNA
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
AI: 50S ribosomal protein L9
AJ: 50S ribosomal protein L13
AK: 50S ribosomal protein L14
AL: 50S ribosomal protein L15
AM: 50S ribosomal protein L16
AN: 50S ribosomal protein L17
AO: 50S ribosomal protein L18
AP: 50S ribosomal protein L19
AQ: 50S ribosomal protein L20
AR: 50S ribosomal protein L21
AS: 50S ribosomal protein L22
AT: 50S ribosomal protein L23
AU: 50S ribosomal protein L24
AV: 50S ribosomal protein L25
AW: 50S ribosomal protein L27
AX: 50S ribosomal protein L28
AY: 50S ribosomal protein L29
AZ: 50S ribosomal protein L30
A1: 50S ribosomal protein L31
A2: 50S ribosomal protein L32
A3: 50S ribosomal protein L33
A4: 50S ribosomal protein L34
A5: 50S ribosomal protein L35
BA: 16S ribosomal RNA
BB: 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
BO: 30S ribosomal protein S15
BP: 30S ribosomal protein S16
BQ: 30S ribosomal protein S17
BR: 30S ribosomal protein S18
BS: 30S ribosomal protein S19
BT: 30S ribosomal protein S20
BU: 30S ribosomal protein Thx
BV: tRNA
BW: tRNA
BX: mRNA
CA: 23S ribosomal RNA
CB: 5S ribosomal RNA
CD: 50S ribosomal protein L2
CE: 50S ribosomal protein L3
CF: 50S ribosomal protein L4
CG: 50S ribosomal protein L5
CH: 50S ribosomal protein L6
CI: 50S ribosomal protein L9
CJ: 50S ribosomal protein L13
CK: 50S ribosomal protein L14
CL: 50S ribosomal protein L15
CM: 50S ribosomal protein L16
CN: 50S ribosomal protein L17
CO: 50S ribosomal protein L18
CP: 50S ribosomal protein L19
CQ: 50S ribosomal protein L20
CR: 50S ribosomal protein L21
CS: 50S ribosomal protein L22
CT: 50S ribosomal protein L23
CU: 50S ribosomal protein L24
CV: 50S ribosomal protein L25
CW: 50S ribosomal protein L27
CX: 50S ribosomal protein L28
CY: 50S ribosomal protein L29
CZ: 50S ribosomal protein L30
C1: 50S ribosomal protein L31
C2: 50S ribosomal protein L32
C3: 50S ribosomal protein L33
C4: 50S ribosomal protein L34
C5: 50S ribosomal protein L35
DA: 16S ribosomal RNA
DB: 30S ribosomal protein S2
DC: 30S ribosomal protein S3
DD: 30S ribosomal protein S4
DE: 30S ribosomal protein S5
DF: 30S ribosomal protein S6
DG: 30S ribosomal protein S7
DH: 30S ribosomal protein S8
DI: 30S ribosomal protein S9
DJ: 30S ribosomal protein S10
DK: 30S ribosomal protein S11
DL: 30S ribosomal protein S12
DM: 30S ribosomal protein S13
DN: 30S ribosomal protein S14
DO: 30S ribosomal protein S15
DP: 30S ribosomal protein S16
DQ: 30S ribosomal protein S17
DR: 30S ribosomal protein S18
DS: 30S ribosomal protein S19
DT: 30S ribosomal protein S20
DU: 30S ribosomal protein Thx
DV: tRNA
DW: tRNA
DX: mRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,417,6914477
Polymers4,310,542108
Non-polymers107,1494369
Water00
1
AA: 23S ribosomal RNA
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
AI: 50S ribosomal protein L9
AJ: 50S ribosomal protein L13
AK: 50S ribosomal protein L14
AL: 50S ribosomal protein L15
AM: 50S ribosomal protein L16
AN: 50S ribosomal protein L17
AO: 50S ribosomal protein L18
AP: 50S ribosomal protein L19
AQ: 50S ribosomal protein L20
AR: 50S ribosomal protein L21
AS: 50S ribosomal protein L22
AT: 50S ribosomal protein L23
AU: 50S ribosomal protein L24
AV: 50S ribosomal protein L25
AW: 50S ribosomal protein L27
AX: 50S ribosomal protein L28
AY: 50S ribosomal protein L29
AZ: 50S ribosomal protein L30
A1: 50S ribosomal protein L31
A2: 50S ribosomal protein L32
A3: 50S ribosomal protein L33
A4: 50S ribosomal protein L34
A5: 50S ribosomal protein L35
BA: 16S ribosomal RNA
BB: 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
BO: 30S ribosomal protein S15
BP: 30S ribosomal protein S16
BQ: 30S ribosomal protein S17
BR: 30S ribosomal protein S18
BS: 30S ribosomal protein S19
BT: 30S ribosomal protein S20
BU: 30S ribosomal protein Thx
BV: tRNA
BW: tRNA
BX: mRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,205,6492107
Polymers2,155,27154
Non-polymers50,3792053
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
CA: 23S ribosomal RNA
CB: 5S ribosomal RNA
CD: 50S ribosomal protein L2
CE: 50S ribosomal protein L3
CF: 50S ribosomal protein L4
CG: 50S ribosomal protein L5
CH: 50S ribosomal protein L6
CI: 50S ribosomal protein L9
CJ: 50S ribosomal protein L13
CK: 50S ribosomal protein L14
CL: 50S ribosomal protein L15
CM: 50S ribosomal protein L16
CN: 50S ribosomal protein L17
CO: 50S ribosomal protein L18
CP: 50S ribosomal protein L19
CQ: 50S ribosomal protein L20
CR: 50S ribosomal protein L21
CS: 50S ribosomal protein L22
CT: 50S ribosomal protein L23
CU: 50S ribosomal protein L24
CV: 50S ribosomal protein L25
CW: 50S ribosomal protein L27
CX: 50S ribosomal protein L28
CY: 50S ribosomal protein L29
CZ: 50S ribosomal protein L30
C1: 50S ribosomal protein L31
C2: 50S ribosomal protein L32
C3: 50S ribosomal protein L33
C4: 50S ribosomal protein L34
C5: 50S ribosomal protein L35
DA: 16S ribosomal RNA
DB: 30S ribosomal protein S2
DC: 30S ribosomal protein S3
DD: 30S ribosomal protein S4
DE: 30S ribosomal protein S5
DF: 30S ribosomal protein S6
DG: 30S ribosomal protein S7
DH: 30S ribosomal protein S8
DI: 30S ribosomal protein S9
DJ: 30S ribosomal protein S10
DK: 30S ribosomal protein S11
DL: 30S ribosomal protein S12
DM: 30S ribosomal protein S13
DN: 30S ribosomal protein S14
DO: 30S ribosomal protein S15
DP: 30S ribosomal protein S16
DQ: 30S ribosomal protein S17
DR: 30S ribosomal protein S18
DS: 30S ribosomal protein S19
DT: 30S ribosomal protein S20
DU: 30S ribosomal protein Thx
DV: tRNA
DW: tRNA
DX: mRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,212,0422370
Polymers2,155,27154
Non-polymers56,7712316
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)211.530, 454.440, 620.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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RNA chain , 5 types, 12 molecules AACAABCBBADABVBWDVDWBXDX

#1: RNA chain 23S ribosomal RNA


Mass: 936302.125 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: GenBank: AE017221.1
#2: RNA chain 5S ribosomal RNA


Mass: 38553.000 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: GenBank: AE017221.1
#31: RNA chain 16S ribosomal RNA


Mass: 488431.219 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: GenBank: AE017221.1
#52: RNA chain
tRNA


Mass: 24802.785 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#53: RNA chain mRNA


Mass: 1594.032 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: This sequence is an analogue of naturally occurring bacterial mRNA
Source: (synth.) Synthetic DNA (others)

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

#3: 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: HB27 / References: UniProt: Q72I07
#4: 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: HB27 / References: UniProt: Q72I04
#5: Protein 50S ribosomal protein L4


Mass: 22487.037 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: Q72I05
#6: Protein 50S ribosomal protein L5


Mass: 20944.428 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: Q72I16
#7: 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: HB27 / References: UniProt: Q72I19
#8: Protein 50S ribosomal protein L9


Mass: 16107.884 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: Q72GV5
#9: Protein 50S ribosomal protein L13


Mass: 15568.460 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: Q72IN1
#10: Protein 50S ribosomal protein L14


Mass: 13309.586 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: Q72I14
#11: 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: HB27 / References: UniProt: Q72I23
#12: Protein 50S ribosomal protein L16


Mass: 15148.842 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: Q72I11
#13: 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: HB27 / References: UniProt: Q72I33
#14: Protein 50S ribosomal protein L18


Mass: 10941.865 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: Q72I20
#15: Protein 50S ribosomal protein L19


Mass: 16247.915 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: Q72JU9
#16: Protein 50S ribosomal protein L20


Mass: 13648.081 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: Q72L76
#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: HB27 / References: UniProt: Q72HR2
#18: Protein 50S ribosomal protein L22


Mass: 12678.874 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: Q72I09
#19: 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: HB27 / References: UniProt: Q72I06
#20: 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: HB27 / References: UniProt: Q72I15
#21: Protein 50S ribosomal protein L25


Mass: 21021.145 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: Q72IA7
#22: Protein 50S ribosomal protein L27


Mass: 8587.940 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: Q72HR3
#23: Protein 50S ribosomal protein L28


Mass: 9884.680 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: Q72G84
#24: Protein 50S ribosomal protein L29


Mass: 7457.875 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: Q72I12
#25: 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: HB27 / References: UniProt: Q72I22
#26: 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: HB27 / References: UniProt: Q72JR0
#27: Protein 50S ribosomal protein L32


Mass: 5818.950 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62652
#28: 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: HB27 / References: UniProt: Q72GW3
#29: 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: HB27 / References: UniProt: P80340
#30: 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: HB27 / References: UniProt: Q72L77

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30S ribosomal protein ... , 20 types, 40 molecules BBDBBCDCBDDDBEDEBFDFBGDGBHDHBIDIBJDJBKDKBLDLBMDMBNDNBODOBPDP...

#32: 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: HB27 / References: UniProt: P62662
#33: Protein 30S ribosomal protein S3


Mass: 22862.430 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62663
#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: HB27 / References: UniProt: P62664
#35: Protein 30S ribosomal protein S5


Mass: 16460.193 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62665
#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: HB27 / References: UniProt: P62666
#37: 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: HB27 / References: UniProt: P62667
#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: HB27 / References: UniProt: P62668
#39: 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: HB27 / References: UniProt: P62669
#40: 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: HB27 / References: UniProt: P62653
#41: Protein 30S ribosomal protein S11


Mass: 12014.666 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62654
#42: Protein 30S ribosomal protein S12


Mass: 13604.119 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P61941
#43: Protein 30S ribosomal protein S13


Mass: 13308.508 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62655
#44: Protein 30S ribosomal protein S14


Mass: 7027.529 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62656
#45: 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: HB27 / References: UniProt: P62657
#46: 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: HB27 / References: UniProt: P62238
#47: Protein 30S ribosomal protein S17


Mass: 11721.919 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62658
#48: 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: HB27 / References: UniProt: P62659
#49: 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: HB27 / References: UniProt: P62660
#50: Protein 30S ribosomal protein S20


Mass: 10907.060 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62661
#51: Protein/peptide 30S ribosomal protein Thx


Mass: 2960.475 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62613

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Non-polymers , 3 types, 4369 molecules

#54: Chemical ChemComp-BLS / BLASTICIDIN S


Mass: 422.439 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H26N8O5 / Comment: antibiotic*YM
#55: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4363 / Source method: obtained synthetically / Formula: Mg
#56: Chemical
ChemComp-ZN / ZINC ION


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

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Details

Has protein modificationY

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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: 3.46 Å3/Da / Density % sol: 64.47 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Mix complex 1:1 with solution containing 4% PEG 20000, 8% MPD, 0.2M KSCN, 0.1M Tris-HCl , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 8, 2012
RadiationMonochromator: Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. all: 810608 / Num. obs: 810608 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3.4→50 Å / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.6.4_486)refinement
CNSrefinement
CBASSdata collection
XDSdata reduction
XSCALEdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4→49.981 Å / SU ML: 0.51 / σ(F): 1.99 / Phase error: 26.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.268 16210 2 %
Rwork0.2314 --
obs0.2321 810607 99.83 %
all-810608 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.314 Å2 / ksol: 0.284 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.1655 Å20 Å20 Å2
2---3.2449 Å20 Å2
3---0.0795 Å2
Refinement stepCycle: LAST / Resolution: 3.4→49.981 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26017 63546 4393 0 93956
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003314014
X-RAY DIFFRACTIONf_angle_d0.613470136
X-RAY DIFFRACTIONf_dihedral_angle_d18.973169548
X-RAY DIFFRACTIONf_chiral_restr0.05459626
X-RAY DIFFRACTIONf_plane_restr0.00325156
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.43860.39595120.352825397X-RAY DIFFRACTION96
3.4386-3.47910.35845390.338626334X-RAY DIFFRACTION100
3.4791-3.52150.34525450.325326363X-RAY DIFFRACTION100
3.5215-3.56610.37125390.329826291X-RAY DIFFRACTION100
3.5661-3.6130.37495340.32926367X-RAY DIFFRACTION100
3.613-3.66240.35765450.332226339X-RAY DIFFRACTION100
3.6624-3.71480.3315280.309326381X-RAY DIFFRACTION100
3.7148-3.77020.32325360.285226344X-RAY DIFFRACTION100
3.7702-3.82910.30825420.283526361X-RAY DIFFRACTION100
3.8291-3.89180.34625440.309926335X-RAY DIFFRACTION100
3.8918-3.95890.31955230.294126339X-RAY DIFFRACTION100
3.9589-4.03090.2735510.248826387X-RAY DIFFRACTION100
4.0309-4.10840.30235300.24826449X-RAY DIFFRACTION100
4.1084-4.19220.27515470.234426374X-RAY DIFFRACTION100
4.1922-4.28330.27325380.226126458X-RAY DIFFRACTION100
4.2833-4.38290.25335330.216526419X-RAY DIFFRACTION100
4.3829-4.49240.24965440.214826492X-RAY DIFFRACTION100
4.4924-4.61380.2575430.208126433X-RAY DIFFRACTION100
4.6138-4.74940.27455380.206526491X-RAY DIFFRACTION100
4.7494-4.90260.25435400.199226487X-RAY DIFFRACTION100
4.9026-5.07770.23035410.191226466X-RAY DIFFRACTION100
5.0777-5.28080.22445410.178726598X-RAY DIFFRACTION100
5.2808-5.52080.21655380.174326489X-RAY DIFFRACTION100
5.5208-5.81150.22035490.172826612X-RAY DIFFRACTION100
5.8115-6.1750.21715390.176326621X-RAY DIFFRACTION100
6.175-6.65070.23695410.178326673X-RAY DIFFRACTION100
6.6507-7.31820.21085470.170926752X-RAY DIFFRACTION100
7.3182-8.37280.20875500.184426809X-RAY DIFFRACTION100
8.3728-10.53270.23815500.216726996X-RAY DIFFRACTION100
10.5327-49.98670.26715630.253627540X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -60.5979 Å / Origin y: 46.6264 Å / Origin z: 70.6353 Å
111213212223313233
T0.0151 Å2-0.0032 Å2-0.079 Å2-0.0892 Å20.0222 Å2--0.0396 Å2
L0.0078 °20.02 °20.0237 °2-0.1328 °20.0983 °2--0.0715 °2
S0.0019 Å °-0.0199 Å °0.0099 Å °-0.049 Å °-0.0097 Å °0.0162 Å °-0.0603 Å °-0.0241 Å °0.0053 Å °
Refinement TLS groupSelection details: all

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