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- PDB-4wsm: Complex of 70S ribosome with tRNA-Leu and mRNA with G-U mismatch ... -

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Basic information

Entry
Database: PDB / ID: 4wsm
TitleComplex of 70S ribosome with tRNA-Leu and mRNA with G-U mismatch in the first position in the A- and P-sites
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 27
  • (tRNA-Leu) x 3
  • 16S ribosomal RNA
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • mRNA
KeywordsRIBOSOME / translation / mismatch
Function / homology
Function and homology information


large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit ...large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / 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 L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L28 / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L18, bacterial-type / : / Ribosomal protein L6, bacterial-type / Ribosomal protein S3, bacterial-type / Ribosomal protein S14/S29 / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein L5, bacterial-type / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / 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 L14P, bacterial-type / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal L28 family / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L16 / Ribosomal protein L28/L24 / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S16 / Ribosomal protein L30, bacterial-type / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / L28p-like / : / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein L27 / Ribosomal protein S6 superfamily / Ribosomal L27 protein / Ribosomal protein S12, bacterial-type / Ribosomal protein L20 / Ribosomal L32p protein family / Ribosomal protein L19 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein L21 / Ribosomal protein L32p / Large ribosomal subunit protein uL24, C-terminal domain / Ribosomal protein L17
Similarity search - Domain/homology
: / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 ...: / : / : / : / 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 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 K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsRozov, A. / Demeshkina, N. / Yusupov, M. / Yusupova, G.
CitationJournal: Nat Commun / Year: 2015
Title: Structural insights into the translational infidelity mechanism.
Authors: Rozov, A. / Demeshkina, N. / Westhof, E. / Yusupov, M. / Yusupova, G.
History
DepositionOct 28, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)4,555,4991448
Polymers4,522,683108
Non-polymers32,8151340
Water22,8251267
1
13: 16S ribosomal RNA
1E: 30S ribosomal protein S2
2E: 30S ribosomal protein S3
3E: 30S ribosomal protein S4
4E: 30S ribosomal protein S5
5E: 30S ribosomal protein S6
6E: 30S ribosomal protein S7
7E: 30S ribosomal protein S8
8E: 30S ribosomal protein S9
1I: 30S ribosomal protein S10
2I: 30S ribosomal protein S11
3I: 30S ribosomal protein S12
4I: 30S ribosomal protein S13
5I: 30S ribosomal protein S14 type Z
6I: 30S ribosomal protein S15
7I: 30S ribosomal protein S16
8I: 30S ribosomal protein S17
9I: 30S ribosomal protein S18
AI: 30S ribosomal protein S19
BI: 30S ribosomal protein S20
1F: 30S ribosomal protein Thx
1K: tRNA-Leu
2K: tRNA-Leu
3K: tRNA-Leu
4K: mRNA
1H: 23S ribosomal RNA
16: 5S ribosomal RNA
11: 50S ribosomal protein L2
21: 50S ribosomal protein L3
31: 50S ribosomal protein L4
41: 50S ribosomal protein L5
51: 50S ribosomal protein L6
61: 50S ribosomal protein L9
58: 50S ribosomal protein L13
68: 50S ribosomal protein L14
78: 50S ribosomal protein L15
88: 50S ribosomal protein L16
98: 50S ribosomal protein L17
A8: 50S ribosomal protein L18
B8: 50S ribosomal protein L19
C8: 50S ribosomal protein L20
D8: 50S ribosomal protein L21
E8: 50S ribosomal protein L22
F8: 50S ribosomal protein L23
G8: 50S ribosomal protein L24
H8: 50S ribosomal protein L25
I8: 50S ribosomal protein L27
J8: 50S ribosomal protein L28
K8: 50S ribosomal protein L29
L8: 50S ribosomal protein L30
M8: 50S ribosomal protein L31
N8: 50S ribosomal protein L32
P8: 50S ribosomal protein L34
Q8: 50S ribosomal protein L35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,278,187742
Polymers2,261,34254
Non-polymers16,845688
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
1G: 16S ribosomal RNA
12: 30S ribosomal protein S2
22: 30S ribosomal protein S3
32: 30S ribosomal protein S4
42: 30S ribosomal protein S5
52: 30S ribosomal protein S6
62: 30S ribosomal protein S7
72: 30S ribosomal protein S8
82: 30S ribosomal protein S9
1A: 30S ribosomal protein S10
2A: 30S ribosomal protein S11
3A: 30S ribosomal protein S12
4A: 30S ribosomal protein S13
5A: 30S ribosomal protein S14 type Z
6A: 30S ribosomal protein S15
7A: 30S ribosomal protein S16
8A: 30S ribosomal protein S17
9A: 30S ribosomal protein S18
AA: 30S ribosomal protein S19
BA: 30S ribosomal protein S20
1B: 30S ribosomal protein Thx
1L: tRNA-Leu
2L: tRNA-Leu
3L: tRNA-Leu
4L: mRNA
14: 23S ribosomal RNA
1J: 5S ribosomal RNA
19: 50S ribosomal protein L2
29: 50S ribosomal protein L3
39: 50S ribosomal protein L4
49: 50S ribosomal protein L5
59: 50S ribosomal protein L6
69: 50S ribosomal protein L9
15: 50S ribosomal protein L13
25: 50S ribosomal protein L14
35: 50S ribosomal protein L15
45: 50S ribosomal protein L16
55: 50S ribosomal protein L17
65: 50S ribosomal protein L18
75: 50S ribosomal protein L19
85: 50S ribosomal protein L20
95: 50S ribosomal protein L21
A5: 50S ribosomal protein L22
B5: 50S ribosomal protein L23
C5: 50S ribosomal protein L24
D5: 50S ribosomal protein L25
E5: 50S ribosomal protein L27
F5: 50S ribosomal protein L28
G5: 50S ribosomal protein L29
H5: 50S ribosomal protein L30
I5: 50S ribosomal protein L31
J5: 50S ribosomal protein L32
L5: 50S ribosomal protein L34
M5: 50S ribosomal protein L35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,277,312706
Polymers2,261,34254
Non-polymers15,970652
Water23413
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)209.500, 449.900, 618.700
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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RNA chain , 7 types, 14 molecules 131G1K1L2K2L3K3L4K4L1H14161J

#1: RNA chain 16S ribosomal RNA


Mass: 493958.281 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: 155076
#22: RNA chain tRNA-Leu


Mass: 28122.697 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: GenBank: 675819288
#23: RNA chain tRNA-Leu


Mass: 28138.738 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria)
#24: RNA chain tRNA-Leu


Mass: 28094.645 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: GenBank: 675819288
#25: RNA chain mRNA


Mass: 18627.367 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Thermus thermophilus (bacteria)
#26: RNA chain 23S ribosomal RNA


Mass: 948539.875 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: 48268
#27: 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 / ATCC 27634 / DSM 579 / References: GenBank: 55771382

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30S ribosomal protein ... , 20 types, 40 molecules 1E122E223E324E425E526E627E728E821I1A2I2A3I3A4I4A5I5A6I6A7I7A...

#2: 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 / ATCC 27634 / DSM 579 / References: UniProt: P80371
#3: 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 / ATCC 27634 / DSM 579 / References: UniProt: P80372
#4: Protein 30S ribosomal protein S4


Mass: 24373.447 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: 17583.416 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: 18050.973 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: A0A0M9AFS9*PLUS
#9: Protein 30S ribosomal protein S9


Mass: 14410.614 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80374
#10: 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 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHN7
#11: 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 / ATCC 27634 / DSM 579 / References: UniProt: P80376
#12: 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 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHN3
#13: 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 / ATCC 27634 / DSM 579 / References: UniProt: P80377
#14: Protein 30S ribosomal protein S14 type Z


Mass: 7158.725 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: A0A0N0BLP2*PLUS
#15: 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 / ATCC 27634 / DSM 579 / References: UniProt: Q5SJ76
#16: 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 / ATCC 27634 / DSM 579 / References: UniProt: Q5SJH3
#17: 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 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP7, UniProt: A0A0N0BLS5*PLUS
#18: 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 / ATCC 27634 / DSM 579 / References: UniProt: Q5SLQ0
#19: 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 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP2
#20: 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 / ATCC 27634 / DSM 579 / References: UniProt: P80380
#21: Protein/peptide 30S ribosomal protein Thx / S31


Mass: 3350.030 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

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50S ribosomal protein ... , 27 types, 54 molecules 11192129313941495159616958156825783588459855A865B875C885D895...

#28: 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 / ATCC 27634 / DSM 579 / References: UniProt: P60405
#29: 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 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHN8
#30: Protein 50S ribosomal protein L4 / L1e


Mass: 23271.914 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHN9
#31: 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 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ0
#32: 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 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ3, UniProt: P0DOY8*PLUS
#33: 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 / ATCC 27634 / DSM 579 / References: UniProt: Q5SLQ1
#34: 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 / ATCC 27634 / DSM 579 / References: UniProt: P60488
#35: 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
#36: 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 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ7
#37: 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
#38: 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 / ATCC 27634 / DSM 579 / References: UniProt: Q9Z9H5
#39: Protein 50S ribosomal protein L18 / TL24


Mass: 12639.845 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ4
#40: 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 / ATCC 27634 / DSM 579 / References: UniProt: P60490
#41: 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 / ATCC 27634 / DSM 579 / References: UniProt: P60491
#42: 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
#43: Protein 50S ribosomal protein L22


Mass: 12808.055 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP3
#44: 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 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP0
#45: 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 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP9
#46: Protein 50S ribosomal protein L25 / TL5


Mass: 23238.572 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHZ1
#47: Protein 50S ribosomal protein L27


Mass: 9557.126 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
#48: 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 / ATCC 27634 / DSM 579 / References: UniProt: P60494
#49: 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 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP6
#50: 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 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ6
#51: 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 / ATCC 27634 / DSM 579 / References: UniProt: Q5SJE1
#52: 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 / ATCC 27634 / DSM 579 / References: UniProt: P80339
#53: 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 / ATCC 27634 / DSM 579 / References: UniProt: P80340
#54: 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 / ATCC 27634 / DSM 579 / References: UniProt: Q5SKU1

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Non-polymers , 3 types, 2607 molecules

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


Mass: 24.305 Da / Num. of mol.: 1334 / Source method: obtained synthetically / Formula: Mg
#56: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 1267 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.22 Å3/Da / Density % sol: 61.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: Tris-acetate, KSCN, PEG 550MME, PEG 20K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→200 Å / Num. obs: 867119 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 58 % / Biso Wilson estimate: 98.404 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.537 / Rrim(I) all: 0.541 / Χ2: 0.605 / Net I/σ(I): 9.1 / Num. measured all: 50295385
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
3.3-3.40.4835.0011.51390816473863738355.049100
3.4-3.50.5764.281.82351617765661656424.32100
3.5-3.60.6533.5962.2311580058590585653.631100
3.6-3.70.7492.9392.72276041252449524342.967100
3.7-3.80.8142.4663.31246051347100470742.4999.9
3.8-3.90.8622.2133.85215573442401423712.23599.9
3.9-40.891.8534.36183834038284382431.87399.9
4-50.971.0487.66132101262372852371621.05799.9
5-60.9910.59713.7169445521053211052690.602100
6-7.50.9960.42918.39514560470943709220.432100
7.5-100.9980.2226.22304332643343433350.222100
10-200.9990.11336.34192709228153281510.114100
20-500.9990.08743.98265218398539290.08798.6
50-1000.9970.13324.3342542701760.13665.2
1000.930.13612.837346110.14723.9

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TVE, 3TVF

3tve
PDB Unreleased entry

3tvf
PDB Unreleased entry


Resolution: 3.3→153.31 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rwork0.1853 --
obs0.2313 866987 100 %
Refinement stepCycle: LAST / Resolution: 3.3→153.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms90183 206640 2607 0 299430

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