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- PDB-5e81: Structure of T. thermophilus 70S ribosome complex with mRNA and t... -

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Basic information

Entry
Database: PDB / ID: 5.0E+81
TitleStructure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with wobble pair
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 28
  • (tRNA-Lys) x 2
  • 16S ribosomal RNA
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • mRNA
  • tRNA-fMet
KeywordsRIBOSOME / translation / mismatch
Function / homology
Function and homology information


large ribosomal subunit / regulation of translation / 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 ...large ribosomal subunit / regulation of translation / 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 L1, bacterial-type / 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 ...30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein / Ribosomal protein L1, bacterial-type / 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 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
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS14 ...IRON/SULFUR CLUSTER / : / : / : / : / 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 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 uS12 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bTHX / 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 bS18 / Small ribosomal subunit protein uS19 / 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 / 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 / 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 / Large ribosomal subunit protein uL1 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS18 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein uL1 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL24 / 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 bL20 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL17
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsRozov, A. / Demeshkina, N. / Khusainov, I. / Yusupov, M. / Yusupova, G.
CitationJournal: Nat Commun / Year: 2016
Title: Novel base-pairing interactions at the tRNA wobble position crucial for accurate reading of the genetic code.
Authors: Rozov, A. / Demeshkina, N. / Khusainov, I. / Westhof, E. / Yusupov, M. / Yusupova, G.
History
DepositionOct 13, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2016Group: Database references / Structure summary
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.ptnr1_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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.ptnr2_symmetry / _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-Lys
2K: tRNA-fMet
3K: tRNA-Lys
4K: mRNA
1H: 23S ribosomal RNA
16: 5S ribosomal RNA
71: 50S ribosomal protein L1
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-Lys
2L: tRNA-fMet
3L: tRNA-Lys
4L: mRNA
14: 23S ribosomal RNA
1J: 5S ribosomal RNA
79: 50S ribosomal protein L1
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
J5: 50S ribosomal protein L32
L5: 50S ribosomal protein L34
M5: 50S ribosomal protein L35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,556,8321518
Polymers4,521,767109
Non-polymers35,0651409
Water67,0523722
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-Lys
2K: tRNA-fMet
3K: tRNA-Lys
4K: mRNA
1H: 23S ribosomal RNA
16: 5S ribosomal RNA
71: 50S ribosomal protein L1
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)2,284,280830
Polymers2,265,03455
Non-polymers19,246775
Water64936
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-Lys
2L: tRNA-fMet
3L: tRNA-Lys
4L: mRNA
14: 23S ribosomal RNA
1J: 5S ribosomal RNA
79: 50S ribosomal protein L1
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
J5: 50S ribosomal protein L32
L5: 50S ribosomal protein L34
M5: 50S ribosomal protein L35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,272,552688
Polymers2,256,73354
Non-polymers15,819634
Water57632
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)209.200, 448.500, 619.900
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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RNA chain , 7 types, 14 molecules 131G1K1L2K2L3K3L4K4L1H14161J

#1: RNA chain 16S ribosomal RNA


Mass: 493040.781 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: GenBank: 155076
#22: RNA chain tRNA-Lys


Mass: 24612.725 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 821329311
#23: RNA chain tRNA-fMet


Mass: 24860.953 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria)
#24: RNA chain tRNA-Lys


Mass: 24378.408 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria)
#25: RNA chain mRNA


Mass: 8901.496 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#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 HB8 (bacteria) / References: GenBank: 55771382
#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 HB8 (bacteria) / References: GenBank: 46197919

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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 HB8 (bacteria) / References: UniProt: P62662, UniProt: P80371*PLUS
#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 HB8 (bacteria) / References: UniProt: P62663, UniProt: P80372*PLUS
#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 HB8 (bacteria) / References: UniProt: P62664, UniProt: P80373*PLUS
#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 HB8 (bacteria) / References: UniProt: P62665, UniProt: Q5SHQ5*PLUS
#6: Protein 30S ribosomal protein S6


Mass: 11988.753 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P62666, UniProt: Q5SLP8*PLUS
#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 HB8 (bacteria) / References: UniProt: P62667, UniProt: P17291*PLUS
#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 HB8 (bacteria) / References: UniProt: P62668, UniProt: P0DOY9*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 HB8 (bacteria) / 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 HB8 (bacteria) / References: UniProt: P62653, UniProt: Q5SHN7*PLUS
#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 HB8 (bacteria) / References: UniProt: P62654, UniProt: P80376*PLUS
#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 HB8 (bacteria) / References: UniProt: P61941, UniProt: Q5SHN3*PLUS
#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 HB8 (bacteria) / References: UniProt: P62655, UniProt: P80377*PLUS
#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 HB8 (bacteria) / References: UniProt: P62656, UniProt: P0DOY6*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 HB8 (bacteria) / References: UniProt: P62657, UniProt: Q5SJ76*PLUS
#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 HB8 (bacteria) / References: UniProt: P62238, UniProt: Q5SJH3*PLUS
#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 HB8 (bacteria) / References: UniProt: Q5SHP7, UniProt: P0DOY7*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 HB8 (bacteria) / References: UniProt: P62659, UniProt: Q5SLQ0*PLUS
#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 HB8 (bacteria) / References: UniProt: P62660, UniProt: Q5SHP2*PLUS
#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 HB8 (bacteria) / References: UniProt: P80380
#21: Protein/peptide 30S ribosomal protein Thx


Mass: 3350.030 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P62612, UniProt: Q5SIH3*PLUS

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50S ribosomal protein ... , 28 types, 55 molecules 717911192129313941495159616958156825783588459855A865B875C885...

#28: Protein 50S ribosomal protein L1


Mass: 24867.699 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q72GV9, UniProt: Q5SLP7*PLUS
#29: Protein 50S ribosomal protein L2


Mass: 30532.551 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q72I07, UniProt: P60405*PLUS
#30: Protein 50S ribosomal protein L3


Mass: 22450.213 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q72I04, UniProt: Q5SHN8*PLUS
#31: 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 HB8 (bacteria) / References: UniProt: Q5SHN9
#32: Protein 50S ribosomal protein L5


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


Mass: 19568.926 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q72I19, UniProt: P0DOY8*PLUS
#34: Protein 50S ribosomal protein L9


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


Mass: 15927.903 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q72IN1, UniProt: P60488*PLUS
#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 HB8 (bacteria) / References: UniProt: Q5SHP8
#37: Protein 50S ribosomal protein L15


Mass: 16319.142 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q72I23, UniProt: Q5SHQ7*PLUS
#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 HB8 (bacteria) / References: UniProt: P60489
#39: Protein 50S ribosomal protein L17


Mass: 13750.148 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q72I33, UniProt: Q9Z9H5*PLUS
#40: Protein 50S ribosomal protein L18


Mass: 12639.845 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q72I20, UniProt: Q5SHQ4*PLUS
#41: Protein 50S ribosomal protein L19


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


Mass: 13779.275 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q72L76, UniProt: P60491*PLUS
#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 HB8 (bacteria) / References: UniProt: Q72HR2, UniProt: P60492*PLUS
#44: Protein 50S ribosomal protein L22


Mass: 12808.055 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q72I09, UniProt: Q5SHP3*PLUS
#45: Protein 50S ribosomal protein L23


Mass: 10759.808 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q72I06, UniProt: Q5SHP0*PLUS
#46: Protein 50S ribosomal protein L24


Mass: 12085.611 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q72I15, UniProt: Q5SHP9*PLUS
#47: Protein 50S ribosomal protein L25 / General stress protein CTC


Mass: 23238.572 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q72IA7, UniProt: Q5SHZ1*PLUS
#48: Protein 50S ribosomal protein L27


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


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


Mass: 8670.258 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q72I12, UniProt: Q5SHP6*PLUS
#51: Protein 50S ribosomal protein L30


Mass: 6799.126 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q72I22, UniProt: Q5SHQ6*PLUS
#52: Protein 50S ribosomal protein L31


Mass: 8300.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q72JR0, UniProt: Q5SJE1*PLUS
#53: Protein 50S ribosomal protein L32


Mass: 6722.050 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P80339
#54: 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 HB8 (bacteria) / References: UniProt: P80340
#55: Protein 50S ribosomal protein L35


Mass: 7506.178 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q72L77, UniProt: Q5SKU1*PLUS

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Non-polymers , 4 types, 5131 molecules

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


Mass: 24.305 Da / Num. of mol.: 1403 / Source method: obtained synthetically / Formula: Mg
#57: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#58: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#59: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3722 / 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: 3.21 Å3/Da / Density % sol: 61.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 20000, PEG 550mme, KSCN, Tris-OAc / PH range: 7.5

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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 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.95→170 Å / Num. obs: 1208590 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 55.9 % / Biso Wilson estimate: 86.5 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.319 / Rrim(I) all: 0.322 / Χ2: 0.986 / Net I/σ(I): 15.38 / Num. measured all: 67576455
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
2.95-3.030.5045.1911.03497239288980889675.237100
3.03-3.110.6693.8071.54491518786626866093.841100
3.11-3.20.7762.7972.25478024184345843312.822100
3.2-3.30.8572.1393.02457116181966819592.158100
3.3-3.410.9031.6593.82414592079434794271.675100
3.41-3.530.9391.3834.85439104276862768621.396100
3.53-3.660.9631.0696.33428573774231742301.079100
3.66-3.810.9790.7868.38408222871515715140.793100
3.81-3.980.9870.58610.89386596268539685360.591100
3.98-4.170.9910.4613.11349582165588655870.464100
4.17-4.40.9940.36416.59346058962418624180.367100
4.4-4.660.9960.29620.67343374359160591600.299100
4.66-4.990.9970.24724.08317269355614556140.249100
4.99-5.390.9980.19828.52285642251812518120.199100
5.39-5.90.9980.16732.26258438047763477620.169100
5.9-6.60.9990.15436.11251529043325433250.155100
6.6-7.620.9990.12143.48214649638275382750.122100
7.62-9.330.9990.09452.51173129532532325270.095100
9.33-13.1910.06771.02143232625386253860.068100
13.190.9980.0468573753014356142890.04699.5

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WQ1

4wq1


Resolution: 2.95→147.011 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2418 1999 0.17 %
Rwork0.1958 1206285 -
obs0.1959 1208284 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 360.79 Å2 / Biso mean: 98.1495 Å2 / Biso min: 26.87 Å2
Refinement stepCycle: final / Resolution: 2.95→147.011 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms89085 203611 5145 0 297841
Biso mean--73.57 --
Num. residues----20667
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012322347
X-RAY DIFFRACTIONf_angle_d2.054486180
X-RAY DIFFRACTIONf_chiral_restr0.07660652
X-RAY DIFFRACTIONf_plane_restr0.0125127
X-RAY DIFFRACTIONf_dihedral_angle_d18.776149174
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.95-3.02380.43221420.38558554785689
3.0238-3.10550.37941410.32298561085751
3.1055-3.19690.33221430.2738575185894
3.1969-3.30010.311420.24278575485896
3.3001-3.41810.28381420.23248578785929
3.4181-3.5550.25971410.22148588286023
3.555-3.71680.27231430.21118583285975
3.7168-3.91270.24241420.18288594786089
3.9127-4.15790.21731430.17638608486227
4.1579-4.47890.20861430.17068619886341
4.4789-4.92970.23441430.16478625986402
4.9297-5.64310.20241440.16148650886652
5.6431-7.10970.22351440.18348685286996
7.1097-147.19370.22271460.18988827488420

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