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- PDB-5el4: Structure of T. thermophilus 70S ribosome complex with mRNA and t... -

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Basic information

Entry
Database: PDB / ID: 5el4
TitleStructure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with a U-U mismatch in the first position
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 28
  • (tRNA-Lys) x 4
  • 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 uS8 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 ...IRON/SULFUR CLUSTER / : / : / 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 / Large ribosomal subunit protein uL1 / 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 HB8 (bacteria)
Escherichia coli K-12 (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 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
DepositionNov 4, 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.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-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
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)4,528,8191321
Polymers4,498,518108
Non-polymers30,3011213
Water35,5441973
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)2,282,745729
Polymers2,265,95355
Non-polymers16,791674
Water37821
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
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)2,246,075592
Polymers2,232,56553
Non-polymers13,510539
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)208.900, 447.800, 617.500
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Details13+1E+2E+3E+4E+5E+6E+7E+8E+1I+2I+3I+4I+5I+6I+7I+8I+9I+AI+BI+1F+1K+2K+3K+4K+1H+16+71+11+21+31+41+51+61+58+68+78+88+98+A8+B8+C8+D8+E8+F8+G8+H8+I8+J8+K8+L8+N8+P8+Q8+M8

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Components

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RNA chain , 9 types, 14 molecules 131G1K2K2L3K4K4L1H14161J1L3L

#1: RNA chain 16S ribosomal RNA


Mass: 493997.312 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: GenBank: 55771382
#22: RNA chain tRNA-Lys


Mass: 24612.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: GenBank: 937517453
#23: RNA chain tRNA-fMet


Mass: 24862.945 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria)
#24: RNA chain tRNA-Lys


Mass: 24378.408 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: GenBank: 937517453
#25: RNA chain mRNA


Mass: 8862.456 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: 55771382
#56: RNA chain tRNA-Lys


Mass: 24392.434 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: GenBank: 937517453
#57: RNA chain tRNA-Lys


Mass: 24378.408 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: GenBank: 937517453

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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: 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 HB8 (bacteria) / 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 HB8 (bacteria) / 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 HB8 (bacteria) / 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 HB8 (bacteria) / 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 HB8 (bacteria) / 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 HB8 (bacteria) / 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 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: 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 HB8 (bacteria) / 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 HB8 (bacteria) / 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 HB8 (bacteria) / 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 HB8 (bacteria) / 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 HB8 (bacteria) / 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 HB8 (bacteria) / 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 HB8 (bacteria) / 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 HB8 (bacteria) / 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 HB8 (bacteria) / 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 HB8 (bacteria) / 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 HB8 (bacteria) / References: UniProt: Q5SIH3

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50S ribosomal protein ... , 28 types, 54 molecules 7111192129313941495159616958156825783588459855A865B875C885D8...

#28: Protein 50S ribosomal protein L1


Mass: 24867.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SLP7
#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: P60405
#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: Q5SHN8
#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: Q5SHQ3, 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: P60488
#36: Protein 50S ribosomal protein L14


Mass: 13323.612 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus 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: Q5SHQ7
#38: Protein 50S ribosomal protein L16


Mass: 15993.909 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus 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: Q9Z9H5
#40: 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 HB8 (bacteria) / References: UniProt: Q5SHQ4
#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: P60491
#43: Protein 50S ribosomal protein L21


Mass: 11069.153 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P60492
#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: Q5SHP3
#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: Q5SHP0
#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: Q5SHP9
#47: 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 HB8 (bacteria) / References: UniProt: Q5SHZ1
#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: Q5SHP6
#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: Q5SHQ6
#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: Q5SJE1
#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: Q5SKU1

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Non-polymers , 4 types, 3186 molecules

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


Mass: 24.305 Da / Num. of mol.: 1207 / Source method: obtained synthetically / Formula: Mg
#59: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


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


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


Mass: 18.015 Da / Num. of mol.: 1973 / 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: 61.68 %
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: Feb 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.15→200 Å / Num. obs: 992033 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 109.9 % / Biso Wilson estimate: 96.38 Å2 / Rmerge F obs: 0.996 / Rmerge(I) obs: 0.314 / Χ2: 1.033 / Net I/σ(I): 31.6 / Num. measured all: 109004697
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
3.15-3.250.3073.8870.97176842588222882073.976100
3.25-3.40.6493.3761.852691421136721136643.413100
3.4-3.50.8032.9192.69498394665382653802.939100
3.5-3.60.8682.6113.48561134758331583272.625100
3.6-3.70.9232.3464.75731453052184521842.355100
3.7-40.9661.5397.09175665541271891271891.545100
4-50.9930.64215.35324220282361892361870.644100
5-100.9990.23339.11298268122186282186280.234100
10-5010.07389.71422711131983319830.073100
50-2000.9930.0862.4148023152840.08290.2

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Processing

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

4wq1


Resolution: 3.15→151.531 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2511 2000 0.2 %
Rwork0.1934 985228 -
obs0.1935 987228 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 223.08 Å2 / Biso mean: 106.0187 Å2 / Biso min: 35.02 Å2
Refinement stepCycle: final / Resolution: 3.15→151.531 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms88352 202753 3200 0 294305
Biso mean--79.73 --
Num. residues----20524
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01318824
X-RAY DIFFRACTIONf_angle_d1.715479583
X-RAY DIFFRACTIONf_chiral_restr0.06960330
X-RAY DIFFRACTIONf_plane_restr0.00824947
X-RAY DIFFRACTIONf_dihedral_angle_d18.798148421
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
3.15-3.22880.39791420.32776993270074
3.2288-3.31610.33161420.28286998570127
3.3161-3.41370.31241420.25436992270064
3.4137-3.52390.31091420.23197000470146
3.5239-3.64980.27671420.21897005570197
3.6498-3.7960.26631420.20467012570267
3.796-3.96870.26411430.18567006170204
3.9687-4.1780.22141420.17897023670378
4.178-4.43980.25811430.17757025170394
4.4398-4.78260.24661420.17297027670418
4.7826-5.26390.25291440.16497049170635
5.2639-6.02560.21521430.16257063570778
6.0256-7.59170.23181450.18647099171136
7.5917-151.70680.22961460.19237226472410

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