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- PDB-5e7k: Structure of T. thermophilus 70S ribosome complex with mRNA and c... -

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Basic information

Entry
Database: PDB / ID: 5e7k
TitleStructure of T. thermophilus 70S ribosome complex with mRNA and cognate tRNALys in the A-site
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 28
  • (tRNALys) x 4
  • 16S rRNA
  • 23S rRNA
  • 5S rRNA
  • mRNA
  • tRNAfMet
KeywordsRIBOSOME / translation / mismatch
Function / homology
Function and homology information


large ribosomal subunit / regulation of translation / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / large ribosomal subunit rRNA binding / transferase activity / cytosolic small ribosomal subunit / ribosomal large subunit assembly / cytosolic large ribosomal subunit ...large ribosomal subunit / regulation of translation / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / large ribosomal subunit rRNA binding / transferase activity / cytosolic small ribosomal subunit / ribosomal large subunit assembly / cytosolic large ribosomal subunit / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / zinc ion binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L1, bacterial-type / 30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / : / Ribosomal protein S14, type Z ...Ribosomal protein L1, bacterial-type / 30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / : / Ribosomal protein S14, type Z / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1 / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein L31 type A / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / : / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L32p, bacterial type / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / : / : / Ribosomal protein L28 / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein S14/S29 / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein L20 signature. / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L34, conserved site / Ribosomal L28 family / Ribosomal protein L34 signature. / Ribosomal protein L28/L24 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L30, bacterial-type / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein L16 / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / : / L28p-like / Ribosomal protein L20 / Ribosomal protein S15, bacterial-type / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L21 / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L19 / Ribosomal protein L19 / Ribosomal protein S6
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 ...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 uL1 / 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 (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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 12, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2016Group: 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

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Assembly

Deposited unit
13: 16S rRNA
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: tRNALys
2K: tRNAfMet
3K: tRNALys
4K: mRNA
1H: 23S rRNA
16: 5S rRNA
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 rRNA
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: tRNALys
2L: tRNAfMet
3L: tRNALys
4L: mRNA
14: 23S rRNA
1J: 5S rRNA
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)4,551,9111253
Polymers4,523,287109
Non-polymers28,6241144
Water24,5541363
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13: 16S rRNA
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: tRNALys
2K: tRNAfMet
3K: tRNALys
4K: mRNA
1H: 23S rRNA
16: 5S rRNA
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)2,281,360686
Polymers2,265,61455
Non-polymers15,746631
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
1G: 16S rRNA
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: tRNALys
2L: tRNAfMet
3L: tRNALys
4L: mRNA
14: 23S rRNA
1J: 5S rRNA
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)2,270,551567
Polymers2,257,67354
Non-polymers12,878513
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)209.500, 450.100, 621.600
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 , 9 types, 14 molecules 131G1K2K2L3K4K4L1H14161J1L3L

#1: RNA chain 16S rRNA


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 tRNALys


Mass: 24251.479 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 836716955
#23: RNA chain tRNAfMet


Mass: 24861.938 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 857137982
#24: RNA chain tRNALys


Mass: 24378.408 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 836716955
#25: RNA chain mRNA


Mass: 8885.496 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#26: RNA chain 23S rRNA


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 rRNA


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 tRNALys


Mass: 24596.682 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 836716955
#57: RNA chain tRNALys


Mass: 24392.434 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 836716955

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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, 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: P27150, 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: 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, 2507 molecules

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


Mass: 24.305 Da / Num. of mol.: 1138 / 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.: 1363 / 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: 3.24 Å3/Da / Density % sol: 62.03 %
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: Dec 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→200 Å / Num. obs: 955810 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 108.7 % / Biso Wilson estimate: 102.2 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.375 / Χ2: 0.997 / Net I/σ(I): 37.7 / Num. measured all: 103886962
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
3.2-3.30.3724.2971.1335993483735837294.352100
3.3-3.50.7463.3122.28122701301402621402523.331100
3.5-3.70.8782.3563.61116337591115981115962.367100
3.7-40.951.4785.86130553411284101284071.485100
4-50.9880.71812.24260410122385012384990.721100
5-60.9970.45824.04146906211058561058560.46100
6-7.50.9990.32934.791133010571301713010.33100
7.5-100.9990.18853.48665496843563435630.188100
10-5010.08288.53483222832320323200.082100
50-173.7190.05392.31188643162870.05390.8

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Processing

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

4wq1


Resolution: 3.2→173.719 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2579 1999 0.21 %
Rwork0.1914 953730 -
obs0.1916 955729 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 216.74 Å2 / Biso mean: 107.4619 Å2 / Biso min: 33.61 Å2
Refinement stepCycle: final / Resolution: 3.2→173.719 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms89071 202855 2521 0 294447
Biso mean--79.81 --
Num. residues----20625
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01319055
X-RAY DIFFRACTIONf_angle_d1.67479136
X-RAY DIFFRACTIONf_chiral_restr0.06860453
X-RAY DIFFRACTIONf_plane_restr0.00925084
X-RAY DIFFRACTIONf_dihedral_angle_d18.789148727
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
3.2-3.280.32611420.27426768467826
3.28-3.36870.32951410.25826764567786
3.3687-3.46790.29771430.24976773967882
3.4679-3.57980.31531420.23796775067892
3.5798-3.70780.30011420.2246784067982
3.7078-3.85620.24961420.20246784167983
3.8562-4.03170.26771430.18376794468087
4.0317-4.24430.24921420.17816792568067
4.2443-4.51030.26151430.17256799568138
4.5103-4.85850.24271430.16536812568268
4.8585-5.34750.26581420.1636817668318
5.3475-6.12130.22981430.16346840068543
6.1213-7.71220.24371450.19226868568830
7.7122-173.97540.24271460.19596998170127

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