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- PDB-4v6g: Initiation complex of 70S ribosome with two tRNAs and mRNA. -

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Basic information

Entry
Database: PDB / ID: 4v6g
TitleInitiation complex of 70S ribosome with two tRNAs and mRNA.
Components
  • (30S RIBOSOMAL PROTEIN ...) x 20
  • (50S ribosomal protein ...) x 28
  • 16S RRNA (E.COLI NUMBERING)
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • MRNA
  • TRNA FMET (UNMODIFIED BASES)
KeywordsRIBOSOME / tRNA / mRNA
Function / homology
Function and homology information


large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / small ribosomal subunit rRNA binding ...large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / small ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / zinc ion binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / : / Ribosomal protein S14, type Z / Ribosomal protein L31 type A ...30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / : / Ribosomal protein S14, type Z / Ribosomal protein L31 type A / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / : / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L32p, bacterial type / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L28 / Ribosomal protein L35, non-mitochondrial / : / Ribosomal protein L5, bacterial-type / Ribosomal protein L18, bacterial-type / : / Ribosomal protein S19, bacterial-type / Ribosomal protein S3, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / 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 S14/S29 / Ribosomal protein L20 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal L28 family / Ribosomal protein L33 superfamily / Ribosomal protein L16 / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein L28/L24 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L30, bacterial-type / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / : / L28p-like / Ribosomal protein S15, bacterial-type / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein S12, bacterial-type / Ribosomal protein L20 / Ribosomal L32p protein family / Ribosomal protein L19 / Ribosomal protein L19 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L19 superfamily / Ribosomal protein L21 / Ribosomal protein L32p
Similarity search - Domain/homology
: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL6 ...: / : / : / 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 / Small ribosomal subunit protein uS14 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL34 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL29 / 30S ribosomal protein S17 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL5 / 30S ribosomal protein S14 type Z / 30S ribosomal protein S8 / 50S ribosomal protein L6 / Large ribosomal subunit protein uL18 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL25 / Small ribosomal subunit protein bTHX / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein bL31 / Small ribosomal subunit protein bS16 / Large ribosomal subunit protein bL35 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS18 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein bL17
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
Escherichia coli (E. coli)
Synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsJenner, L.B. / Yusupova, G. / Yusupov, M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Structural aspects of messenger RNA reading frame maintenance by the ribosome.
Authors: Jenner, L.B. / Demeshkina, N. / Yusupova, G. / Yusupov, M.
History
DepositionJul 10, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 3I9B, 3I9C, 3I9D, 3I9E
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Sep 20, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type / struct_ref_seq / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_PDB_ins_code / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_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.ptnr2_symmetry / _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.ptnr2_symmetry / _struct_conn_type.id / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details
Revision 1.3Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: ndb_struct_na_base_pair / ndb_struct_na_base_pair_step ...ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_entry_details / pdbx_modification_feature / pdbx_validate_symm_contact / struct_conn / struct_conn_type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AA: 16S RRNA (E.COLI NUMBERING)
AE: 30S RIBOSOMAL PROTEIN S2
AF: 30S RIBOSOMAL PROTEIN S3
AG: 30S RIBOSOMAL PROTEIN S4
AH: 30S RIBOSOMAL PROTEIN S5
AI: 30S RIBOSOMAL PROTEIN S6
AJ: 30S RIBOSOMAL PROTEIN S7
AK: 30S RIBOSOMAL PROTEIN S8
AL: 30S RIBOSOMAL PROTEIN S9
AM: 30S RIBOSOMAL PROTEIN S10
AN: 30S RIBOSOMAL PROTEIN S11
AO: 30S RIBOSOMAL PROTEIN S12
AP: 30S RIBOSOMAL PROTEIN S13
AQ: 30S RIBOSOMAL PROTEIN S14
AR: 30S RIBOSOMAL PROTEIN S15
AS: 30S RIBOSOMAL PROTEIN S16
AT: 30S RIBOSOMAL PROTEIN S17
AU: 30S RIBOSOMAL PROTEIN S18
AV: 30S RIBOSOMAL PROTEIN S19
AW: 30S RIBOSOMAL PROTEIN S20
AX: 30S RIBOSOMAL PROTEIN THX
AC: TRNA FMET (UNMODIFIED BASES)
AD: TRNA FMET (UNMODIFIED BASES)
A1: MRNA
BA: 23S ribosomal RNA
BB: 5S ribosomal RNA
BD: 50S ribosomal protein L2
BE: 50S ribosomal protein L3
BF: 50S ribosomal protein L4
BG: 50S ribosomal protein L5
BH: 50S ribosomal protein L6
BK: 50S ribosomal protein L9
BM: 50S ribosomal protein L13
BN: 50S ribosomal protein L14
BO: 50S ribosomal protein L15
BP: 50S ribosomal protein L16
B0: 50S ribosomal protein L17
BQ: 50S ribosomal protein L18
BR: 50S ribosomal protein L19
B1: 50S ribosomal protein L20
B2: 50S ribosomal protein L21
BS: 50S ribosomal protein L22
BT: 50S ribosomal protein L23
BU: 50S ribosomal protein L24
BV: 50S ribosomal protein L25
B3: 50S ribosomal protein L27
BZ: 50S ribosomal protein L28
BW: 50S ribosomal protein L29
BX: 50S ribosomal protein L30
B4: 50S ribosomal protein L31
B5: 50S ribosomal protein L32
B6: 50S ribosomal protein L33
B7: 50S ribosomal protein L34
B8: 50S ribosomal protein L35
CA: 16S RRNA (E.COLI NUMBERING)
CE: 30S RIBOSOMAL PROTEIN S2
CF: 30S RIBOSOMAL PROTEIN S3
CG: 30S RIBOSOMAL PROTEIN S4
CH: 30S RIBOSOMAL PROTEIN S5
CI: 30S RIBOSOMAL PROTEIN S6
CJ: 30S RIBOSOMAL PROTEIN S7
CK: 30S RIBOSOMAL PROTEIN S8
CL: 30S RIBOSOMAL PROTEIN S9
CM: 30S RIBOSOMAL PROTEIN S10
CN: 30S RIBOSOMAL PROTEIN S11
CO: 30S RIBOSOMAL PROTEIN S12
CP: 30S RIBOSOMAL PROTEIN S13
CQ: 30S RIBOSOMAL PROTEIN S14
CR: 30S RIBOSOMAL PROTEIN S15
CS: 30S RIBOSOMAL PROTEIN S16
CT: 30S RIBOSOMAL PROTEIN S17
CU: 30S RIBOSOMAL PROTEIN S18
CV: 30S RIBOSOMAL PROTEIN S19
CW: 30S RIBOSOMAL PROTEIN S20
CX: 30S RIBOSOMAL PROTEIN THX
CC: TRNA FMET (UNMODIFIED BASES)
CD: TRNA FMET (UNMODIFIED BASES)
C1: MRNA
DA: 23S ribosomal RNA
DB: 5S ribosomal RNA
DD: 50S ribosomal protein L2
DE: 50S ribosomal protein L3
DF: 50S ribosomal protein L4
DG: 50S ribosomal protein L5
DH: 50S ribosomal protein L6
DK: 50S ribosomal protein L9
DM: 50S ribosomal protein L13
DN: 50S ribosomal protein L14
DO: 50S ribosomal protein L15
DP: 50S ribosomal protein L16
D0: 50S ribosomal protein L17
DQ: 50S ribosomal protein L18
DR: 50S ribosomal protein L19
D1: 50S ribosomal protein L20
D2: 50S ribosomal protein L21
DS: 50S ribosomal protein L22
DT: 50S ribosomal protein L23
DU: 50S ribosomal protein L24
DV: 50S ribosomal protein L25
D3: 50S ribosomal protein L27
DZ: 50S ribosomal protein L28
DW: 50S ribosomal protein L29
DX: 50S ribosomal protein L30
D4: 50S ribosomal protein L31
D5: 50S ribosomal protein L32
D6: 50S ribosomal protein L33
D7: 50S ribosomal protein L34
D8: 50S ribosomal protein L35
CB: TRNA FMET (UNMODIFIED BASES)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,520,2142768
Polymers4,455,340109
Non-polymers64,8742659
Water00
1
AA: 16S RRNA (E.COLI NUMBERING)
AE: 30S RIBOSOMAL PROTEIN S2
AF: 30S RIBOSOMAL PROTEIN S3
AG: 30S RIBOSOMAL PROTEIN S4
AH: 30S RIBOSOMAL PROTEIN S5
AI: 30S RIBOSOMAL PROTEIN S6
AJ: 30S RIBOSOMAL PROTEIN S7
AK: 30S RIBOSOMAL PROTEIN S8
AL: 30S RIBOSOMAL PROTEIN S9
AM: 30S RIBOSOMAL PROTEIN S10
AN: 30S RIBOSOMAL PROTEIN S11
AO: 30S RIBOSOMAL PROTEIN S12
AP: 30S RIBOSOMAL PROTEIN S13
AQ: 30S RIBOSOMAL PROTEIN S14
AR: 30S RIBOSOMAL PROTEIN S15
AS: 30S RIBOSOMAL PROTEIN S16
AT: 30S RIBOSOMAL PROTEIN S17
AU: 30S RIBOSOMAL PROTEIN S18
AV: 30S RIBOSOMAL PROTEIN S19
AW: 30S RIBOSOMAL PROTEIN S20
AX: 30S RIBOSOMAL PROTEIN THX
AC: TRNA FMET (UNMODIFIED BASES)
AD: TRNA FMET (UNMODIFIED BASES)
A1: MRNA
BA: 23S ribosomal RNA
BB: 5S ribosomal RNA
BD: 50S ribosomal protein L2
BE: 50S ribosomal protein L3
BF: 50S ribosomal protein L4
BG: 50S ribosomal protein L5
BH: 50S ribosomal protein L6
BK: 50S ribosomal protein L9
BM: 50S ribosomal protein L13
BN: 50S ribosomal protein L14
BO: 50S ribosomal protein L15
BP: 50S ribosomal protein L16
B0: 50S ribosomal protein L17
BQ: 50S ribosomal protein L18
BR: 50S ribosomal protein L19
B1: 50S ribosomal protein L20
B2: 50S ribosomal protein L21
BS: 50S ribosomal protein L22
BT: 50S ribosomal protein L23
BU: 50S ribosomal protein L24
BV: 50S ribosomal protein L25
B3: 50S ribosomal protein L27
BZ: 50S ribosomal protein L28
BW: 50S ribosomal protein L29
BX: 50S ribosomal protein L30
B4: 50S ribosomal protein L31
B5: 50S ribosomal protein L32
B6: 50S ribosomal protein L33
B7: 50S ribosomal protein L34
B8: 50S ribosomal protein L35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,245,0861274
Polymers2,215,26954
Non-polymers29,8171220
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
CA: 16S RRNA (E.COLI NUMBERING)
CE: 30S RIBOSOMAL PROTEIN S2
CF: 30S RIBOSOMAL PROTEIN S3
CG: 30S RIBOSOMAL PROTEIN S4
CH: 30S RIBOSOMAL PROTEIN S5
CI: 30S RIBOSOMAL PROTEIN S6
CJ: 30S RIBOSOMAL PROTEIN S7
CK: 30S RIBOSOMAL PROTEIN S8
CL: 30S RIBOSOMAL PROTEIN S9
CM: 30S RIBOSOMAL PROTEIN S10
CN: 30S RIBOSOMAL PROTEIN S11
CO: 30S RIBOSOMAL PROTEIN S12
CP: 30S RIBOSOMAL PROTEIN S13
CQ: 30S RIBOSOMAL PROTEIN S14
CR: 30S RIBOSOMAL PROTEIN S15
CS: 30S RIBOSOMAL PROTEIN S16
CT: 30S RIBOSOMAL PROTEIN S17
CU: 30S RIBOSOMAL PROTEIN S18
CV: 30S RIBOSOMAL PROTEIN S19
CW: 30S RIBOSOMAL PROTEIN S20
CX: 30S RIBOSOMAL PROTEIN THX
CC: TRNA FMET (UNMODIFIED BASES)
CD: TRNA FMET (UNMODIFIED BASES)
C1: MRNA
DA: 23S ribosomal RNA
DB: 5S ribosomal RNA
DD: 50S ribosomal protein L2
DE: 50S ribosomal protein L3
DF: 50S ribosomal protein L4
DG: 50S ribosomal protein L5
DH: 50S ribosomal protein L6
DK: 50S ribosomal protein L9
DM: 50S ribosomal protein L13
DN: 50S ribosomal protein L14
DO: 50S ribosomal protein L15
DP: 50S ribosomal protein L16
D0: 50S ribosomal protein L17
DQ: 50S ribosomal protein L18
DR: 50S ribosomal protein L19
D1: 50S ribosomal protein L20
D2: 50S ribosomal protein L21
DS: 50S ribosomal protein L22
DT: 50S ribosomal protein L23
DU: 50S ribosomal protein L24
DV: 50S ribosomal protein L25
D3: 50S ribosomal protein L27
DZ: 50S ribosomal protein L28
DW: 50S ribosomal protein L29
DX: 50S ribosomal protein L30
D4: 50S ribosomal protein L31
D5: 50S ribosomal protein L32
D6: 50S ribosomal protein L33
D7: 50S ribosomal protein L34
D8: 50S ribosomal protein L35
CB: TRNA FMET (UNMODIFIED BASES)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,275,1281494
Polymers2,240,07155
Non-polymers35,0571439
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)210.460, 452.180, 626.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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RNA chain , 5 types, 13 molecules AACAACADCCCDCBA1C1BADABBDB

#1: RNA chain 16S RRNA (E.COLI NUMBERING)


Mass: 492467.500 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: GenBank: M26923.1
#22: RNA chain
TRNA FMET (UNMODIFIED BASES)


Mass: 24801.801 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#23: RNA chain MRNA


Mass: 8227.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others)
#24: RNA chain 23S ribosomal RNA


Mass: 942506.062 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: GenBank: AP008226.1
#25: RNA chain 5S ribosomal RNA


Mass: 39540.617 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: GenBank: X01554.1

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30S RIBOSOMAL PROTEIN ... , 20 types, 40 molecules AECEAFCFAGCGAHCHAICIAJCJAKCKALCLAMCMANCNAOCOAPCPAQCQARCRASCS...

#2: Protein 30S RIBOSOMAL PROTEIN S2


Mass: 29317.703 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80371
#3: Protein 30S RIBOSOMAL PROTEIN S3


Mass: 26751.076 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80372
#4: Protein 30S RIBOSOMAL PROTEIN S4


Mass: 24373.447 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80373
#5: Protein 30S RIBOSOMAL PROTEIN S5


Mass: 17583.416 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHQ5
#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 (bacteria) / Strain: HB8 / References: UniProt: Q5SLP8
#7: Protein 30S RIBOSOMAL PROTEIN S7


Mass: 18050.973 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P17291
#8: Protein 30S RIBOSOMAL PROTEIN S8


Mass: 15868.570 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHQ2, 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 (bacteria) / Strain: HB8 / References: UniProt: P80374
#10: Protein 30S RIBOSOMAL PROTEIN S10


Mass: 11954.968 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHN7
#11: Protein 30S RIBOSOMAL PROTEIN S11


Mass: 13737.868 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80376
#12: Protein 30S RIBOSOMAL PROTEIN S12


Mass: 14637.384 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHN3
#13: Protein 30S RIBOSOMAL PROTEIN S13


Mass: 14338.861 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80377
#14: Protein 30S RIBOSOMAL PROTEIN S14


Mass: 7158.725 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
References: UniProt: P24320, UniProt: Q5SHQ1, 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 (bacteria) / Strain: HB8 / References: UniProt: Q5SJ76
#16: Protein 30S RIBOSOMAL PROTEIN S16


Mass: 10409.983 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SJH3
#17: Protein 30S RIBOSOMAL PROTEIN S17


Mass: 12325.655 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / 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 (bacteria) / Strain: HB8 / References: UniProt: Q5SLQ0
#19: Protein 30S RIBOSOMAL PROTEIN S19


Mass: 10605.464 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHP2
#20: Protein 30S RIBOSOMAL PROTEIN S20


Mass: 11736.143 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / 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 (bacteria) / Strain: HB8 / References: UniProt: Q5SIH3

+
50S ribosomal protein ... , 28 types, 56 molecules BDDDBEDEBFDFBGDGBHDHBKDKBMDMBNDNBODOBPDPB0D0BQDQBRDRB1D1B2D2...

#26: Protein 50S ribosomal protein L2


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


Mass: 22450.213 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHN8
#28: Protein 50S ribosomal protein L4 / L1e


Mass: 23271.914 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHN9
#29: Protein 50S ribosomal protein L5


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


Mass: 19568.926 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHQ3, UniProt: P0DOY8*PLUS
#31: Protein 50S ribosomal protein L9


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


Mass: 15927.903 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P60488
#33: Protein 50S ribosomal protein L14


Mass: 13323.612 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHP8
#34: Protein 50S ribosomal protein L15


Mass: 16319.142 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHQ7
#35: Protein 50S ribosomal protein L16


Mass: 15993.909 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P60489
#36: Protein 50S ribosomal protein L17


Mass: 13750.148 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q9Z9H5
#37: Protein 50S ribosomal protein L18 / TL24


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


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


Mass: 13779.275 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P60491
#40: Protein 50S ribosomal protein L21


Mass: 11069.153 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P60492
#41: Protein 50S ribosomal protein L22


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


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


Mass: 12085.611 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHP9
#44: Protein 50S ribosomal protein L25 / TL5


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


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


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


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


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


Mass: 8300.543 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SJE1
#50: Protein 50S ribosomal protein L32


Mass: 6722.050 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80339
#51: Protein 50S ribosomal protein L33


Mass: 6632.896 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P35871
#52: Protein/peptide 50S ribosomal protein L34


Mass: 6132.449 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80340
#53: Protein 50S ribosomal protein L35


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

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Non-polymers , 2 types, 2659 molecules

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


Mass: 24.305 Da / Num. of mol.: 2653 / Source method: obtained synthetically / Formula: Mg
#55: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn

-
Details

Has protein modificationY

-
Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.37 Å3/Da / Density % sol: 63.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 4% PEG20K, 4% PEGMME 550, 100mM Tris/HAc, 200mM KSCN, pH 7.5, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 10, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→300 Å / Num. all: 743905 / Num. obs: 719306 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.36 % / Biso Wilson estimate: 96.091 Å2 / Rmerge(I) obs: 0.285 / Rsym value: 0.177 / Net I/σ(I): 7.13
Reflection shellResolution: 3.5→3.6 Å / Redundancy: 12.1 % / Rmerge(I) obs: 0.568 / Mean I/σ(I) obs: 1.98 / Num. unique all: 53168 / Rsym value: 0.568 / % possible all: 88.9

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.005data extraction
XDSdata scaling
XDSdata reduction
XSCALEdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3I8F, 3I8G, 3I8H, 3I8I

3i8f
PDB Unreleased entry

3i8g
PDB Unreleased entry

3i8h
PDB Unreleased entry

3i8i
PDB Unreleased entry


Resolution: 3.5→300 Å / Occupancy max: 8 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.252 22133 -RANDOM
Rwork0.213 ---
all-719306 --
obs-719306 96.7 %-
Displacement parametersBiso max: 201.53 Å2 / Biso mean: 126.967 Å2 / Biso min: 0 Å2
Refinement stepCycle: LAST / Resolution: 3.5→300 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19242 36382 1219 0 56843
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008245
X-RAY DIFFRACTIONc_angle_deg1.4001
LS refinement shellResolution: 3.5→3.52 Å
RfactorNum. reflection
Rfree0.3482 446
Rwork0.3243 -
obs-14249

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