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- PDB-6n1d: X-ray Crystal complex showing Spontaneous Ribosomal Translocation... -

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Basic information

Entry
Database: PDB / ID: 6n1d
TitleX-ray Crystal complex showing Spontaneous Ribosomal Translocation of mRNA and tRNAs into a Chimeric Hybrid State
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 30
  • 16S rRNA
  • 23S rRNA
  • 5s rRNA
  • A tRNA
  • P-tRNA
  • mRNA
KeywordsRIBOSOME
Function / homology
Function and homology information


regulation of translation / large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding ...regulation of translation / large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / zinc ion binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein / Ribosomal protein 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 L36 signature. / 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 / Ribosomal protein L9, N-terminal domain superfamily / 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 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 / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / 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 L33 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 / Ribosomal L28 family / Ribosomal protein L33 superfamily / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L16 / Ribosomal protein S18, conserved site / Ribosomal protein L28/L24 / 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
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL1 / Large ribosomal subunit protein bL27 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein bS16 ...IRON/SULFUR CLUSTER / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL1 / Large ribosomal subunit protein bL27 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bTHX / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL31 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL35
Similarity search - Component
Biological speciesThermus thermophilus HB27 (bacteria)
Thermus thermophilus (bacteria)
Escherichia coli (E. coli)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsNoller, H.F. / Donohue, J.P. / Lancaster, L. / Zhou, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM118156 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2019
Title: Spontaneous ribosomal translocation of mRNA and tRNAs into a chimeric hybrid state.
Authors: Zhou, J. / Lancaster, L. / Donohue, J.P. / Noller, H.F.
History
DepositionNov 8, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 1, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 3, 2019Group: Data collection / Non-polymer description / Structure summary
Category: chem_comp / entity
Item: _chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight
Revision 2.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.2Oct 11, 2023Group: 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_label_atom_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_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
Revision 2.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A16S: 16S rRNA
A23S: 23S rRNA
A5S: 5s rRNA
AL01: 50S ribosomal protein L1
AL02: 50S ribosomal protein L2
AL03: 50S ribosomal protein L3
AL04: 50S ribosomal protein L4
AL05: 50S ribosomal protein L5
AL06: 50S ribosomal protein L6
AL09: 50S ribosomal protein L9
AL13: 50S ribosomal protein L13
AL14: 50S ribosomal protein L14
AL15: 50S ribosomal protein L15
AL16: 50S ribosomal protein L16
AL17: 50S ribosomal protein L17
AL18: 50S ribosomal protein L18
AL19: 50S ribosomal protein L19
AL20: 50S ribosomal protein L20
AL21: 50S ribosomal protein L21
AL22: 50S ribosomal protein L22
AL23: 50S ribosomal protein L23
AL24: 50S ribosomal protein L24
AL25: 50S ribosomal protein L25
AL27: 50S ribosomal protein L27
AL28: 50S ribosomal protein L28
AL29: 50S ribosomal protein L29
AL30: 50S ribosomal protein L30
AL31: 50S ribosomal protein L31
AL32: 50S ribosomal protein L32
AL33: 50S ribosomal protein L33
AL34: 50S ribosomal protein L34
AL35: 50S ribosomal protein L35
AL36: 50S ribosomal protein L36
AMRN: mRNA
APTN: P-tRNA
AS02: 30S ribosomal protein S2
AS03: 30S ribosomal protein S3
AS04: 30S ribosomal protein S4
AS05: 30S ribosomal protein S5
AS06: 30S ribosomal protein S6
AS07: 30S ribosomal protein S7
AS08: 30S ribosomal protein S8
AS09: 30S ribosomal protein S9
AS10: 30S ribosomal protein S10
AS11: 30S ribosomal protein S11
AS12: 30S ribosomal protein S12
AS13: 30S ribosomal protein S13
AS14: 30S ribosomal protein S14 type Z
AS15: 30S ribosomal protein S15
AS16: 30S ribosomal protein S16
AS17: 30S ribosomal protein S17
AS18: 30S ribosomal protein S18
AS19: 30S ribosomal protein S19
AS20: 30S ribosomal protein S20
ATHX: 30S ribosomal protein Thx
B16S: 16S rRNA
B23S: 23S rRNA
B5S: 5s rRNA
BATN: A tRNA
BL01: 50S ribosomal protein L1
BL02: 50S ribosomal protein L2
BL03: 50S ribosomal protein L3
BL04: 50S ribosomal protein L4
BL05: 50S ribosomal protein L5
BL06: 50S ribosomal protein L6
BL09: 50S ribosomal protein L9
BL13: 50S ribosomal protein L13
BL14: 50S ribosomal protein L14
BL15: 50S ribosomal protein L15
BL16: 50S ribosomal protein L16
BL17: 50S ribosomal protein L17
BL18: 50S ribosomal protein L18
BL19: 50S ribosomal protein L19
BL20: 50S ribosomal protein L20
BL21: 50S ribosomal protein L21
BL22: 50S ribosomal protein L22
BL23: 50S ribosomal protein L23
BL24: 50S ribosomal protein L24
BL25: 50S ribosomal protein L25
BL27: 50S ribosomal protein L27
BL28: 50S ribosomal protein L28
BL29: 50S ribosomal protein L29
BL30: 50S ribosomal protein L30
BL31: 50S ribosomal protein L31
BL32: 50S ribosomal protein L32
BL33: 50S ribosomal protein L33
BL34: 50S ribosomal protein L34
BL35: 50S ribosomal protein L35
BL36: 50S ribosomal protein L36
BMRN: mRNA
BPTN: P-tRNA
BS02: 30S ribosomal protein S2
BS03: 30S ribosomal protein S3
BS04: 30S ribosomal protein S4
BS05: 30S ribosomal protein S5
BS06: 30S ribosomal protein S6
BS07: 30S ribosomal protein S7
BS08: 30S ribosomal protein S8
BS09: 30S ribosomal protein S9
BS10: 30S ribosomal protein S10
BS11: 30S ribosomal protein S11
BS12: 30S ribosomal protein S12
BS13: 30S ribosomal protein S13
BS14: 30S ribosomal protein S14 type Z
BS15: 30S ribosomal protein S15
BS16: 30S ribosomal protein S16
BS17: 30S ribosomal protein S17
BS18: 30S ribosomal protein S18
BS19: 30S ribosomal protein S19
BS20: 30S ribosomal protein S20
BTHX: 30S ribosomal protein Thx
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,451,770472
Polymers4,442,341111
Non-polymers9,429361
Water00
1
A16S: 16S rRNA
A23S: 23S rRNA
A5S: 5s rRNA
AL01: 50S ribosomal protein L1
AL02: 50S ribosomal protein L2
AL03: 50S ribosomal protein L3
AL04: 50S ribosomal protein L4
AL05: 50S ribosomal protein L5
AL06: 50S ribosomal protein L6
AL09: 50S ribosomal protein L9
AL13: 50S ribosomal protein L13
AL14: 50S ribosomal protein L14
AL15: 50S ribosomal protein L15
AL16: 50S ribosomal protein L16
AL17: 50S ribosomal protein L17
AL18: 50S ribosomal protein L18
AL19: 50S ribosomal protein L19
AL20: 50S ribosomal protein L20
AL21: 50S ribosomal protein L21
AL22: 50S ribosomal protein L22
AL23: 50S ribosomal protein L23
AL24: 50S ribosomal protein L24
AL25: 50S ribosomal protein L25
AL27: 50S ribosomal protein L27
AL28: 50S ribosomal protein L28
AL29: 50S ribosomal protein L29
AL30: 50S ribosomal protein L30
AL31: 50S ribosomal protein L31
AL32: 50S ribosomal protein L32
AL33: 50S ribosomal protein L33
AL34: 50S ribosomal protein L34
AL35: 50S ribosomal protein L35
AL36: 50S ribosomal protein L36
AMRN: mRNA
APTN: P-tRNA
AS02: 30S ribosomal protein S2
AS03: 30S ribosomal protein S3
AS04: 30S ribosomal protein S4
AS05: 30S ribosomal protein S5
AS06: 30S ribosomal protein S6
AS07: 30S ribosomal protein S7
AS08: 30S ribosomal protein S8
AS09: 30S ribosomal protein S9
AS10: 30S ribosomal protein S10
AS11: 30S ribosomal protein S11
AS12: 30S ribosomal protein S12
AS13: 30S ribosomal protein S13
AS14: 30S ribosomal protein S14 type Z
AS15: 30S ribosomal protein S15
AS16: 30S ribosomal protein S16
AS17: 30S ribosomal protein S17
AS18: 30S ribosomal protein S18
AS19: 30S ribosomal protein S19
AS20: 30S ribosomal protein S20
ATHX: 30S ribosomal protein Thx
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,211,177197
Polymers2,207,39855
Non-polymers3,779142
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B16S: 16S rRNA
B23S: 23S rRNA
B5S: 5s rRNA
BATN: A tRNA
BL01: 50S ribosomal protein L1
BL02: 50S ribosomal protein L2
BL03: 50S ribosomal protein L3
BL04: 50S ribosomal protein L4
BL05: 50S ribosomal protein L5
BL06: 50S ribosomal protein L6
BL09: 50S ribosomal protein L9
BL13: 50S ribosomal protein L13
BL14: 50S ribosomal protein L14
BL15: 50S ribosomal protein L15
BL16: 50S ribosomal protein L16
BL17: 50S ribosomal protein L17
BL18: 50S ribosomal protein L18
BL19: 50S ribosomal protein L19
BL20: 50S ribosomal protein L20
BL21: 50S ribosomal protein L21
BL22: 50S ribosomal protein L22
BL23: 50S ribosomal protein L23
BL24: 50S ribosomal protein L24
BL25: 50S ribosomal protein L25
BL27: 50S ribosomal protein L27
BL28: 50S ribosomal protein L28
BL29: 50S ribosomal protein L29
BL30: 50S ribosomal protein L30
BL31: 50S ribosomal protein L31
BL32: 50S ribosomal protein L32
BL33: 50S ribosomal protein L33
BL34: 50S ribosomal protein L34
BL35: 50S ribosomal protein L35
BL36: 50S ribosomal protein L36
BMRN: mRNA
BPTN: P-tRNA
BS02: 30S ribosomal protein S2
BS03: 30S ribosomal protein S3
BS04: 30S ribosomal protein S4
BS05: 30S ribosomal protein S5
BS06: 30S ribosomal protein S6
BS07: 30S ribosomal protein S7
BS08: 30S ribosomal protein S8
BS09: 30S ribosomal protein S9
BS10: 30S ribosomal protein S10
BS11: 30S ribosomal protein S11
BS12: 30S ribosomal protein S12
BS13: 30S ribosomal protein S13
BS14: 30S ribosomal protein S14 type Z
BS15: 30S ribosomal protein S15
BS16: 30S ribosomal protein S16
BS17: 30S ribosomal protein S17
BS18: 30S ribosomal protein S18
BS19: 30S ribosomal protein S19
BS20: 30S ribosomal protein S20
BTHX: 30S ribosomal protein Thx
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,240,593275
Polymers2,234,94356
Non-polymers5,650219
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)207.450, 442.870, 613.000
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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RNA chain , 6 types, 11 molecules A16SB16SA23SB23SA5SB5SAMRNBMRNAPTNBPTNBATN

#1: RNA chain 16S rRNA


Mass: 492773.656 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: GenBank: 46197919
#2: RNA chain 23S rRNA


Mass: 937014.688 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / Strain: HB27 / ATCC BAA-163 / DSM 7039
#3: RNA chain 5s rRNA


Mass: 38553.000 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: GenBank: 46197919
#34: RNA chain mRNA


Mass: 5562.422 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#35: RNA chain P-tRNA


Mass: 24616.760 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#56: RNA chain A tRNA


Mass: 27544.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)

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50S ribosomal protein ... , 30 types, 60 molecules AL01BL01AL02BL02AL03BL03AL04BL04AL05BL05AL06BL06AL09BL09AL13BL13AL14BL14AL15BL15AL16BL16AL17BL17AL18BL18AL19BL19AL20BL20...

#4: Protein 50S ribosomal protein L1


Mass: 24741.523 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: A0A1J1EJ43
#5: Protein 50S ribosomal protein L2


Mass: 30532.551 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72I07
#6: Protein 50S ribosomal protein L3


Mass: 22450.213 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72I04
#7: Protein 50S ribosomal protein L4


Mass: 22744.279 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72I05
#8: Protein 50S ribosomal protein L5


Mass: 20944.428 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / References: UniProt: Q72I16
#9: Protein 50S ribosomal protein L6


Mass: 19568.926 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72I19
#10: Protein 50S ribosomal protein L9


Mass: 16436.205 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72GV5
#11: Protein 50S ribosomal protein L13


Mass: 15927.903 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72IN1
#12: Protein 50S ribosomal protein L14


Mass: 13309.586 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / References: UniProt: Q72I14
#13: Protein 50S ribosomal protein L15


Mass: 16319.142 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / References: UniProt: Q72I23
#14: Protein 50S ribosomal protein L16


Mass: 15977.909 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72I11
#15: Protein 50S ribosomal protein L17


Mass: 13750.148 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72I33
#16: Protein 50S ribosomal protein L18


Mass: 12508.649 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72I20
#17: Protein 50S ribosomal protein L19


Mass: 17217.867 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72JU9
#18: Protein 50S ribosomal protein L20


Mass: 13779.275 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72L76
#19: Protein 50S ribosomal protein L21


Mass: 11069.153 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / References: UniProt: Q72HR2
#20: Protein 50S ribosomal protein L22


Mass: 12808.055 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72I09
#21: Protein 50S ribosomal protein L23


Mass: 10759.808 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72I06
#22: Protein 50S ribosomal protein L24


Mass: 12085.611 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72I15
#23: Protein 50S ribosomal protein L25 / General stress protein CTC


Mass: 23238.572 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72IA7
#24: Protein 50S ribosomal protein L27


Mass: 9397.878 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P60493
#25: Protein 50S ribosomal protein L28


Mass: 11032.174 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72G84
#26: Protein 50S ribosomal protein L29


Mass: 8670.258 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72I12
#27: Protein 50S ribosomal protein L30


Mass: 6799.126 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72I22
#28: Protein 50S ribosomal protein L31


Mass: 8300.543 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72JR0
#29: Protein 50S ribosomal protein L32


Mass: 6590.854 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80339
#30: Protein 50S ribosomal protein L33


Mass: 6632.896 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72GW3
#31: 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) / References: UniProt: P80340
#32: Protein 50S ribosomal protein L35


Mass: 7374.981 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72L77
#33: Protein/peptide 50S ribosomal protein L36


Mass: 4435.411 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / References: UniProt: Q72I28

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30S ribosomal protein ... , 20 types, 40 molecules AS02BS02AS03BS03AS04BS04AS05BS05AS06BS06AS07BS07AS08BS08AS09BS09AS10BS10AS11BS11AS12BS12AS13BS13AS14BS14AS15BS15AS16BS16...

#36: Protein 30S ribosomal protein S2


Mass: 29186.506 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62662
#37: Protein 30S ribosomal protein S3


Mass: 26619.881 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62663
#38: Protein 30S ribosomal protein S4


Mass: 24242.254 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / References: UniProt: P62664
#39: Protein 30S ribosomal protein S5


Mass: 17452.221 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62665
#40: Protein 30S ribosomal protein S6


Mass: 11988.753 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / References: UniProt: P62666
#41: Protein 30S ribosomal protein S7


Mass: 17919.775 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / References: UniProt: P62667
#42: Protein 30S ribosomal protein S8


Mass: 15868.570 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / References: UniProt: P62668
#43: Protein 30S ribosomal protein S9


Mass: 14429.661 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62669
#44: Protein 30S ribosomal protein S10


Mass: 11823.772 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62653
#45: Protein 30S ribosomal protein S11


Mass: 13606.672 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62654
#46: Protein 30S ribosomal protein S12


Mass: 14506.188 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P61941
#47: Protein 30S ribosomal protein S13


Mass: 14207.666 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62655
#48: Protein 30S ribosomal protein S14 type Z


Mass: 7027.529 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / References: UniProt: P62656
#49: Protein 30S ribosomal protein S15


Mass: 10447.213 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / References: UniProt: P62657
#50: Protein 30S ribosomal protein S16


Mass: 10409.983 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62238
#51: Protein 30S ribosomal protein S17


Mass: 12193.475 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62658
#52: Protein 30S ribosomal protein S18


Mass: 10127.102 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62659
#53: Protein 30S ribosomal protein S19


Mass: 10474.269 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62660
#54: Protein 30S ribosomal protein S20


Mass: 11590.920 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62661
#55: Protein/peptide 30S ribosomal protein Thx


Mass: 3218.835 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62613

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Non-polymers , 2 types, 361 molecules

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


Mass: 24.305 Da / Num. of mol.: 359 / Source method: obtained synthetically / Formula: Mg
#58: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4

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Details

Has protein modificationY

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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: 3.23 Å3/Da / Density % sol: 61.87 %
Crystal growTemperature: 295 K / Method: liquid diffusion / pH: 7
Details: pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03315 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03315 Å / Relative weight: 1
ReflectionResolution: 3.2→100 Å / Num. obs: 874708 / % possible obs: 95.5 % / Redundancy: 2.87 % / CC1/2: 0.987 / Rrim(I) all: 0.309 / Rsym value: 0.278 / Net I/av σ(I): 3.94 / Net I/σ(I): 3.94
Reflection shellResolution: 3.2→3.3 Å / Redundancy: 2.49 % / Mean I/σ(I) obs: 0.82 / CC1/2: 0.182 / % possible all: 95

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4V67

4v67


Resolution: 3.2→100 Å / SU ML: 0.59 / Data cutoff low absF: 1.34 / Cross valid method: FREE R-VALUE / Phase error: 34.93
RfactorNum. reflection% reflectionSelection details
Rfree0.321 43730 5 %random 5%
Rwork0.268 ---
obs0.271 874593 95.5 %-
Solvent computationVDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.2→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms94725 199983 375 0 295083
LS refinement shellResolution: 3.2→3.3 Å
Num. reflection% reflection
Rfree4395 5 %
Rwork82287 -
obs-95 %

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