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- PDB-5hau: Crystal structure of antimicrobial peptide Bac7(1-19) bound to th... -

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Basic information

Entry
Database: PDB / ID: 5hau
TitleCrystal structure of antimicrobial peptide Bac7(1-19) bound to the Thermus thermophilus 70S ribosome
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 31
  • 16S Ribosomal RNA
  • 23S Ribosomal RNA
  • 5S Ribosomal RNA
  • Cathelicidin-3
  • Chimera protein of 50S ribosomal protein L9 and Elongation factor G
  • P-site tRNA
  • mRNAMessenger RNA
KeywordsRibosome/Antibiotic / Bac7 / antimicrobial peptide / antibiotic / 70S ribosome / inhibition of translation / peptidyl transferase inhibitors / 50S ribosomal subunit / peptide exit tunnel / Ribosome-Antibiotic Complex
Function / homology
Function and homology information


translation elongation factor activity / large ribosomal subunit rRNA binding / large ribosomal subunit / regulation of translation / small ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome ...translation elongation factor activity / large ribosomal subunit rRNA binding / large ribosomal subunit / regulation of translation / small ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / defense response to bacterium / ribonucleoprotein complex / translation / mRNA binding / GTPase activity / GTP binding / zinc ion binding / extracellular region / metal ion binding / cytoplasm
Similarity search - Function
Cathelicidin / Cathelicidins signature 1. / Cathelicidin, conserved site / Cathelicidins signature 2. / Cathelicidin-like / : / Translation elongation factor EFG/EF2 / Elongation factor G, domain III / EFG, domain V / Cystatin superfamily ...Cathelicidin / Cathelicidins signature 1. / Cathelicidin, conserved site / Cathelicidins signature 2. / Cathelicidin-like / : / Translation elongation factor EFG/EF2 / Elongation factor G, domain III / EFG, domain V / Cystatin superfamily / Elongation Factor G, domain II / Elongation Factor G, domain III / Ribosomal protein L1, bacterial-type / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / 30S ribosomal protein Thx / 30S ribosomal protein Thx / Elongation factor G C-terminus / 30S ribosomal protein / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein L10 / EF-G domain III/V-like / : / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Ribosomal protein S14, type Z / Ribosomal protein L1, conserved site / Ribosomal protein L1 / Ribosomal protein L1 signature. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Translation elongation factor EFTu-like, domain 2 / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Elongation factor Tu domain 2 / Ribosomal protein L1p/L10e family / Ribosomal protein L11, bacterial-type / Ribosomal protein L31 type A / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L11, conserved site / Ribosomal protein L10-like domain superfamily / Ribosomal protein L10P / Ribosomal protein L10 / Ribosomal protein L11 signature. / Ribosomal protein L11, N-terminal / 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 protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11, RNA binding domain / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein S14/S29 / Ribosomal protein L36 signature. / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L32p, bacterial type / 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 L28 / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L20 signature. / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature.
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / 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 ...GUANOSINE-5'-DIPHOSPHATE / 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 / Cathelicidin-3 / 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 / Elongation factor G / 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 bL36 / 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 uL11 / Large ribosomal subunit protein uL1 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS18 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein bL17
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
Escherichia coli (E. coli)
Thermus thermophilus HB8 (bacteria)
Enterobacteria phage T4 (virus)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsGagnon, M.G. / Roy, R.N. / Lomakin, I.B. / Florin, T. / Mankin, A.S. / Steitz, T.A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM022778 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM106386 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: Structures of proline-rich peptides bound to the ribosome reveal a common mechanism of protein synthesis inhibition.
Authors: Gagnon, M.G. / Roy, R.N. / Lomakin, I.B. / Florin, T. / Mankin, A.S. / Steitz, T.A.
History
DepositionDec 30, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Feb 5, 2020Group: Derived calculations / Category: pdbx_struct_assembly_gen / Item: _pdbx_struct_assembly_gen.asym_id_list
Revision 1.4Mar 6, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / 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_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1A: 23S Ribosomal RNA
1B: 5S Ribosomal RNA
1C: 50S ribosomal protein L1
1D: 50S ribosomal protein L2
1E: 50S ribosomal protein L3
1F: 50S ribosomal protein L4
1G: 50S ribosomal protein L5
1H: 50S ribosomal protein L6
1J: 50S ribosomal protein L10
1K: 50S ribosomal protein L11
1L: 50S ribosomal protein L13
1M: 50S ribosomal protein L14
1N: 50S ribosomal protein L15
1O: 50S ribosomal protein L16
1P: 50S ribosomal protein L17
1Q: 50S ribosomal protein L18
1R: 50S ribosomal protein L19
1S: 50S ribosomal protein L20
1T: 50S ribosomal protein L21
1U: 50S ribosomal protein L22
1V: 50S ribosomal protein L23
1W: 50S ribosomal protein L24
1X: 50S ribosomal protein L25
1Y: 50S ribosomal protein L27
1Z: 50S ribosomal protein L28
10: 50S ribosomal protein L29
11: 50S ribosomal protein L30
12: 50S ribosomal protein L31
13: 50S ribosomal protein L32
14: 50S ribosomal protein L33
15: 50S ribosomal protein L34
16: 50S ribosomal protein L35
17: 50S ribosomal protein L36
1a: 16S Ribosomal RNA
1b: 30S ribosomal protein S2
1c: 30S ribosomal protein S3
1d: 30S ribosomal protein S4
1e: 30S ribosomal protein S5
1f: 30S ribosomal protein S6
1g: 30S ribosomal protein S7
1h: 30S ribosomal protein S8
1i: 30S ribosomal protein S9
1j: 30S ribosomal protein S10
1k: 30S ribosomal protein S11
1l: 30S ribosomal protein S12
1m: 30S ribosomal protein S13
1n: 30S ribosomal protein S14 type Z
1o: 30S ribosomal protein S15
1p: 30S ribosomal protein S16
1q: 30S ribosomal protein S17
1r: 30S ribosomal protein S18
1s: 30S ribosomal protein S19
1t: 30S ribosomal protein S20
1u: 30S ribosomal protein Thx
1z: Chimera protein of 50S ribosomal protein L9 and Elongation factor G
1y: mRNA
1w: P-site tRNA
1x: Cathelicidin-3
2A: 23S Ribosomal RNA
2B: 5S Ribosomal RNA
2C: 50S ribosomal protein L1
2D: 50S ribosomal protein L2
2E: 50S ribosomal protein L3
2F: 50S ribosomal protein L4
2G: 50S ribosomal protein L5
2H: 50S ribosomal protein L6
2J: 50S ribosomal protein L10
2K: 50S ribosomal protein L11
2L: 50S ribosomal protein L13
2M: 50S ribosomal protein L14
2N: 50S ribosomal protein L15
2O: 50S ribosomal protein L16
2P: 50S ribosomal protein L17
2Q: 50S ribosomal protein L18
2R: 50S ribosomal protein L19
2S: 50S ribosomal protein L20
2T: 50S ribosomal protein L21
2U: 50S ribosomal protein L22
2V: 50S ribosomal protein L23
2W: 50S ribosomal protein L24
2X: 50S ribosomal protein L25
2Y: 50S ribosomal protein L27
2Z: 50S ribosomal protein L28
20: 50S ribosomal protein L29
21: 50S ribosomal protein L30
22: 50S ribosomal protein L31
23: 50S ribosomal protein L32
24: 50S ribosomal protein L33
25: 50S ribosomal protein L34
26: 50S ribosomal protein L35
27: 50S ribosomal protein L36
2a: 16S Ribosomal RNA
2b: 30S ribosomal protein S2
2c: 30S ribosomal protein S3
2d: 30S ribosomal protein S4
2e: 30S ribosomal protein S5
2f: 30S ribosomal protein S6
2g: 30S ribosomal protein S7
2h: 30S ribosomal protein S8
2i: 30S ribosomal protein S9
2j: 30S ribosomal protein S10
2k: 30S ribosomal protein S11
2l: 30S ribosomal protein S12
2m: 30S ribosomal protein S13
2n: 30S ribosomal protein S14 type Z
2o: 30S ribosomal protein S15
2p: 30S ribosomal protein S16
2q: 30S ribosomal protein S17
2r: 30S ribosomal protein S18
2s: 30S ribosomal protein S19
2t: 30S ribosomal protein S20
2u: 30S ribosomal protein Thx
2z: Chimera protein of 50S ribosomal protein L9 and Elongation factor G
2y: mRNA
2w: P-site tRNA
2x: Cathelicidin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,713,1502061
Polymers4,663,891116
Non-polymers49,2591945
Water44,3352461
1
1A: 23S Ribosomal RNA
1B: 5S Ribosomal RNA
1C: 50S ribosomal protein L1
1D: 50S ribosomal protein L2
1E: 50S ribosomal protein L3
1F: 50S ribosomal protein L4
1G: 50S ribosomal protein L5
1H: 50S ribosomal protein L6
1J: 50S ribosomal protein L10
1K: 50S ribosomal protein L11
1L: 50S ribosomal protein L13
1M: 50S ribosomal protein L14
1N: 50S ribosomal protein L15
1O: 50S ribosomal protein L16
1P: 50S ribosomal protein L17
1Q: 50S ribosomal protein L18
1R: 50S ribosomal protein L19
1S: 50S ribosomal protein L20
1T: 50S ribosomal protein L21
1U: 50S ribosomal protein L22
1V: 50S ribosomal protein L23
1W: 50S ribosomal protein L24
1X: 50S ribosomal protein L25
1Y: 50S ribosomal protein L27
1Z: 50S ribosomal protein L28
10: 50S ribosomal protein L29
11: 50S ribosomal protein L30
12: 50S ribosomal protein L31
13: 50S ribosomal protein L32
14: 50S ribosomal protein L33
15: 50S ribosomal protein L34
16: 50S ribosomal protein L35
17: 50S ribosomal protein L36
1a: 16S Ribosomal RNA
1b: 30S ribosomal protein S2
1c: 30S ribosomal protein S3
1d: 30S ribosomal protein S4
1e: 30S ribosomal protein S5
1f: 30S ribosomal protein S6
1g: 30S ribosomal protein S7
1h: 30S ribosomal protein S8
1i: 30S ribosomal protein S9
1j: 30S ribosomal protein S10
1k: 30S ribosomal protein S11
1l: 30S ribosomal protein S12
1m: 30S ribosomal protein S13
1n: 30S ribosomal protein S14 type Z
1o: 30S ribosomal protein S15
1p: 30S ribosomal protein S16
1q: 30S ribosomal protein S17
1r: 30S ribosomal protein S18
1s: 30S ribosomal protein S19
1t: 30S ribosomal protein S20
1u: 30S ribosomal protein Thx
1z: Chimera protein of 50S ribosomal protein L9 and Elongation factor G
1y: mRNA
1w: P-site tRNA
1x: Cathelicidin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,359,4071147
Polymers2,331,94658
Non-polymers27,4611089
Water59433
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
2A: 23S Ribosomal RNA
2B: 5S Ribosomal RNA
2C: 50S ribosomal protein L1
2D: 50S ribosomal protein L2
2E: 50S ribosomal protein L3
2F: 50S ribosomal protein L4
2G: 50S ribosomal protein L5
2H: 50S ribosomal protein L6
2J: 50S ribosomal protein L10
2K: 50S ribosomal protein L11
2L: 50S ribosomal protein L13
2M: 50S ribosomal protein L14
2N: 50S ribosomal protein L15
2O: 50S ribosomal protein L16
2P: 50S ribosomal protein L17
2Q: 50S ribosomal protein L18
2R: 50S ribosomal protein L19
2S: 50S ribosomal protein L20
2T: 50S ribosomal protein L21
2U: 50S ribosomal protein L22
2V: 50S ribosomal protein L23
2W: 50S ribosomal protein L24
2X: 50S ribosomal protein L25
2Y: 50S ribosomal protein L27
2Z: 50S ribosomal protein L28
20: 50S ribosomal protein L29
21: 50S ribosomal protein L30
22: 50S ribosomal protein L31
23: 50S ribosomal protein L32
24: 50S ribosomal protein L33
25: 50S ribosomal protein L34
26: 50S ribosomal protein L35
27: 50S ribosomal protein L36
2a: 16S Ribosomal RNA
2b: 30S ribosomal protein S2
2c: 30S ribosomal protein S3
2d: 30S ribosomal protein S4
2e: 30S ribosomal protein S5
2f: 30S ribosomal protein S6
2g: 30S ribosomal protein S7
2h: 30S ribosomal protein S8
2i: 30S ribosomal protein S9
2j: 30S ribosomal protein S10
2k: 30S ribosomal protein S11
2l: 30S ribosomal protein S12
2m: 30S ribosomal protein S13
2n: 30S ribosomal protein S14 type Z
2o: 30S ribosomal protein S15
2p: 30S ribosomal protein S16
2q: 30S ribosomal protein S17
2r: 30S ribosomal protein S18
2s: 30S ribosomal protein S19
2t: 30S ribosomal protein S20
2u: 30S ribosomal protein Thx
2z: Chimera protein of 50S ribosomal protein L9 and Elongation factor G
2y: mRNA
2w: P-site tRNA
2x: Cathelicidin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,353,743914
Polymers2,331,94658
Non-polymers21,798856
Water52229
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)208.782, 449.030, 619.335
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11segid S031 or segid S071 or segid S091 or segid...
21segid S032 or segid S072 or segid S092 or segid...
12segid 16S1 and resid 71:95
22segid 16S2 and resid 71:95
13segid 16S1 and resid 1386:1477
23segid 16S2 and resid 1386:1477
14segid S021 or segid S041 or segid S051 or segid...
24segid S022 or segid S042 or segid S052 or segid...
15segid EFG1 and resid -66:7
25segid EFG1 and resid 8:802
35segid EFG2 and resid -66:7
45segid EFG2 and resid 8:802
16segid L011 or (segid 23S1 and resid 2117:2214)
26segid L012 or (segid 23S2 and resid 2117:2214)
17(segid L*1 and not ((segid L091 and resid 41:146) or...
27(segid L*2 and not ((segid L092 and resid 41:146) or...
18segid mRN1
28segid mRN2
19segid PtR1
29segid PtR2
110segid BAC1
210segid BAC2

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth seq-ID
111segid S031 or segid S071 or segid S091 or segid...0
211segid S032 or segid S072 or segid S092 or segid...0
112segid 16S1 and resid 71:950
212segid 16S2 and resid 71:950
113segid 16S1 and resid 1386:14770
213segid 16S2 and resid 1386:14770
114segid S021 or segid S041 or segid S051 or segid...0
214segid S022 or segid S042 or segid S052 or segid...0
115segid EFG1 and resid -66:70
215segid EFG1 and resid 8:8020
315segid EFG2 and resid -66:70
415segid EFG2 and resid 8:8020
116segid L011 or (segid 23S1 and resid 2117:2214)0
216segid L012 or (segid 23S2 and resid 2117:2214)0
117(segid L*1 and not ((segid L091 and resid 41:146) or...0
217(segid L*2 and not ((segid L092 and resid 41:146) or...0
118segid mRN10
218segid mRN20
119segid PtR10
219segid PtR20
1110segid BAC10
2110segid BAC20

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10

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Components

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RNA chain , 5 types, 10 molecules 1A2A1B2B1a2a1y2y1w2w

#1: RNA chain 23S Ribosomal RNA /


Mass: 947895.375 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: GenBank: 55771382
#2: RNA chain 5S Ribosomal RNA /


Mass: 39188.371 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: GenBank: 55771382
#34: RNA chain 16S Ribosomal RNA /


Mass: 493652.156 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: GenBank: 55771382
#56: RNA chain mRNA / Messenger RNA


Mass: 7804.735 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: IDT-Synthesized 24-nt M-F-Stop mRNA / Source: (synth.) Enterobacteria phage T4 (virus)
#57: RNA chain P-site tRNA


Mass: 24846.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Initiator Methionine tRNA / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE-600 / Production host: Escherichia coli (E. coli) / Strain (production host): MRE-600

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50S ribosomal protein ... , 31 types, 62 molecules 1C2C1D2D1E2E1F2F1G2G1H2H1J2J1K2K1L2L1M2M1N2N1O2O1P2P1Q2Q1R2R...

#3: Protein 50S ribosomal protein L1 /


Mass: 24872.721 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SLP7
#4: Protein 50S ribosomal protein L2 /


Mass: 30532.551 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P60405
#5: Protein 50S ribosomal protein L3 /


Mass: 22450.213 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHN8
#6: 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHN9
#7: Protein 50S ribosomal protein L5 /


Mass: 21061.596 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ0
#8: Protein 50S ribosomal protein L6 /


Mass: 19568.926 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ3, UniProt: P0DOY8*PLUS
#9: Protein 50S ribosomal protein L10 /


Mass: 18586.639 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q8VVE3
#10: Protein 50S ribosomal protein L11 /


Mass: 15526.111 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SLP6
#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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P60488
#12: Protein 50S ribosomal protein L14 /


Mass: 13323.612 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP8
#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 HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ7
#14: Protein 50S ribosomal protein L16 /


Mass: 15993.909 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P60489
#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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q9Z9H5
#16: 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ4
#17: Protein 50S ribosomal protein L19 /


Mass: 17188.830 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P60490
#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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P60491
#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 HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P60492
#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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP3
#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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP0
#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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP9
#23: 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHZ1
#24: Protein 50S ribosomal protein L27 /


Mass: 9529.074 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P60493
#25: Protein 50S ribosomal protein L28 /


Mass: 11004.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P60494
#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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP6
#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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ6
#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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SJE1
#29: Protein 50S ribosomal protein L32 /


Mass: 6722.050 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P35871
#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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80340
#32: Protein 50S ribosomal protein L35 /


Mass: 7506.178 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SKU1
#33: Protein/peptide 50S ribosomal protein L36 / / Ribosomal protein B


Mass: 4435.411 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHR2

-
30S ribosomal protein ... , 20 types, 40 molecules 1b2b1c2c1d2d1e2e1f2f1g2g1h2h1i2i1j2j1k2k1l2l1m2m1n2n1o2o1p2p...

#35: Protein 30S ribosomal protein S2 /


Mass: 29317.703 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80371
#36: Protein 30S ribosomal protein S3 /


Mass: 26751.076 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80372
#37: Protein 30S ribosomal protein S4 /


Mass: 24373.447 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80373
#38: Protein 30S ribosomal protein S5 /


Mass: 17583.416 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ5
#39: 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SLP8
#40: Protein 30S ribosomal protein S7 /


Mass: 18050.973 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P17291
#41: 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 HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ2, UniProt: A0A0M9AFS9*PLUS
#42: Protein 30S ribosomal protein S9 /


Mass: 14410.614 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80374
#43: Protein 30S ribosomal protein S10 /


Mass: 11954.968 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHN7
#44: Protein 30S ribosomal protein S11 /


Mass: 13737.868 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80376
#45: Protein 30S ribosomal protein S12 /


Mass: 14637.384 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHN3
#46: Protein 30S ribosomal protein S13 /


Mass: 14338.861 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80377
#47: Protein 30S ribosomal protein S14 type Z / Ribosome


Mass: 7158.725 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ1, UniProt: A0A0N0BLP2*PLUS
#48: Protein 30S ribosomal protein S15 /


Mass: 10578.407 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SJ76
#49: Protein 30S ribosomal protein S16 /


Mass: 10409.983 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SJH3
#50: Protein 30S ribosomal protein S17 /


Mass: 12325.655 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP7, UniProt: A0A0N0BLS5*PLUS
#51: Protein 30S ribosomal protein S18 /


Mass: 10258.299 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SLQ0
#52: Protein 30S ribosomal protein S19 /


Mass: 10605.464 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP2
#53: Protein 30S ribosomal protein S20 /


Mass: 11736.143 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80380
#54: Protein/peptide 30S ribosomal protein Thx / Ribosome / S31


Mass: 3350.030 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SIH3

-
Protein / Protein/peptide , 2 types, 4 molecules 1z2z1x2x

#55: Protein Chimera protein of 50S ribosomal protein L9 and Elongation factor G / / EF-G


Mass: 84416.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: L9-EFG protein fusion / Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / Gene: rplI, TTHA0242, fusA, fus, TTHA1695 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Star / References: UniProt: Q5SLQ1, UniProt: Q5SHN5
#58: Protein/peptide Cathelicidin-3 / / Bactenecin-7 / Bac7 / PR-59


Mass: 4218.171 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: GenScript-Synthesized peptide Bac7(1-35) / Source: (synth.) Bos taurus (cattle) / References: UniProt: P19661

-
Non-polymers , 5 types, 4406 molecules

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


Mass: 24.305 Da / Num. of mol.: 1929 / Source method: obtained synthetically / Formula: Mg
#60: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#61: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#62: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#63: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2461 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.66 % / Description: Long needles
Crystal growTemperature: 292 K / Method: vapor diffusion
Details: 0.15M Arginine-HCl, 0.1M Tris-HCl pH 7.3-7.6, 2.6-2.9% PEG-20K, 9-10% MPD, 0.5 mM BME
PH range: 7.3-7.6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 16, 2015 / Details: S/N 60-0112-F
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 1150981 / Num. obs: 1140965 / % possible obs: 99.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): -3 / Redundancy: 4.642 % / Biso Wilson estimate: 55.67 Å2 / Rmerge F obs: 0.986 / Rmerge(I) obs: 0.263 / Rrim(I) all: 0.296 / Χ2: 0.979 / Net I/σ(I): 7.04 / Num. measured all: 5295862
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3-3.181.1981.348126791846351810740.3711.35698.1
3.18-3.40.7572.238289841736021732820.6090.8599.8
3.4-3.670.5273.167514591619091611580.7580.59399.5
3.67-4.020.3444.766746091491421479850.8820.38899.2
4.02-4.490.2466.856408191350521348240.9410.27699.8
4.49-5.170.1729.275345471196411182760.9690.19498.9
5.17-6.320.1311.984874101015881013180.9830.14699.7
6.32-8.860.08316.6135830279278781610.9920.09498.6
8.86-49.6580.0336.9920705346134448870.9990.03497.3

-
Processing

Software
NameVersionClassificationNB
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Coot0.8.1model building
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→49.478 Å / FOM work R set: 0.8142 / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2645 57144 5.01 %
Rwork0.2082 1082580 -
obs0.2111 1139724 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 278.29 Å2 / Biso mean: 60.08 Å2 / Biso min: 4.52 Å2
Refinement stepCycle: final / Resolution: 3→49.478 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms105235 196675 4335 139 306384
Biso mean--45.04 31.73 -
Num. residues----22627
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005330831
X-RAY DIFFRACTIONf_angle_d0.962490269
X-RAY DIFFRACTIONf_chiral_restr0.04261646
X-RAY DIFFRACTIONf_plane_restr0.00527834
X-RAY DIFFRACTIONf_dihedral_angle_d15.714151105
Refine LS restraints NCS
Ens-IDDom-IDNumberRefine-IDRmsType
1118408X-RAY DIFFRACTION11.931TORSIONAL
1218408X-RAY DIFFRACTION11.931TORSIONAL
21420X-RAY DIFFRACTION11.931TORSIONAL
22420X-RAY DIFFRACTION11.931TORSIONAL
312148X-RAY DIFFRACTION11.931TORSIONAL
322148X-RAY DIFFRACTION11.931TORSIONAL
4135359X-RAY DIFFRACTION11.931TORSIONAL
4235359X-RAY DIFFRACTION11.931TORSIONAL
516273X-RAY DIFFRACTION11.931TORSIONAL
526273X-RAY DIFFRACTION11.931TORSIONAL
536273X-RAY DIFFRACTION11.931TORSIONAL
546273X-RAY DIFFRACTION11.931TORSIONAL
611104X-RAY DIFFRACTION11.931TORSIONAL
621104X-RAY DIFFRACTION11.931TORSIONAL
7132503X-RAY DIFFRACTION11.931TORSIONAL
7232503X-RAY DIFFRACTION11.931TORSIONAL
81114X-RAY DIFFRACTION11.931TORSIONAL
82114X-RAY DIFFRACTION11.931TORSIONAL
911724X-RAY DIFFRACTION11.931TORSIONAL
921724X-RAY DIFFRACTION11.931TORSIONAL
101166X-RAY DIFFRACTION11.931TORSIONAL
102166X-RAY DIFFRACTION11.931TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3-3.03410.373818910.3318355743746598
3.0341-3.06980.35818460.307355843743098
3.0698-3.10720.351219080.295358593776799
3.1072-3.14650.339918760.28443613538011100
3.1465-3.18790.337418920.27533603237924100
3.1879-3.23160.336418740.27343609737971100
3.2316-3.27780.324919090.26763614938058100
3.2778-3.32670.312518790.24923613038009100
3.3267-3.37860.314918450.24533606937914100
3.3786-3.4340.304519110.24293607737988100
3.434-3.49320.295419080.23623613238040100
3.4932-3.55670.283419600.23223595737917100
3.5567-3.62510.28318280.2267360243785299
3.6251-3.69910.281919070.2193358303773799
3.6991-3.77950.283419070.2185355793748698
3.7795-3.86740.265618460.2034360933793999
3.8674-3.9640.267518870.20453616638053100
3.964-4.07120.255319140.19543619338107100
4.0712-4.19090.250719550.19113623138186100
4.1909-4.32610.250419180.19323616538083100
4.3261-4.48060.253719240.18813624938173100
4.4806-4.65990.237419380.18163615038088100
4.6599-4.87180.237119120.1794359283784099
4.8718-5.12840.23619040.1747356563756098
5.1284-5.44930.228419220.16593639038312100
5.4493-5.86950.224219380.16423636738305100
5.8695-6.4590.228219430.17233646638409100
6.459-7.3910.233118850.1749360353792098
7.391-9.30170.229120080.1807364183842699
9.3017-49.4850.226719090.1999368453875498

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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