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- PDB-4v8j: Crystal structure of the bacterial ribosome ram mutation G347U. -

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Basic information

Entry
Database: PDB / ID: 4v8j
TitleCrystal structure of the bacterial ribosome ram mutation G347U.
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 30
  • 16S rRNA
  • 23S rRNA23S ribosomal RNA
  • 5S rRNA5S ribosomal RNA
  • messenger RNA
  • tRNA-Phe
  • tRNA-fMet
KeywordsRIBOSOME / Protein biosynthesis / ribosomes / RNA / tRNA / transfer / ribosomal ambiguity mutations / ram / 30S / 70S / 16S / ribosomal subunit / PAROMOMYCIN as crystallization agent
Function / homology
Function and homology information


large ribosomal subunit / regulation of translation / small ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex ...large ribosomal subunit / regulation of translation / small ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / zinc ion binding / metal ion binding / cytoplasm
Similarity search - Function
Ribosomal protein L1, bacterial-type / 30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein S14, type Z / Ribosomal protein L1, conserved site ...Ribosomal protein L1, bacterial-type / 30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein S14, type Z / Ribosomal protein L1, conserved site / Ribosomal protein L1 / Ribosomal protein L1 signature. / 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 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. / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S4, bacterial-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L33 superfamily / : / Ribosomal protein L30, bacterial-type / Ribosomal protein L16 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / L28p-like / Ribosomal protein L20 / Ribosomal protein S16 / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L21 / Ribosomal protein L27
Similarity search - Domain/homology
PAROMOMYCIN / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 ...PAROMOMYCIN / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein 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 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 uL1 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS18 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein bL17
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.9 Å
AuthorsFagan, C.E. / Dunkle, J.A. / Maehigashi, T. / Dunham, C.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Reorganization of an intersubunit bridge induced by disparate 16S ribosomal ambiguity mutations mimics an EF-Tu-bound state.
Authors: Fagan, C.E. / Dunkle, J.A. / Maehigashi, T. / Dang, M.N. / Devaraj, A. / Miles, S.J. / Qin, D. / Fredrick, K. / Dunham, C.M.
History
DepositionDec 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 3V6U, 3V6V, 3V6W, 3V6X
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AA: 16S rRNA
AB: 30S ribosomal protein S2
AC: 30S ribosomal protein S3
AD: 30S ribosomal protein S4
AE: 30S ribosomal protein S5
AF: 30S ribosomal protein S6
AG: 30S ribosomal protein S7
AH: 30S ribosomal protein S8
AI: 30S ribosomal protein S9
AJ: 30S ribosomal protein S10
AK: 30S ribosomal protein S11
AL: 30S ribosomal protein S12
AM: 30S ribosomal protein S13
AN: 30S ribosomal protein S14
AO: 30S ribosomal protein S15
AP: 30S ribosomal protein S16
AQ: 30S ribosomal protein S17
AR: 30S ribosomal protein S18
AS: 30S ribosomal protein S19
AT: 30S ribosomal protein S20
AU: 30S ribosomal protein THX
AW: tRNA-Phe
AV: tRNA-fMet
AY: tRNA-Phe
AX: messenger RNA
BA: 23S rRNA
BB: 5S rRNA
BC: 50S ribosomal protein L1
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
BI: 50S ribosomal protein L9
BN: 50S ribosomal protein L13
BO: 50S ribosomal protein L14
BP: 50S ribosomal protein L15
BQ: 50S ribosomal protein L16
BR: 50S ribosomal protein L17
BS: 50S ribosomal protein L18
BT: 50S ribosomal protein L19
BU: 50S ribosomal protein L20
BV: 50S ribosomal protein L21
BW: 50S ribosomal protein L22
BX: 50S ribosomal protein L23
BY: 50S ribosomal protein L24
BZ: 50S ribosomal protein L25
B0: 50S ribosomal protein L27
B1: 50S ribosomal protein L28
B2: 50S ribosomal protein L29
B3: 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
B9: 50S ribosomal protein L36
CA: 16S rRNA
CB: 30S ribosomal protein S2
CC: 30S ribosomal protein S3
CD: 30S ribosomal protein S4
CE: 30S ribosomal protein S5
CF: 30S ribosomal protein S6
CG: 30S ribosomal protein S7
CH: 30S ribosomal protein S8
CI: 30S ribosomal protein S9
CJ: 30S ribosomal protein S10
CK: 30S ribosomal protein S11
CL: 30S ribosomal protein S12
CM: 30S ribosomal protein S13
CN: 30S ribosomal protein S14
CO: 30S ribosomal protein S15
CP: 30S ribosomal protein S16
CQ: 30S ribosomal protein S17
CR: 30S ribosomal protein S18
CS: 30S ribosomal protein S19
CT: 30S ribosomal protein S20
CU: 30S ribosomal protein THX
CW: tRNA-Phe
CV: tRNA-fMet
CY: tRNA-Phe
CX: messenger RNA
DA: 23S rRNA
DB: 5S rRNA
DC: 50S ribosomal protein L1
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
DI: 50S ribosomal protein L9
DN: 50S ribosomal protein L13
DO: 50S ribosomal protein L14
DP: 50S ribosomal protein L15
DQ: 50S ribosomal protein L16
DR: 50S ribosomal protein L17
DS: 50S ribosomal protein L18
DT: 50S ribosomal protein L19
DU: 50S ribosomal protein L20
DV: 50S ribosomal protein L21
DW: 50S ribosomal protein L22
DX: 50S ribosomal protein L23
DY: 50S ribosomal protein L24
DZ: 50S ribosomal protein L25
D0: 50S ribosomal protein L27
D1: 50S ribosomal protein L28
D2: 50S ribosomal protein L29
D3: 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
D9: 50S ribosomal protein L36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,570,456860
Polymers4,550,977114
Non-polymers19,479746
Water0
1
AA: 16S rRNA
AB: 30S ribosomal protein S2
AC: 30S ribosomal protein S3
AD: 30S ribosomal protein S4
AE: 30S ribosomal protein S5
AF: 30S ribosomal protein S6
AG: 30S ribosomal protein S7
AH: 30S ribosomal protein S8
AI: 30S ribosomal protein S9
AJ: 30S ribosomal protein S10
AK: 30S ribosomal protein S11
AL: 30S ribosomal protein S12
AM: 30S ribosomal protein S13
AN: 30S ribosomal protein S14
AO: 30S ribosomal protein S15
AP: 30S ribosomal protein S16
AQ: 30S ribosomal protein S17
AR: 30S ribosomal protein S18
AS: 30S ribosomal protein S19
AT: 30S ribosomal protein S20
AU: 30S ribosomal protein THX
AW: tRNA-Phe
AV: tRNA-fMet
AY: tRNA-Phe
AX: messenger RNA
BA: 23S rRNA
BB: 5S rRNA
BC: 50S ribosomal protein L1
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
BI: 50S ribosomal protein L9
BN: 50S ribosomal protein L13
BO: 50S ribosomal protein L14
BP: 50S ribosomal protein L15
BQ: 50S ribosomal protein L16
BR: 50S ribosomal protein L17
BS: 50S ribosomal protein L18
BT: 50S ribosomal protein L19
BU: 50S ribosomal protein L20
BV: 50S ribosomal protein L21
BW: 50S ribosomal protein L22
BX: 50S ribosomal protein L23
BY: 50S ribosomal protein L24
BZ: 50S ribosomal protein L25
B0: 50S ribosomal protein L27
B1: 50S ribosomal protein L28
B2: 50S ribosomal protein L29
B3: 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
B9: 50S ribosomal protein L36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,285,203429
Polymers2,275,48857
Non-polymers9,715372
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
CA: 16S rRNA
CB: 30S ribosomal protein S2
CC: 30S ribosomal protein S3
CD: 30S ribosomal protein S4
CE: 30S ribosomal protein S5
CF: 30S ribosomal protein S6
CG: 30S ribosomal protein S7
CH: 30S ribosomal protein S8
CI: 30S ribosomal protein S9
CJ: 30S ribosomal protein S10
CK: 30S ribosomal protein S11
CL: 30S ribosomal protein S12
CM: 30S ribosomal protein S13
CN: 30S ribosomal protein S14
CO: 30S ribosomal protein S15
CP: 30S ribosomal protein S16
CQ: 30S ribosomal protein S17
CR: 30S ribosomal protein S18
CS: 30S ribosomal protein S19
CT: 30S ribosomal protein S20
CU: 30S ribosomal protein THX
CW: tRNA-Phe
CV: tRNA-fMet
CY: tRNA-Phe
CX: messenger RNA
DA: 23S rRNA
DB: 5S rRNA
DC: 50S ribosomal protein L1
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
DI: 50S ribosomal protein L9
DN: 50S ribosomal protein L13
DO: 50S ribosomal protein L14
DP: 50S ribosomal protein L15
DQ: 50S ribosomal protein L16
DR: 50S ribosomal protein L17
DS: 50S ribosomal protein L18
DT: 50S ribosomal protein L19
DU: 50S ribosomal protein L20
DV: 50S ribosomal protein L21
DW: 50S ribosomal protein L22
DX: 50S ribosomal protein L23
DY: 50S ribosomal protein L24
DZ: 50S ribosomal protein L25
D0: 50S ribosomal protein L27
D1: 50S ribosomal protein L28
D2: 50S ribosomal protein L29
D3: 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
D9: 50S ribosomal protein L36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,285,252431
Polymers2,275,48857
Non-polymers9,764374
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)210.197, 446.163, 620.953
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 , 6 types, 14 molecules AACAAWAYCWCYAVCVAXCXBADABBDB

#1: RNA chain 16S rRNA /


Mass: 493919.250 Da / Num. of mol.: 2 / Mutation: G347U / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: GenBank: AP008226.1
#22: RNA chain
tRNA-Phe


Mass: 24485.539 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: E-SITE TRNA PHE OR A-SITE TRNA PHE / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: GenBank: AP012306.1
#23: RNA chain tRNA-fMet


Mass: 24802.785 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: P-SITE TRNA-FMET / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: GenBank: AP012306.1
#24: RNA chain messenger RNA /


Mass: 7827.775 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: RNA oligonucleotide
#25: RNA chain 23S rRNA / 23S ribosomal RNA


Mass: 948240.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: GenBank: AP008226.1
#26: RNA chain 5S rRNA / 5S ribosomal RNA


Mass: 39494.535 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: GenBank: AP008226.1

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

#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: A0A0M9AFS9*PLUS
#9: Protein 30S ribosomal protein S9 /


Mass: 14410.614 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (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: Q5SHQ1, UniProt: A0A0N0BLP2*PLUS
#15: Protein 30S ribosomal protein S15 /


Mass: 10578.407 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (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: A0A0N0BLS5*PLUS
#18: Protein 30S ribosomal protein S18 /


Mass: 10258.299 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (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 / Ribosome


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

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

#27: Protein 50S ribosomal protein L1 /


Mass: 24872.721 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q5SLP7
#28: 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) / References: UniProt: P60405
#29: 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) / References: UniProt: Q5SHN8
#30: Protein 50S ribosomal protein L4 /


Mass: 23271.914 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q5SHN9
#31: 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) / References: UniProt: Q5SHQ0
#32: 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) / References: UniProt: Q5SHQ3, UniProt: P0DOY8*PLUS
#33: 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) / References: UniProt: Q5SLQ1
#34: 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) / References: UniProt: P60488
#35: 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) / References: UniProt: Q5SHP8
#36: 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) / References: UniProt: Q5SHQ7
#37: 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) / References: UniProt: P60489
#38: 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) / References: UniProt: Q9Z9H5
#39: Protein 50S ribosomal protein L18 /


Mass: 12639.845 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q5SHQ4
#40: 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) / References: UniProt: P60490
#41: 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) / References: UniProt: P60491
#42: 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) / References: UniProt: P60492
#43: 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) / References: UniProt: Q5SHP3
#44: 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) / References: UniProt: Q5SHP0
#45: 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) / References: UniProt: Q5SHP9
#46: Protein 50S ribosomal protein L25 /


Mass: 23238.572 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q5SHZ1
#47: 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) / References: UniProt: P60493
#48: 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) / References: UniProt: P60494
#49: 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) / References: UniProt: Q5SHP6
#50: 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) / References: UniProt: Q5SHQ6
#51: 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) / References: UniProt: Q5SJE1
#52: 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) / References: UniProt: P80339
#53: 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) / References: UniProt: P35871
#54: Protein/peptide 50S ribosomal protein L34 /


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


Mass: 7506.178 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q5SKU1
#56: 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 (bacteria) / References: UniProt: Q5SHR2

-
Non-polymers , 3 types, 746 molecules

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


Mass: 24.305 Da / Num. of mol.: 740 / Source method: obtained synthetically / Formula: Mg
#58: Chemical ChemComp-PAR / PAROMOMYCIN / PAROMOMYCIN I, AMMINOSIDIN, CATENULIN, CRESTOMYCIN, MONOMYCIN A, NEOMYCIN E / Paromomycin


Mass: 615.628 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H45N5O14 / Comment: Antimicrobial, medication*YM
#59: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

-
Sample preparation

CrystalDensity Matthews: 3.52 Å3/Da / Density % sol: 65.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 3.5-4.5% PEG 20K, 3.5-4.5% PEG550 MME, 0.1M TRIS-ACETATE, 0.2M KSCN, 10MM MGCL2, PH 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 22, 2011 / Details: MIRRORS
RadiationMonochromator: KOHZU DIAMOND MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3.9→50 Å / Num. obs: 497544 / % possible obs: 94.3 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Rmerge(I) obs: 0.354 / Net I/σ(I): 5.7
Reflection shellResolution: 3.9→4.1 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.409 / Mean I/σ(I) obs: 1.8 / % possible all: 90.9

-
Processing

Software
NameVersionClassificationNB
PHENIX(phenix.refine: 1.8.1_1168)refinement
PDB_EXTRACT3.1data extraction
XDSdata scaling
PHENIX(phenix.refine: 1.7_641)model building
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHENIX1.7_641phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.9→50 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.5 / σ(F): 1.99 / Phase error: 25.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2692 22067 4.44 %
Rwork0.242 --
obs0.2432 496744 94.34 %
all-526847 -
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.704 Å20 Å20 Å2
2--7.0673 Å2-0 Å2
3---23.1822 Å2
Refinement stepCycle: LAST / Resolution: 3.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19156 36123 412 0 55691
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008317247
X-RAY DIFFRACTIONf_angle_d1.203474389
X-RAY DIFFRACTIONf_dihedral_angle_d17.354148011
X-RAY DIFFRACTIONf_chiral_restr0.08660134
X-RAY DIFFRACTIONf_plane_restr0.01225787
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.9-3.94430.36436250.344511959X-RAY DIFFRACTION72
3.9443-3.99070.34078140.300215837X-RAY DIFFRACTION96
3.9907-4.03930.33598330.300215876X-RAY DIFFRACTION95
4.0393-4.09040.30838280.292815746X-RAY DIFFRACTION95
4.0904-4.14420.28468340.285415800X-RAY DIFFRACTION95
4.1442-4.2010.32558440.284515844X-RAY DIFFRACTION95
4.201-4.2610.3068240.27715689X-RAY DIFFRACTION95
4.261-4.32450.29598330.268515722X-RAY DIFFRACTION95
4.3245-4.39210.28168190.263515761X-RAY DIFFRACTION95
4.3921-4.4640.26794960.262716131X-RAY DIFFRACTION95
4.464-4.54090.26594440.252916036X-RAY DIFFRACTION95
4.5409-4.62350.26474900.255816009X-RAY DIFFRACTION95
4.6235-4.71230.26915530.248615989X-RAY DIFFRACTION94
4.7123-4.80840.26996190.247315863X-RAY DIFFRACTION94
4.8084-4.91290.27247190.245715680X-RAY DIFFRACTION94
4.9129-5.02710.27228250.246515706X-RAY DIFFRACTION94
5.0271-5.15270.2688160.232415599X-RAY DIFFRACTION94
5.1527-5.29180.25268120.229215614X-RAY DIFFRACTION94
5.2918-5.44740.25528150.220815709X-RAY DIFFRACTION94
5.4474-5.62290.25448180.225415848X-RAY DIFFRACTION95
5.6229-5.82360.2668090.228615964X-RAY DIFFRACTION96
5.8236-6.05640.25588280.226916036X-RAY DIFFRACTION96
6.0564-6.33150.26878470.231716197X-RAY DIFFRACTION97
6.3315-6.66460.27118370.234416273X-RAY DIFFRACTION97
6.6646-7.0810.25066740.219116379X-RAY DIFFRACTION97
7.081-7.62590.2485410.215316474X-RAY DIFFRACTION96
7.6259-8.390.24576140.216216428X-RAY DIFFRACTION96
8.39-9.59630.24216870.217416287X-RAY DIFFRACTION96
9.5963-12.06140.23047700.210416280X-RAY DIFFRACTION95
12.0614-49.47190.25567990.238215941X-RAY DIFFRACTION91
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.14280.0377-0.07070.20880.06690.2157-0.00680.0232-0.12330.017-0.0648-0.03940.13220.0322-0.30.40050.1267-0.21690.2644-0.18460.341-10.729941.384497.9438
20.08590.0030.02650.0571-0.02490.05950.02120.12210.0013-0.1325-0.0394-0.0171-0.01490.0625-0.01360.27170.0656-0.02720.2031-0.00580.0667-11.1561116.588973.9014
30.2064-0.0190.10010.10770.02610.27630.01520.0996-0.0248-0.1844-0.07390.17410.0291-0.135-0.1040.54470.0825-0.35160.409-0.16380.5245-88.4103102.975361.5308
40.03790.0306-0.01590.0670.02830.08730.0044-0.0004-0.02630.01750.0021-0.03210.03680.0303-0.03240.12630.0303-0.07680.0752-0.04660.0996-15.370184.1893111.7218
50.0018-0.00060.00240.0012-0.00150.0034-0.0045-00.0001-0.0032-0.0027-0.00420.00360.002300.08450.0215-0.02530.075-0.01620.0529-44.349274.070552.7166
60.0003-0.00010.00030.0002-0.00020.00040.0030.001-0.001-0.00110.0005-0.00010.0004-0.0002-00.2370.013-0.01470.2339-0.01750.232-22.59364.376856.2149
70.0006-0.00090.00060.0011-0.00050.0007-0.00090.00050.0011-0.0069-0.0018-0.00240.00230-00.12890.0197-0.00250.1274-0.00270.1311-25.431667.790853.1189
80.0004-0.0002-0.00010.0001-0.00020.0001-0.00090.00030.0016-0.0014-0.0027-0.00060.00040.000100.0429-0.00170.00220.0483-0.00010.0462-15.978775.240287.6357
90.00030.00030.00040.0020.00130.0009-0.0003-0.00090.00080.0032-0.0008-0.00030.0006-0.0026-0.00130.01950.0116-0.01410.0188-0.01610.0244-43.838268.1045104.5596
100.0003-0.0002-0.00010.0003-0.00020.0003-0.00070.0004-0.00290.0029-0.00140.00090.0013-0.002400.1162-0.0084-0.01440.119-0.00580.1204-54.18551.722699.25
110.0006-0.00090.00040.0012-0.00040.0022-0.00130.00020.0035-0.0014-0.0058-0.00880.00020.005200.11770.0022-0.00720.1046-0.00040.11125.135843.5696126.6649
120.0004-0.0003-0.00040.00050.00010.0005-0.0010.00030.00080-0.00180.00010.00070.001100.18110.0074-0.00740.1797-0.00050.17934.824644.1381118.2834
130.00050-00.000500.0004-0.00090.0004-0.00060.0001-0-0.0013-0.0001-0.000200.62730.0080.00330.62760.0010.635948.415853.2178117.0539
140.0093-0.0091-0.00210.01010.00550.01230.02120.01870.0093-0.0086-0.0084-0.01080.01050.0044-0.00050.4040.0565-0.01630.3573-0.04640.3485.276955.716870.9682
150.18910.03610.02890.226-0.09370.15240.02940.19620.0107-0.2205-0.029-0.15860.04890.0680.13060.31120.09540.09940.33960.21410.2579-63.815613.5612-69.7907
160.0708-0.00770.01250.04080.01090.0604-0.0353-0.01250.11220.02970.0066-0.0456-0.09820.0250.02170.166-0.0202-0.10560.0208-0.00430.1557-63.28836.51786.0243
170.1947-0.0508-0.02410.2284-0.02620.153-0.00590.02260.2150.01710.05510.0939-0.2097-0.16720.05530.42360.24540.01250.30910.08010.4193-140.445550.1746-7.0043
180.06110.00780.02110.1119-0.03240.0844-0.00370.0283-0.0108-0.0429-0.0121-0.03940.01870.0378-0.02920.03930.0164-0.00390.01880.02650.0235-67.8475-0.9224-27.2384
190.0013-0.00140.00030.00160.00020.0010.001-0.00260.0011-0.00430.0026-0.0056-0.00560.0021-00.0560.01820.0080.03880.01510.0471-96.552458.8328-35.8799
200.0002-0.0001-0.00020.0001-00.00020.0010.00420.002-0.00320.0014-0.00150.00020.000700.18050.010800.17450.02090.1762-74.657155.2766-45.3788
210.0007-0.0008-0.00050.00120.00010.0008-0.00430.0011-0.0017-0.0018-0.0030.0049-0.00160.002100.05790.00140.01610.0510.01420.0672-77.656458.1616-42.0557
220.00020.0003-0.00030.0003-0.00010.00020.0008-0.00190.0029-0.0003-0.0002-0.0043-0.00140.0042-00.0399-0.00730.00170.03830.00020.0381-68.664323.4684-35.8405
230.00020.00010.00010.0002-0.00010.00030.0010.0003-0.00010-0.0005-0.0009-0.00030.00090.0033-0.00040.00090.0024-0.00010.00440.0002-96.67846.9008-42.4878
240.00020.0001-00.00030.00010.0001-0.00010.00120.0002-0.0016-0.00060.00290.0005-0.0028-00.0258-0.0042-0.00830.03590.00980.0304-107.124513.5168-58.1677
250.00060.0002-0.00090.0019-0.00080.00140.0040.00020.00060.00330.008-0.0059-0.00040.0011-00.0382-0.00180.01340.0370.0050.0432-28.5753-15.2067-68.6176
260.00040.0004-0.00030.0004-0.00010.00060.002-0.0004-0.0010.00030.0011-0.00340.00170.0013-00.04090.00480.01060.04350.00410.0426-18.4898-7.3697-68.5502
270.00040.0001-00.000300.0003-0.00010.00040.00140.0003-0.0013-0.0002-0.00030.001600.1767-0.00380.00520.1755-0.00390.181-4.7893-5.5794-58.8097
280.00360.0068-0.00840.0249-0.00410.02090.0190.00340.01520.00330.0041-0.0129-0.0113-0.00120.02510.3556-0.02240.02180.33180.06780.3601-47.329640.1393-55.0127
290.00410.00320.00050.00990.00170.00580.0010.00310.00110.00240.01530.00480.00270.002100.1411-0.0312-0.0180.19630.04540.2112-97.2433116.278185.8557
300.00950.0018-0.00120.0016-0.0030.002-0.0012-0.0162-0.02050.00870.00090.0130.0094-0.003700.292-0.0112-0.00060.41650.02250.4198-124.3016150.9949155.7852
310.06540.0439-0.04160.0976-0.01550.1252-0.00010.04880.0764-0.07630.02220.1062-0.1194-0.10470.02880.25730.0161-0.08150.160.02240.1721-49.3862192.82697.5771
320.0011-0.00020.00030.00270.00170.00160.0002-0.00680.00170.00770.0030.00460.0033-0.004800.23460.00930.01570.19650.01680.212611.2643231.305589.7236
330.0193-0.0104-0.00680.0131-0.00880.0246-0.01060.0114-0.0382-0.00160.00320.04660.04-0.0456-0.01550.0511-0.0363-0.01330.0962-0.00290.1162-84.7486118.854170.8812
340.0733-0.06370.15050.01910.03230.13060.0248-0.1080.03490.17320.06930.03810.0922-0.02830.6543-0.1332-0.0064-0.37320.0626-0.0335-0.0158-17.0796131.9085169.0426
350.0025-0.00210.00090.00850.00320.0069-0.00750.0079-0.0111-0.0039-0.0135-0.00420.01120.0018-0.00070.06810.0129-0.04990.1324-0.00260.1273-113.1212141.8527129.3069
360.0008-0.00120.00090.0029-0.0020.0062-0.00460.0051-0.0039-0.0052-0.00320.00380.0018-0.0032-0.00770.0419-0.0356-0.01570.06280.0060.0357-151.0206-73.79162.8152
370.00080.00010.0003-00.0004-0.00020.00460.0008-0.0055-0.00350.00330.01440.0016-0.00960.00090.18440.0067-0.0150.250.01890.2411-177.84-45.420738.3129
380.0730.01740.01520.136-0.01990.12180.0127-0.08430.05710.11330.0170.113-0.0907-0.11820.06710.22040.05790.00670.1734-0.06270.1743-102.289311.604881.8908
390.0013-0.0004-00.001-0.00080.0019-0.00390.0008-0.0047-0.003-0.00510.00340.0052-0.0018-00.1153-0.0106-0.01860.1133-0.02660.0979-39.718319.912119.696
400.02150.0112-0.01910.0427-0.00030.03620.0020.0060.0054-0.0177-0.00430.0223-0.0049-0.0203-0.00220.0036-0.0091-0.00490.0248-0.00430.0172-138.3971-59.37585.8332
410.0599-0.02540.0592-0.0041-0.06120.0924-0.0075-0.0838-0.1062-0.0578-0.0211-0.09090.1736-0.02270.5218-0.20630.0521-0.0845-0.2224-0.1859-0.2126-70.7967-58.924219.3407
420.0041-0.0016-0.00010.00630.00150.00250.00340.00540.00440.00530.0041-0.0086-0.00110.00490.00970.02950.0254-0.01160.06250.01010.0429-166.4788-18.246630.2054
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1((chain AA and (resid 5:560)) or (chain AD)
2X-RAY DIFFRACTION2((chain AA and ((resid 561:587) or (resid
3X-RAY DIFFRACTION3((chain AA and (resid 921:1400)) or (chain
4X-RAY DIFFRACTION4(chain AA and (resid 1401:1534))
5X-RAY DIFFRACTION5(chain AE and (resid 5:69))
6X-RAY DIFFRACTION6(chain AE and (resid 70:101))
7X-RAY DIFFRACTION7(chain AE and (resid 102:155))
8X-RAY DIFFRACTION8(chain AL and (resid 5:28))
9X-RAY DIFFRACTION9(chain AL and (resid 29:105))
10X-RAY DIFFRACTION10(chain AL and (resid 106:129))
11X-RAY DIFFRACTION11(chain AT and (resid 8:50))
12X-RAY DIFFRACTION12(chain AT and (resid 51:83))
13X-RAY DIFFRACTION13(chain AT and (resid 84:106))
14X-RAY DIFFRACTION14(chain AA and (resid 588:653))
15X-RAY DIFFRACTION15((chain CA and (resid 5:560)) or (chain CD)
16X-RAY DIFFRACTION16((chain CA and ((resid 561:587) or (resid
17X-RAY DIFFRACTION17((chain CA and (resid 921:1400)) or (chain
18X-RAY DIFFRACTION18(chain CA and (resid 1401:1534))
19X-RAY DIFFRACTION19(chain CE and (resid 5:69))
20X-RAY DIFFRACTION20(chain CE and (resid 70:101))
21X-RAY DIFFRACTION21(chain CE and (resid 102:155))
22X-RAY DIFFRACTION22(chain CL and (resid 5:28))
23X-RAY DIFFRACTION23(chain CL and (resid 29:105))
24X-RAY DIFFRACTION24(chain CL and (resid 106:129))
25X-RAY DIFFRACTION25(chain CT and (resid 8:50))
26X-RAY DIFFRACTION26(chain CT and (resid 51:83))
27X-RAY DIFFRACTION27(chain CT and (resid 84:106))
28X-RAY DIFFRACTION28(chain CA and (resid 588:653))
29X-RAY DIFFRACTION29((chain BB and (resid 70:107)) or (chain BZ
30X-RAY DIFFRACTION30((chain BB and (resid 1:69)) or (chain BB and
31X-RAY DIFFRACTION31((chain BA and (resid 2109:2238)) or (chain
32X-RAY DIFFRACTION32(chain BI and (resid 54:145))
33X-RAY DIFFRACTION33((chain BA and (resid 912:952)) or (chain BZ
34X-RAY DIFFRACTION34((chain BA and (resid 10:911)) or (chain BA
35X-RAY DIFFRACTION35((chain BA and (resid 2308:2330)) or (chain
36X-RAY DIFFRACTION36((chain DB and (resid 70:107)) or (chain DZ
37X-RAY DIFFRACTION37((chain DB and (resid 1:69)) or (chain DB and
38X-RAY DIFFRACTION38((chain DA and (resid 2109:2238)) or (chain
39X-RAY DIFFRACTION39(chain DI and (resid 54:145))
40X-RAY DIFFRACTION40((chain DA and (resid 912:952)) or (chain DZ
41X-RAY DIFFRACTION41((chain DA and (resid 10:911)) or (chain DA
42X-RAY DIFFRACTION42((chain DA and (resid 2308:2330)) or (chain

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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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