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- PDB-4v4g: Crystal structure of five 70s ribosomes from Escherichia Coli in ... -

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Basic information

Entry
Database: PDB / ID: 4v4g
TitleCrystal structure of five 70s ribosomes from Escherichia Coli in complex with protein Y.
Components
  • (30S ribosomal protein ...) x 19
  • (50S ribosomal protein ...) x 29
  • 16S ribosomal RNA
  • 23S RIBOSOMAL RNA
  • 5S RIBOSOMAL RNA
  • general stress protein Ctc
  • protein Y
KeywordsRIBOSOME / 30S RIBOSOMAL SUBUNIT / PROTEIN-RNA COMPLEX / PROTEIN-PROTEIN COMPLEX / RNA-RNA COMPLEX
Function / homologyRNA / RNA (> 10) / RNA (> 100) / RNA (> 1000)
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 11.5 Å
AuthorsVila-Sanjurjo, A. / Schuwirth, B.S. / Hau, C.W. / Cate, J.H.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2004
Title: Structural basis for the control of translation initiation during stress.
Authors: Vila-Sanjurjo, A. / Schuwirth, B.S. / Hau, C.W. / Cate, J.H.
History
DepositionOct 6, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 1VOQ, 1VOR, 1VOS, 1VOU, 1VOV, 1VOW, 1VOX, 1VOY, 1VOZ, 1VP0
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Sep 20, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 400COMPOUND THIS FILE, 1VOQ, CONTAINS THE 30S SUBUNIT OF ONE 70S RIBOSOME. THE ENTIRE CRYSTAL ...COMPOUND THIS FILE, 1VOQ, CONTAINS THE 30S SUBUNIT OF ONE 70S RIBOSOME. THE ENTIRE CRYSTAL STRUCTURE CONTAINS FIVE 70S RIBOSOMES AND ARE DEPOSITED UNDER: 70S RIBOSOME ONE: 1VOQ (30S SUBUNIT), 1VOR (50S SUBUNIT) 70S RIBOSOME TWO: 1VOS (30S SUBUNIT), 1VOU (50S SUBUNIT) 70S RIBOSOME THREE: 1VOV (30S SUBUNIT), 1VOW (50S SUBUNIT) 70S RIBOSOME FOUR: 1VOX (30S SUBUNIT), 1VOY (50S SUBUNIT) 70S RIBOSOME FIVE: 1VOZ (30S SUBUNIT), 1VP0 (50S SUBUNIT)
Remark 999SEQUENCE The 30S subunit is modelled based on 1PNS which are derived mainly from 1J5E, the T. ...SEQUENCE The 30S subunit is modelled based on 1PNS which are derived mainly from 1J5E, the T. thermophilus 30S subunit, with modifications to the rRNA to make it match E. coli insertions and deletions. The sequence of this subunit represent that of pdb entry, 1J5E. As a result, no dbref was provided. Some residues are not at link distance. Distance of O3*-P bond is 3.20 for residue (A A 919 ) and residue (A U 920 ). Distance of O3*-P bond is 3.21 for residue (A U 1393 ) and residue (A A 1394 ). Distance of O3*-P bond is 5.27 for residue (A G 1443 ) and residue (A U 1445 ). Distance of O3*-P bond is 6.64 for residue (A G 1458 ) and residue (A A 1460 ). Distance of C-N bond is 5.58 for residue (L SER 22 ) and residue (L LYS 23 ). Distance of C-N bond is 4.55 for residue (M GLY 89 ) and residue (M LEU 90 ). The short contacts listed at remark 500 may not be complete since this file only represents one tenth of the entire crystal structure.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AA: 16S ribosomal RNA
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
Aa: protein Y
BB: 23S RIBOSOMAL RNA
BA: 5S RIBOSOMAL RNA
BD: 50S ribosomal protein L2
BE: 50S ribosomal protein L3
BF: 50S ribosomal protein L4
BG: 50S ribosomal protein L5
BH: 50S ribosomal protein L6
BI: 50S ribosomal protein L9
BJ: 50S ribosomal protein L11
BK: 50S ribosomal protein L13
BL: 50S ribosomal protein L14
BM: 50S ribosomal protein L15
BN: 50S ribosomal protein L16
BO: 50S ribosomal protein L17
BP: 50S ribosomal protein L18
BQ: 50S ribosomal protein L19
BR: 50S ribosomal protein L20
BS: 50S ribosomal protein L21
BT: 50S ribosomal protein L22
BU: 50S ribosomal protein L23
BV: 50S ribosomal protein L24
BW: general stress protein Ctc
BX: 50S ribosomal protein L27
BY: 50S ribosomal protein L29
BZ: 50S ribosomal protein L30
B1: 50S ribosomal protein L31
B2: 50S ribosomal protein L32
B3: 50S ribosomal protein L33
B4: 50S ribosomal protein L34
B5: 50S ribosomal protein L35
B6: 50S ribosomal protein L36
B7: 50S ribosomal protein L1P
CA: 16S ribosomal RNA
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
Ca: protein Y
DB: 23S RIBOSOMAL RNA
DA: 5S RIBOSOMAL RNA
DD: 50S ribosomal protein L2
DE: 50S ribosomal protein L3
DF: 50S ribosomal protein L4
DG: 50S ribosomal protein L5
DH: 50S ribosomal protein L6
DI: 50S ribosomal protein L9
DJ: 50S ribosomal protein L11
DK: 50S ribosomal protein L13
DL: 50S ribosomal protein L14
DM: 50S ribosomal protein L15
DN: 50S ribosomal protein L16
DO: 50S ribosomal protein L17
DP: 50S ribosomal protein L18
DQ: 50S ribosomal protein L19
DR: 50S ribosomal protein L20
DS: 50S ribosomal protein L21
DT: 50S ribosomal protein L22
DU: 50S ribosomal protein L23
DV: 50S ribosomal protein L24
DW: general stress protein Ctc
DX: 50S ribosomal protein L27
DY: 50S ribosomal protein L29
DZ: 50S ribosomal protein L30
D1: 50S ribosomal protein L31
D2: 50S ribosomal protein L32
D3: 50S ribosomal protein L33
D4: 50S ribosomal protein L34
D5: 50S ribosomal protein L35
D6: 50S ribosomal protein L36
D7: 50S ribosomal protein L1P
EA: 16S ribosomal RNA
EB: 30S ribosomal protein S2
EC: 30S ribosomal protein S3
ED: 30S ribosomal protein S4
EE: 30S ribosomal protein S5
EF: 30S ribosomal protein S6
EG: 30S ribosomal protein S7
EH: 30S ribosomal protein S8
EI: 30S ribosomal protein S9
EJ: 30S ribosomal protein S10
EK: 30S ribosomal protein S11
EL: 30S ribosomal protein S12
EM: 30S ribosomal protein S13
EN: 30S ribosomal protein S14
EO: 30S ribosomal protein S15
EP: 30S ribosomal protein S16
EQ: 30S ribosomal protein S17
ER: 30S ribosomal protein S18
ES: 30S ribosomal protein S19
ET: 30S ribosomal protein S20
Ea: protein Y
FB: 23S RIBOSOMAL RNA
FA: 5S RIBOSOMAL RNA
FD: 50S ribosomal protein L2
FE: 50S ribosomal protein L3
FF: 50S ribosomal protein L4
FG: 50S ribosomal protein L5
FH: 50S ribosomal protein L6
FI: 50S ribosomal protein L9
FJ: 50S ribosomal protein L11
FK: 50S ribosomal protein L13
FL: 50S ribosomal protein L14
FM: 50S ribosomal protein L15
FN: 50S ribosomal protein L16
FO: 50S ribosomal protein L17
FP: 50S ribosomal protein L18
FQ: 50S ribosomal protein L19
FR: 50S ribosomal protein L20
FS: 50S ribosomal protein L21
FT: 50S ribosomal protein L22
FU: 50S ribosomal protein L23
FV: 50S ribosomal protein L24
FW: general stress protein Ctc
FX: 50S ribosomal protein L27
FY: 50S ribosomal protein L29
FZ: 50S ribosomal protein L30
F1: 50S ribosomal protein L31
F2: 50S ribosomal protein L32
F3: 50S ribosomal protein L33
F4: 50S ribosomal protein L34
F5: 50S ribosomal protein L35
F6: 50S ribosomal protein L36
F7: 50S ribosomal protein L1P
GA: 16S ribosomal RNA
GB: 30S ribosomal protein S2
GC: 30S ribosomal protein S3
GD: 30S ribosomal protein S4
GE: 30S ribosomal protein S5
GF: 30S ribosomal protein S6
GG: 30S ribosomal protein S7
GH: 30S ribosomal protein S8
GI: 30S ribosomal protein S9
GJ: 30S ribosomal protein S10
GK: 30S ribosomal protein S11
GL: 30S ribosomal protein S12
GM: 30S ribosomal protein S13
GN: 30S ribosomal protein S14
GO: 30S ribosomal protein S15
GP: 30S ribosomal protein S16
GQ: 30S ribosomal protein S17
GR: 30S ribosomal protein S18
GS: 30S ribosomal protein S19
GT: 30S ribosomal protein S20
Ga: protein Y
HB: 23S RIBOSOMAL RNA
HA: 5S RIBOSOMAL RNA
HD: 50S ribosomal protein L2
HE: 50S ribosomal protein L3
HF: 50S ribosomal protein L4
HG: 50S ribosomal protein L5
HH: 50S ribosomal protein L6
HI: 50S ribosomal protein L9
HJ: 50S ribosomal protein L11
HK: 50S ribosomal protein L13
HL: 50S ribosomal protein L14
HM: 50S ribosomal protein L15
HN: 50S ribosomal protein L16
HO: 50S ribosomal protein L17
HP: 50S ribosomal protein L18
HQ: 50S ribosomal protein L19
HR: 50S ribosomal protein L20
HS: 50S ribosomal protein L21
HT: 50S ribosomal protein L22
HU: 50S ribosomal protein L23
HV: 50S ribosomal protein L24
HW: general stress protein Ctc
HX: 50S ribosomal protein L27
HY: 50S ribosomal protein L29
HZ: 50S ribosomal protein L30
H1: 50S ribosomal protein L31
H2: 50S ribosomal protein L32
H3: 50S ribosomal protein L33
H4: 50S ribosomal protein L34
H5: 50S ribosomal protein L35
H6: 50S ribosomal protein L36
H7: 50S ribosomal protein L1P
IA: 16S ribosomal RNA
IB: 30S ribosomal protein S2
IC: 30S ribosomal protein S3
ID: 30S ribosomal protein S4
IE: 30S ribosomal protein S5
IF: 30S ribosomal protein S6
IG: 30S ribosomal protein S7
IH: 30S ribosomal protein S8
II: 30S ribosomal protein S9
IJ: 30S ribosomal protein S10
IK: 30S ribosomal protein S11
IL: 30S ribosomal protein S12
IM: 30S ribosomal protein S13
IN: 30S ribosomal protein S14
IO: 30S ribosomal protein S15
IP: 30S ribosomal protein S16
IQ: 30S ribosomal protein S17
IR: 30S ribosomal protein S18
IS: 30S ribosomal protein S19
IT: 30S ribosomal protein S20
Ia: protein Y
JB: 23S RIBOSOMAL RNA
JA: 5S RIBOSOMAL RNA
JD: 50S ribosomal protein L2
JE: 50S ribosomal protein L3
JF: 50S ribosomal protein L4
JG: 50S ribosomal protein L5
JH: 50S ribosomal protein L6
JI: 50S ribosomal protein L9
JJ: 50S ribosomal protein L11
JK: 50S ribosomal protein L13
JL: 50S ribosomal protein L14
JM: 50S ribosomal protein L15
JN: 50S ribosomal protein L16
JO: 50S ribosomal protein L17
JP: 50S ribosomal protein L18
JQ: 50S ribosomal protein L19
JR: 50S ribosomal protein L20
JS: 50S ribosomal protein L21
JT: 50S ribosomal protein L22
JU: 50S ribosomal protein L23
JV: 50S ribosomal protein L24
JW: general stress protein Ctc
JX: 50S ribosomal protein L27
JY: 50S ribosomal protein L29
JZ: 50S ribosomal protein L30
J1: 50S ribosomal protein L31
J2: 50S ribosomal protein L32
J3: 50S ribosomal protein L33
J4: 50S ribosomal protein L34
J5: 50S ribosomal protein L35
J6: 50S ribosomal protein L36
J7: 50S ribosomal protein L1P


Theoretical massNumber of molelcules
Total (without water)10,637,747265
Polymers10,637,747265
Non-polymers00
Water00
1
AA: 16S ribosomal RNA
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
Aa: protein Y
BB: 23S RIBOSOMAL RNA
BA: 5S RIBOSOMAL RNA
BD: 50S ribosomal protein L2
BE: 50S ribosomal protein L3
BF: 50S ribosomal protein L4
BG: 50S ribosomal protein L5
BH: 50S ribosomal protein L6
BI: 50S ribosomal protein L9
BJ: 50S ribosomal protein L11
BK: 50S ribosomal protein L13
BL: 50S ribosomal protein L14
BM: 50S ribosomal protein L15
BN: 50S ribosomal protein L16
BO: 50S ribosomal protein L17
BP: 50S ribosomal protein L18
BQ: 50S ribosomal protein L19
BR: 50S ribosomal protein L20
BS: 50S ribosomal protein L21
BT: 50S ribosomal protein L22
BU: 50S ribosomal protein L23
BV: 50S ribosomal protein L24
BW: general stress protein Ctc
BX: 50S ribosomal protein L27
BY: 50S ribosomal protein L29
BZ: 50S ribosomal protein L30
B1: 50S ribosomal protein L31
B2: 50S ribosomal protein L32
B3: 50S ribosomal protein L33
B4: 50S ribosomal protein L34
B5: 50S ribosomal protein L35
B6: 50S ribosomal protein L36
B7: 50S ribosomal protein L1P


Theoretical massNumber of molelcules
Total (without water)2,127,54953
Polymers2,127,54953
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
CA: 16S ribosomal RNA
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
Ca: protein Y
DB: 23S RIBOSOMAL RNA
DA: 5S RIBOSOMAL RNA
DD: 50S ribosomal protein L2
DE: 50S ribosomal protein L3
DF: 50S ribosomal protein L4
DG: 50S ribosomal protein L5
DH: 50S ribosomal protein L6
DI: 50S ribosomal protein L9
DJ: 50S ribosomal protein L11
DK: 50S ribosomal protein L13
DL: 50S ribosomal protein L14
DM: 50S ribosomal protein L15
DN: 50S ribosomal protein L16
DO: 50S ribosomal protein L17
DP: 50S ribosomal protein L18
DQ: 50S ribosomal protein L19
DR: 50S ribosomal protein L20
DS: 50S ribosomal protein L21
DT: 50S ribosomal protein L22
DU: 50S ribosomal protein L23
DV: 50S ribosomal protein L24
DW: general stress protein Ctc
DX: 50S ribosomal protein L27
DY: 50S ribosomal protein L29
DZ: 50S ribosomal protein L30
D1: 50S ribosomal protein L31
D2: 50S ribosomal protein L32
D3: 50S ribosomal protein L33
D4: 50S ribosomal protein L34
D5: 50S ribosomal protein L35
D6: 50S ribosomal protein L36
D7: 50S ribosomal protein L1P


Theoretical massNumber of molelcules
Total (without water)2,127,54953
Polymers2,127,54953
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
EA: 16S ribosomal RNA
EB: 30S ribosomal protein S2
EC: 30S ribosomal protein S3
ED: 30S ribosomal protein S4
EE: 30S ribosomal protein S5
EF: 30S ribosomal protein S6
EG: 30S ribosomal protein S7
EH: 30S ribosomal protein S8
EI: 30S ribosomal protein S9
EJ: 30S ribosomal protein S10
EK: 30S ribosomal protein S11
EL: 30S ribosomal protein S12
EM: 30S ribosomal protein S13
EN: 30S ribosomal protein S14
EO: 30S ribosomal protein S15
EP: 30S ribosomal protein S16
EQ: 30S ribosomal protein S17
ER: 30S ribosomal protein S18
ES: 30S ribosomal protein S19
ET: 30S ribosomal protein S20
Ea: protein Y
FB: 23S RIBOSOMAL RNA
FA: 5S RIBOSOMAL RNA
FD: 50S ribosomal protein L2
FE: 50S ribosomal protein L3
FF: 50S ribosomal protein L4
FG: 50S ribosomal protein L5
FH: 50S ribosomal protein L6
FI: 50S ribosomal protein L9
FJ: 50S ribosomal protein L11
FK: 50S ribosomal protein L13
FL: 50S ribosomal protein L14
FM: 50S ribosomal protein L15
FN: 50S ribosomal protein L16
FO: 50S ribosomal protein L17
FP: 50S ribosomal protein L18
FQ: 50S ribosomal protein L19
FR: 50S ribosomal protein L20
FS: 50S ribosomal protein L21
FT: 50S ribosomal protein L22
FU: 50S ribosomal protein L23
FV: 50S ribosomal protein L24
FW: general stress protein Ctc
FX: 50S ribosomal protein L27
FY: 50S ribosomal protein L29
FZ: 50S ribosomal protein L30
F1: 50S ribosomal protein L31
F2: 50S ribosomal protein L32
F3: 50S ribosomal protein L33
F4: 50S ribosomal protein L34
F5: 50S ribosomal protein L35
F6: 50S ribosomal protein L36
F7: 50S ribosomal protein L1P


Theoretical massNumber of molelcules
Total (without water)2,127,54953
Polymers2,127,54953
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
GA: 16S ribosomal RNA
GB: 30S ribosomal protein S2
GC: 30S ribosomal protein S3
GD: 30S ribosomal protein S4
GE: 30S ribosomal protein S5
GF: 30S ribosomal protein S6
GG: 30S ribosomal protein S7
GH: 30S ribosomal protein S8
GI: 30S ribosomal protein S9
GJ: 30S ribosomal protein S10
GK: 30S ribosomal protein S11
GL: 30S ribosomal protein S12
GM: 30S ribosomal protein S13
GN: 30S ribosomal protein S14
GO: 30S ribosomal protein S15
GP: 30S ribosomal protein S16
GQ: 30S ribosomal protein S17
GR: 30S ribosomal protein S18
GS: 30S ribosomal protein S19
GT: 30S ribosomal protein S20
Ga: protein Y
HB: 23S RIBOSOMAL RNA
HA: 5S RIBOSOMAL RNA
HD: 50S ribosomal protein L2
HE: 50S ribosomal protein L3
HF: 50S ribosomal protein L4
HG: 50S ribosomal protein L5
HH: 50S ribosomal protein L6
HI: 50S ribosomal protein L9
HJ: 50S ribosomal protein L11
HK: 50S ribosomal protein L13
HL: 50S ribosomal protein L14
HM: 50S ribosomal protein L15
HN: 50S ribosomal protein L16
HO: 50S ribosomal protein L17
HP: 50S ribosomal protein L18
HQ: 50S ribosomal protein L19
HR: 50S ribosomal protein L20
HS: 50S ribosomal protein L21
HT: 50S ribosomal protein L22
HU: 50S ribosomal protein L23
HV: 50S ribosomal protein L24
HW: general stress protein Ctc
HX: 50S ribosomal protein L27
HY: 50S ribosomal protein L29
HZ: 50S ribosomal protein L30
H1: 50S ribosomal protein L31
H2: 50S ribosomal protein L32
H3: 50S ribosomal protein L33
H4: 50S ribosomal protein L34
H5: 50S ribosomal protein L35
H6: 50S ribosomal protein L36
H7: 50S ribosomal protein L1P


Theoretical massNumber of molelcules
Total (without water)2,127,54953
Polymers2,127,54953
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
IA: 16S ribosomal RNA
IB: 30S ribosomal protein S2
IC: 30S ribosomal protein S3
ID: 30S ribosomal protein S4
IE: 30S ribosomal protein S5
IF: 30S ribosomal protein S6
IG: 30S ribosomal protein S7
IH: 30S ribosomal protein S8
II: 30S ribosomal protein S9
IJ: 30S ribosomal protein S10
IK: 30S ribosomal protein S11
IL: 30S ribosomal protein S12
IM: 30S ribosomal protein S13
IN: 30S ribosomal protein S14
IO: 30S ribosomal protein S15
IP: 30S ribosomal protein S16
IQ: 30S ribosomal protein S17
IR: 30S ribosomal protein S18
IS: 30S ribosomal protein S19
IT: 30S ribosomal protein S20
Ia: protein Y
JB: 23S RIBOSOMAL RNA
JA: 5S RIBOSOMAL RNA
JD: 50S ribosomal protein L2
JE: 50S ribosomal protein L3
JF: 50S ribosomal protein L4
JG: 50S ribosomal protein L5
JH: 50S ribosomal protein L6
JI: 50S ribosomal protein L9
JJ: 50S ribosomal protein L11
JK: 50S ribosomal protein L13
JL: 50S ribosomal protein L14
JM: 50S ribosomal protein L15
JN: 50S ribosomal protein L16
JO: 50S ribosomal protein L17
JP: 50S ribosomal protein L18
JQ: 50S ribosomal protein L19
JR: 50S ribosomal protein L20
JS: 50S ribosomal protein L21
JT: 50S ribosomal protein L22
JU: 50S ribosomal protein L23
JV: 50S ribosomal protein L24
JW: general stress protein Ctc
JX: 50S ribosomal protein L27
JY: 50S ribosomal protein L29
JZ: 50S ribosomal protein L30
J1: 50S ribosomal protein L31
J2: 50S ribosomal protein L32
J3: 50S ribosomal protein L33
J4: 50S ribosomal protein L34
J5: 50S ribosomal protein L35
J6: 50S ribosomal protein L36
J7: 50S ribosomal protein L1P


Theoretical massNumber of molelcules
Total (without water)2,127,54953
Polymers2,127,54953
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)687.900, 687.900, 1933.3
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

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RNA chain , 3 types, 15 molecules AACAEAGAIABBDBFBHBJBBADAFAHAJA

#1: RNA chain
16S ribosomal RNA


Mass: 495435.469 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#22: RNA chain
23S RIBOSOMAL RNA


Mass: 915854.875 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#23: RNA chain
5S RIBOSOMAL RNA


Mass: 38374.984 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)

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30S ribosomal protein ... , 19 types, 95 molecules ABCBEBGBIBACCCECGCICADCDEDGDIDAECEEEGEIEAFCFEFGFIFAGCGEGGGIG...

#2: Protein
30S ribosomal protein S2


Mass: 26987.271 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#3: Protein
30S ribosomal protein S3


Mass: 22862.430 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#4: Protein
30S ribosomal protein S4


Mass: 24242.254 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#5: Protein
30S ribosomal protein S5


Mass: 16331.079 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#6: Protein
30S ribosomal protein S6


Mass: 11988.753 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#7: Protein
30S ribosomal protein S7


Mass: 17919.775 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#8: Protein
30S ribosomal protein S8


Mass: 15868.570 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#9: Protein
30S ribosomal protein S9


Mass: 14298.466 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#10: Protein
30S ribosomal protein S10


Mass: 11299.176 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#11: Protein
30S ribosomal protein S11


Mass: 12606.369 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#12: Protein
30S ribosomal protein S12


Mass: 13804.311 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#13: Protein
30S ribosomal protein S13


Mass: 14207.666 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#14: Protein
30S ribosomal protein S14


Mass: 7027.529 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#15: Protein
30S ribosomal protein S15


Mass: 10447.213 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#16: Protein
30S ribosomal protein S16


Mass: 9924.469 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#17: Protein
30S ribosomal protein S17


Mass: 12193.475 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#18: Protein
30S ribosomal protein S18


Mass: 8483.172 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#19: Protein
30S ribosomal protein S19


Mass: 9203.743 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#20: Protein
30S ribosomal protein S20


Mass: 10907.060 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)

-
Protein , 2 types, 10 molecules AaCaEaGaIaBWDWFWHWJW

#21: Protein
protein Y


Mass: 10250.834 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#43: Protein
general stress protein Ctc


Mass: 18929.711 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)

+
50S ribosomal protein ... , 29 types, 145 molecules BDDDFDHDJDBEDEFEHEJEBFDFFFHFJFBGDGFGHGJGBHDHFHHHJHBIDIFIHIJI...

#24: Protein
50S ribosomal protein L2


Mass: 29519.994 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#25: Protein
50S ribosomal protein L3


Mass: 21962.529 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#26: Protein
50S ribosomal protein L4


Mass: 21502.346 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#27: Protein
50S ribosomal protein L5


Mass: 20120.586 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#28: Protein
50S ribosomal protein L6


Mass: 18680.418 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#29: Protein
50S ribosomal protein L9


Mass: 5734.673 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#30: Protein
50S ribosomal protein L11


Mass: 14818.137 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#31: Protein
50S ribosomal protein L13


Mass: 15936.398 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#32: Protein
50S ribosomal protein L14


Mass: 14012.183 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#33: Protein
50S ribosomal protein L15


Mass: 15177.267 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#34: Protein
50S ribosomal protein L16


Mass: 14033.465 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#35: Protein
50S ribosomal protein L17


Mass: 12637.677 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#36: Protein
50S ribosomal protein L18


Mass: 11860.560 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#37: Protein
50S ribosomal protein L19


Mass: 14322.516 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#38: Protein
50S ribosomal protein L20


Mass: 13860.079 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#39: Protein
50S ribosomal protein L21


Mass: 11165.743 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#40: Protein
50S ribosomal protein L22


Mass: 14790.375 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#41: Protein
50S ribosomal protein L23


Mass: 10336.936 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#42: Protein
50S ribosomal protein L24


Mass: 12138.118 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#44: Protein
50S ribosomal protein L27


Mass: 9121.521 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#45: Protein
50S ribosomal protein L29


Mass: 7515.659 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#46: Protein
50S ribosomal protein L30


Mass: 6079.235 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#47: Protein
50S ribosomal protein L31


Mass: 8597.846 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#48: Protein
50S ribosomal protein L32


Mass: 6579.690 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#49: Protein
50S ribosomal protein L33


Mass: 6144.174 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#50: Protein/peptide
50S ribosomal protein L34


Mass: 5497.474 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#51: Protein
50S ribosomal protein L35


Mass: 7130.701 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#52: Protein/peptide
50S ribosomal protein L36


Mass: 4134.048 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#53: Protein
50S ribosomal protein L1P


Mass: 24690.396 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.38 Å3/Da / Density % sol: 77.12 %
Crystal growpH: 6.5
Details: 18-22% 2-methyl-2,4-pentanediol (MPD), 0-5% ethanol, 20-25mM MgCl2, 200-320mM NH4Cl, 1mM spermine, 0-0.5mM spermidine, pH 6.0-6.5, pH 6.50
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2ethanol11
3MgCl211
4NH4Cl11
5spermine11
6spermidine11
7H2O11
8MgCl212
9NH4Cl12
10MPD12

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21
31
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.3.111
SYNCHROTRONALS 8.2.121.2
SYNCHROTRONALS 8.2.231.3
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDMar 1, 2004
ADSC QUANTUM 2102CCDMar 1, 2004
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.21
31.31
ReflectionResolution: 11.5→500 Å / Num. obs: 62383 / % possible obs: 93.9 % / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Rsym value: 0.181 / Net I/σ(I): 7.4
Reflection shellResolution: 11.5→11.8 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2 / Rsym value: 0.462 / % possible all: 77.9

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1PNS, 1PNU

1pns
PDB Unreleased entry

1pnu
PDB Unreleased entry


Resolution: 11.5→500 Å / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0
Details: 235 RIGID BODIES REFINEMENT, GROUPED THIS ENTRY. COORDINATES USED FOR SOLVING AND REFINING THIS SUBUNIT COMES FROM PDB ENTRY, 1PNS, WHERE THE SEQUENCE REPRESENTS THAT OF T. THERMOPHILUS.
RfactorNum. reflection% reflectionSelection details
Rfree0.401 6283 -RANDOM
Rwork0.395 ---
obs0.395 62383 93.9 %-
Refinement stepCycle: LAST / Resolution: 11.5→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19749 32799 0 0 52548

+
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