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- PDB-4v8h: Crystal structure of HPF bound to the 70S ribosome. -

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Basic information

Entry
Database: PDB / ID: 4v8h
TitleCrystal structure of HPF bound to the 70S ribosome.
Components
  • (30S Ribosomal Protein ...) x 20
  • (50S Ribosomal Protein ...) x 29
  • 16S Ribosomal RNA
  • 23S Ribosomal RNA
  • 5S Ribosomal RNA
  • Probable sigma(54) modulation protein
KeywordsRIBOSOME / ribosome hibernation factor / YhbH / Protein E / stress response / stationary phase / ribosome hibernation
Function / homology
Function and homology information


dormancy process / negative regulation of translational elongation / ribosomal small subunit binding / large ribosomal subunit / transferase activity / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding ...dormancy process / negative regulation of translational elongation / ribosomal small subunit binding / large ribosomal subunit / transferase activity / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / small ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / zinc ion binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
: / Ribosome hibernation promoting factor/RaiA / Ribosome hibernation promotion factor-like / Sigma 54 modulation protein / S30EA ribosomal protein / 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 ...: / Ribosome hibernation promoting factor/RaiA / Ribosome hibernation promotion factor-like / Sigma 54 modulation protein / S30EA ribosomal protein / 30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / : / Ribosomal protein S14, type Z / Ribosomal protein L31 type A / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / : / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L36 signature. / Ribosomal protein L32p, bacterial type / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L28 / Ribosomal protein L35, non-mitochondrial / : / Ribosomal protein L5, bacterial-type / Ribosomal protein L18, bacterial-type / : / Ribosomal protein S19, bacterial-type / Ribosomal protein S3, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S14/S29 / Ribosomal protein L20 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal L28 family / Ribosomal protein L33 superfamily / Ribosomal protein L16 / Ribosomal protein L28/L24 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L30, bacterial-type / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / : / L28p-like / Ribosomal protein S15, bacterial-type / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L20 / Ribosomal protein S12, bacterial-type
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Ribosome hibernation promoting factor / Large ribosomal subunit protein uL6 ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Ribosome hibernation promoting factor / 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 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS18 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein bL17
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Thermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsPolikanov, Y.S. / Blaha, G.M. / Steitz, T.A.
CitationJournal: Science / Year: 2012
Title: How Hibernation Factors RMF, HPF, and YfiA Turn Off Protein Synthesis.
Authors: Polikanov, Y.S. / Blaha, G.M. / Steitz, T.A.
History
DepositionDec 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 3V26, 3V27, 3V28, 3V29
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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_PDB_ins_code / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_PDB_ins_code / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_PDB_ins_code / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
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
AU: 30S Ribosomal Protein THX
AX: Probable sigma(54) modulation protein
BA: 23S Ribosomal RNA
BB: 5S Ribosomal RNA
BD: 50S Ribosomal Protein L2
BE: 50S Ribosomal Protein L3
BF: 50S Ribosomal Protein L4
BG: 50S Ribosomal Protein L5
BH: 50S Ribosomal Protein L6
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 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
CU: 30S Ribosomal Protein THX
CX: Probable sigma(54) modulation protein
DA: 23S Ribosomal RNA
DB: 5S Ribosomal RNA
DD: 50S Ribosomal Protein L2
DE: 50S Ribosomal Protein L3
DF: 50S Ribosomal Protein L4
DG: 50S Ribosomal Protein L5
DH: 50S Ribosomal Protein L6
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)4,400,3541768
Polymers4,359,383106
Non-polymers40,9701662
Water66,2413677
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
AU: 30S Ribosomal Protein THX
AX: Probable sigma(54) modulation protein
BA: 23S Ribosomal RNA
BB: 5S Ribosomal RNA
BD: 50S Ribosomal Protein L2
BE: 50S Ribosomal Protein L3
BF: 50S Ribosomal Protein L4
BG: 50S Ribosomal Protein L5
BH: 50S Ribosomal Protein L6
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)2,200,979917
Polymers2,179,69253
Non-polymers21,287864
Water57632
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
CU: 30S Ribosomal Protein THX
CX: Probable sigma(54) modulation protein
DA: 23S Ribosomal RNA
DB: 5S Ribosomal RNA
DD: 50S Ribosomal Protein L2
DE: 50S Ribosomal Protein L3
DF: 50S Ribosomal Protein L4
DG: 50S Ribosomal Protein L5
DH: 50S Ribosomal Protein L6
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)2,199,375851
Polymers2,179,69253
Non-polymers19,683798
Water59433
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)208.970, 447.240, 617.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.992929, -0.112328, 0.038404), (-0.037667, -0.008675, -0.999253), (0.112577, -0.993633, 0.004383)245.151001, -190.666, -133.477005
2given(-0.999867, -0.007948, 0.014224), (-0.014059, -0.020413, -0.999693), (0.008236, -0.99976, 0.020298)262.46701, -197.584, -109.677002
3given(-0.999359, -0.032843, 0.014243), (-0.013915, -0.010208, -0.999851), (0.032983, -0.999408, 0.009745)258.919006, -196.100998, -116.818001
4given(-0.999536, -0.023836, 0.018957), (-0.018772, -0.007937, -0.999792), (0.023981, -0.999684, 0.007485)261.484009, -194.932999, -115.667999
5given(-0.99947, -0.031491, 0.008207), (-0.008115, -0.003055, -0.999962), (0.031515, -0.999499, 0.002797)257.890991, -196.024994, -118.111
6given(-0.999489, -0.031727, 0.003937), (-0.003569, -0.011646, -0.999926), (0.03177, -0.999429, 0.011527)256.786011, -198.658997, -116.311996
7given(-0.998855, -0.027426, 0.039195), (-0.035799, -0.114906, -0.992731), (0.031731, -0.992998, 0.113792)266.348999, -202.054001, -87.329697
8given(-0.999739, -0.018881, 0.012833), (-0.012497, -0.017779, -0.999764), (0.019105, -0.999664, 0.017539)261.054993, -197.720001, -112.390999
9given(-0.999936, 0.00296, 0.010946), (-0.011068, -0.045201, -0.998917), (-0.002462, -0.998974, 0.045231)263.113007, -199.666, -102.694
10given(-0.999835, 0.006638, 0.016904), (-0.017089, -0.02903, -0.999432), (-0.006144, -0.999556, 0.029139)264.679993, -198.070999, -105.18

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Components

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RNA chain , 3 types, 6 molecules AACABADABBDB

#1: RNA chain 16S Ribosomal RNA


Mass: 493958.281 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: GenBank: AP008226.1
#23: RNA chain 23S Ribosomal RNA


Mass: 947283.062 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: GenBank: AP008226.1
#24: RNA chain 5S Ribosomal RNA


Mass: 39494.535 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / 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


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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Protein , 1 types, 2 molecules AXCX

#22: Protein Probable sigma(54) modulation protein / ORF3 / ORF95


Mass: 11596.127 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b3203, hpf, JW3170, yhbH / Plasmid: pGS21a-HPF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0AFX0

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50S Ribosomal Protein ... , 29 types, 58 molecules BDDDBEDEBFDFBGDGBHDHBIDIBNDNBODOBPDPBQDQBRDRBSDSBTDTBUDUBVDV...

#25: Protein 50S Ribosomal Protein L2


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


Mass: 22450.213 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHN8
#27: 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) / Strain: HB8 / References: UniProt: Q5SHN9
#28: Protein 50S Ribosomal Protein L5


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


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


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


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


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


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


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


Mass: 13750.148 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q9Z9H5
#36: 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) / Strain: HB8 / References: UniProt: Q5SHQ4
#37: Protein 50S Ribosomal Protein L19


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


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


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


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


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


Mass: 12085.611 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHP9
#43: 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) / Strain: HB8 / References: UniProt: Q5SHZ1
#44: Protein 50S Ribosomal Protein L27


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


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


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


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


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


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


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


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


Mass: 7506.178 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SKU1
#53: 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) / Strain: HB8 / References: UniProt: Q5SHR2

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Non-polymers , 3 types, 5339 molecules

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


Mass: 24.305 Da / Num. of mol.: 1648 / Source method: obtained synthetically / Formula: Mg
#55: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Zn
#56: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3677 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

-
Experimental details

-
Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.31 Å3/Da / Density % sol: 57.42 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 7.6
Details: 0.1-0.2M Arginine-HCl, 0.1M Tris-HCl pH 7.6, 2.5% PEG-20K, 7-12% MPD, 0.5mM BME, VAPOR DIFFUSION, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 6, 2011
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.1→49.9852 Å / Num. obs: 1002309 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 5.06 % / Rmerge(I) obs: 0.228 / Net I/σ(I): 6.01
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
3.1-3.180.0121.01192.5
3.18-3.270.0121.28192.7
3.27-3.360.0121.61193.4
3.36-3.470.0121.88193.9
3.47-3.580.0122.23194.4
3.58-3.710.0122.76195
3.71-3.850.0123.33195.8
3.85-40.0123.98197.2
4-4.180.0124.82199.5
4.18-4.380.0125.74199.7
4.38-4.620.0126.81199.9
4.62-4.90.0127.84199.9
4.9-5.240.0129.06199.9
5.24-5.660.01210.161100
5.66-6.20.01210.881100
6.2-6.930.01211.961100
6.93-80.01214.591100
8-9.80.01217.52199.9
9.8-13.860.01222.031100
13.86-49.98520.01224.63197.2

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.7.2_869refinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
PHENIXmodel building
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WDG and 2WDI

2wdg
PDB Unreleased entry

2wdi
PDB Unreleased entry


Resolution: 3.1→49.979 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.92 / σ(F): 1.33 / Phase error: 25.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2583 49827 5.02 %
Rwork0.2157 --
obs0.2178 993138 95.99 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 20.997 Å2 / ksol: 0.235 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.3427 Å2-0 Å20 Å2
2---2.9373 Å20 Å2
3---11.28 Å2
Refinement stepCycle: LAST / Resolution: 3.1→49.979 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18151 32270 146 294 50861
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014310194
X-RAY DIFFRACTIONf_angle_d1.481463436
X-RAY DIFFRACTIONf_dihedral_angle_d19.806141146
X-RAY DIFFRACTIONf_chiral_restr0.08458333
X-RAY DIFFRACTIONf_plane_restr0.00924878
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.13520.373214200.338227080X-RAY DIFFRACTION83
3.1352-3.17210.36614970.329527841X-RAY DIFFRACTION86
3.1721-3.21080.357114850.311728533X-RAY DIFFRACTION88
3.2108-3.25140.33915490.308129312X-RAY DIFFRACTION90
3.2514-3.29420.335815900.295429968X-RAY DIFFRACTION92
3.2942-3.33930.325715320.282630242X-RAY DIFFRACTION93
3.3393-3.3870.325715700.281230505X-RAY DIFFRACTION93
3.387-3.43750.330316690.273830476X-RAY DIFFRACTION93
3.4375-3.49120.307915810.264630694X-RAY DIFFRACTION94
3.4912-3.54850.305916950.261930738X-RAY DIFFRACTION94
3.5485-3.60960.295215500.249130938X-RAY DIFFRACTION95
3.6096-3.67530.290216860.243530898X-RAY DIFFRACTION95
3.6753-3.74590.276716000.227331149X-RAY DIFFRACTION95
3.7459-3.82240.270116840.231231299X-RAY DIFFRACTION96
3.8224-3.90540.274315490.222931603X-RAY DIFFRACTION96
3.9054-3.99630.264216910.213531858X-RAY DIFFRACTION97
3.9963-4.09610.25217480.203932478X-RAY DIFFRACTION99
4.0961-4.20680.239317370.199332507X-RAY DIFFRACTION100
4.2068-4.33060.242717310.197732612X-RAY DIFFRACTION100
4.3306-4.47030.247117340.193132618X-RAY DIFFRACTION100
4.4703-4.62990.236317450.189232673X-RAY DIFFRACTION100
4.6299-4.81520.230717210.181832732X-RAY DIFFRACTION100
4.8152-5.03410.231417480.178732780X-RAY DIFFRACTION100
5.0341-5.29920.223217230.172232794X-RAY DIFFRACTION100
5.2992-5.63080.21917640.168932845X-RAY DIFFRACTION100
5.6308-6.06490.214417840.168332836X-RAY DIFFRACTION100
6.0649-6.6740.220317220.177533042X-RAY DIFFRACTION100
6.674-7.63680.226217560.1833067X-RAY DIFFRACTION100
7.6368-9.61030.234317930.19533212X-RAY DIFFRACTION100
9.6103-49.98520.236117730.223633981X-RAY DIFFRACTION100

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