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- PDB-1w2b: Trigger Factor ribosome binding domain in complex with 50S -

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Basic information

Entry
Database: PDB / ID: 1w2b
TitleTrigger Factor ribosome binding domain in complex with 50S
Components
  • (50S RIBOSOMAL PROTEIN ...) x 26
  • (RIBOSOMAL PROTEIN ...) x 2
  • 23S RRNA
  • 5S RRNA
  • TRIGGER FACTOR
KeywordsRIBOSOME / RIBOSOME_ASSOCIATED FACTORS / CHAPERONE / NASCENT CHAIN / COTRANSLATIONAL FOLDING / RNA-BINDING / RIBOSOMAL PROTEIN
Function / homology
Function and homology information


'de novo' cotranslational protein folding / stress response to copper ion / ribonuclease P activity / tRNA 5'-leader removal / box C/D methylation guide snoRNP complex / protein unfolding / chaperone-mediated protein folding / protein folding chaperone / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA ...'de novo' cotranslational protein folding / stress response to copper ion / ribonuclease P activity / tRNA 5'-leader removal / box C/D methylation guide snoRNP complex / protein unfolding / chaperone-mediated protein folding / protein folding chaperone / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / peptidylprolyl isomerase / maturation of SSU-rRNA / peptidyl-prolyl cis-trans isomerase activity / small-subunit processome / mRNA splicing, via spliceosome / protein transport / ribosome binding / 5S rRNA binding / response to heat / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / tRNA binding / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / cell cycle / cell division / DNA repair / nucleotide binding / mRNA binding / DNA binding / zinc ion binding / identical protein binding / membrane / cytosol
Similarity search - Function
Trigger factor / Trigger factor, C-terminal / Trigger factor, ribosome-binding, bacterial / Trigger factor ribosome-binding domain superfamily / Bacterial trigger factor protein (TF) / Bacterial trigger factor protein (TF) C-terminus / Trigger factor, C-terminal domain superfamily / Trigger factor/SurA domain superfamily / Single Heli x bin / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A - #60 ...Trigger factor / Trigger factor, C-terminal / Trigger factor, ribosome-binding, bacterial / Trigger factor ribosome-binding domain superfamily / Bacterial trigger factor protein (TF) / Bacterial trigger factor protein (TF) C-terminus / Trigger factor, C-terminal domain superfamily / Trigger factor/SurA domain superfamily / Single Heli x bin / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A - #60 / Ribosomal protein L30/L7, central domain / Ribosomal protein L39 / 50s Ribosomal Protein L19e, Chain O, domain 1 - #10 / N-terminal domain of TfIIb - #30 / Ribosomal protein L21 / Ribosomal Protein L31e; Chain: W; / Ribosomal protein L31 / Nuclear Transport Factor 2; Chain: A, - #80 / Molecule: Ribosomal Protein L15; Chain: K; domain 1 / Molecule: Ribosomal Protein L15; Chain: K; domain 1 - #10 / 3-methyladenine DNA Glycosylase II; Chain A, domain 3 / Ribosomal protein L24 / Ribosomal protein L3; domain 3 / Ribosomal protein L3, domain 3 / Ribosomal protein L15e / Ribosomal protein L15 / Ribosomal Protein L15; Chain: K; domain 2 - #10 / Ribosomal Protein L3; Chain: B; domain 2, / Ribosomal Protein L3; Chain: B; domain 2, - #10 / Ribosomal protein L19e, domain 2 / Ribosomal protein L19e, domain 3 / 50s Ribosomal Protein L19e, Chain O, domain 1 / Ribosomal Protein L4; Chain: A; / Ribosomal protein L4/L1 / Helix Hairpins - #310 / 50S ribosomal protein L10, archaea / Ribosomal Protein L13p; Chain: A; / Ribosomal protein L13 / Atp Synthase Epsilon Chain; Chain: I; / Ribosomal Protein L24e; Chain: T; / Ribosomal Protein L15; Chain: K; domain 2 / Ribosomal Protein L15; Chain: K; domain 2 / Ribosomal protein L19e, archaeal / Ribosomal protein L2; domain 3 / Ribosomal protein L2, domain 3 / Ribosomal protein L15e, archaeal / Ribosomal protein L30, archaeal / Ribosomal protein L6P, archaea / Ribosomal protein L14P, archaeal / Ribosomal protein L21e, archaeal / Ribosomal protein L18e, archaea / Ribosomal protein L10e, archaea / Ribosomal protein L32e, archaeal / Ribosomal protein L3, archaeal / Ribosomal protein L4, archaea / Ribosomal protein L5, archaeal / Ribosomal protein L6 / 50s Ribosomal Protein L5; Chain: A, / Ribosomal protein L5 / Ribosomal protein L30/L7 / Nucleotidyltransferase; domain 5 - #100 / Ribosomal protein L16/L10 / Ribosomal protein L22/L17 / Ribosomal Protein L14 / Ribosomal protein L14/L23 / Outer Surface Protein A; domain 3 / Ribosomal protein L7Ae, archaea / Ribosomal Protein L22; Chain A / Ribosomal Protein L30; Chain: A, / Ribosomal protein L24e / SH3 type barrels. - #30 / Ribosomal protein L30/S12 / Aldehyde Oxidoreductase; domain 3 / DNA repair Rad51/transcription factor NusA, alpha-helical / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / N-terminal domain of TfIIb / Ribosomal protein L2, archaeal-type / Helix-hairpin-helix domain / Ribosomal L15/L27a, N-terminal / Translation factors / Ribosomal protein L23 / 50S ribosomal protein L10, insertion domain superfamily / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / metallochaperone-like domain / TRASH domain / RRM (RNA recognition motif) domain / Peptidyl-prolyl cis-trans isomerase domain superfamily / 60s Ribosomal Protein L30; Chain: A; / Ribosomal protein L44e signature. / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L10e / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature.
Similarity search - Domain/homology
: / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Trigger factor / Large ribosomal subunit protein uL22 ...: / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Trigger factor / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL18 / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein eL8 / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein eL19 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein eL37 / Large ribosomal subunit protein eL42 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein eL15 / Large ribosomal subunit protein eL43
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
HALOARCULA MARISMORTUI (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsFerbitz, L. / Maier, T. / Patzelt, H. / Bukau, B. / Deuerling, E. / Ban, N.
CitationJournal: Nature / Year: 2004
Title: Trigger Factor in Complex with the Ribosome Forms a Molecular Cradle for Nascent Proteins
Authors: Ferbitz, L. / Maier, T. / Patzelt, H. / Bukau, B. / Deuerling, E. / Ban, N.
History
DepositionJul 1, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 12, 2017Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 1.4Dec 13, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "JC" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "JC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
0: 23S RRNA
1: 50S RIBOSOMAL PROTEIN L39E
2: 50S RIBOSOMAL PROTEIN L44E LA, HLA, RIBOSOMAL PROTEIN L44E
5: TRIGGER FACTOR
9: 5S RRNA
A: 50S RIBOSOMAL PROTEIN L2P
B: 50S RIBOSOMAL PROTEIN L3P
C: 50S RIBOSOMAL PROTEIN L4P
D: 50S RIBOSOMAL PROTEIN L5P HMAL5, HL13, RIBOSOMAL PROTEIN L5
E: 50S RIBOSOMAL PROTEIN L6P
F: 50S RIBOSOMAL PROTEIN L7AE
G: 50S RIBOSOMAL PROTEIN L10E
H: 50S RIBOSOMAL PROTEIN L10E
I: 50S RIBOSOMAL PROTEIN L13P
J: 50S RIBOSOMAL PROTEIN L14P
K: 50S RIBOSOMAL PROTEIN L15P
L: 50S RIBOSOMAL PROTEIN L15E
M: 50S RIBOSOMAL PROTEIN L18P
N: 50S RIBOSOMAL PROTEIN L18E
O: 50S RIBOSOMAL PROTEIN L19E
P: 50S RIBOSOMAL PROTEIN L21E
Q: 50S RIBOSOMAL PROTEIN L22P HMAL22, HL23, RIBOSOMAL PROTEIN L22
R: 50S RIBOSOMAL PROTEIN L23P
S: RIBOSOMAL PROTEIN L24
T: 50S RIBOSOMAL PROTEIN L24P
U: 50S RIBOSOMAL PROTEIN L24E
V: 50S RIBOSOMAL PROTEIN L30P
W: 50S RIBOSOMAL PROTEIN L31E
X: 50S RIBOSOMAL PROTEIN L32E
Y: 50S RIBOSOMAL PROTEIN L37AE
Z: RIBOSOMAL PROTEIN L37E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,473,992263
Polymers1,467,75131
Non-polymers6,241232
Water142,0847887
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)210.746, 298.871, 574.173
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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RNA chain , 2 types, 2 molecules 09

#1: RNA chain 23S RRNA


Mass: 946034.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: GenBank: 3377779
#5: RNA chain 5S RRNA


Mass: 39318.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: GenBank: 3377779

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50S RIBOSOMAL PROTEIN ... , 26 types, 26 molecules 12ABCDEFGHIJKLMNOPQRTUVWXY

#2: Protein/peptide 50S RIBOSOMAL PROTEIN L39E / HL39E / HL46E / RIBOSOMAL PROTEIN L39E


Mass: 5844.700 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P22452
#3: Protein 50S RIBOSOMAL PROTEIN L44E LA, HLA, RIBOSOMAL PROTEIN L44E


Mass: 10815.245 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P32411
#6: Protein 50S RIBOSOMAL PROTEIN L2P / RIBOSOMAL PROTEIN L2 / HMAL2 / HL4


Mass: 25237.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P20276
#7: Protein 50S RIBOSOMAL PROTEIN L3P / HMAL3 / HL1 / RIBOSOMAL PROTEIN L3


Mass: 37265.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P20279
#8: Protein 50S RIBOSOMAL PROTEIN L4P / RIBOSOMAL PROTEIN L4 / HMAL4 / HL6


Mass: 26442.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P12735
#9: Protein 50S RIBOSOMAL PROTEIN L5P HMAL5, HL13, RIBOSOMAL PROTEIN L5


Mass: 19420.498 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P14124
#10: Protein 50S RIBOSOMAL PROTEIN L6P / RIBOSOMAL PROTEIN L6 / HMAL6 / HL10


Mass: 19830.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P14135
#11: Protein 50S RIBOSOMAL PROTEIN L7AE / HS6 / RIBOSOMAL PROTEIN L10


Mass: 12600.822 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P12743
#12: Protein 50S RIBOSOMAL PROTEIN L10E / RIBOSOMAL PROTEIN L10 / ACIDIC RIBOSOMAL PROTEIN P0 HOMOLOG / L10E / HMAL10


Mass: 37213.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P15825
#13: Protein 50S RIBOSOMAL PROTEIN L10E / RIBOSOMAL PROTEIN L10E


Mass: 18022.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P60617
#14: Protein 50S RIBOSOMAL PROTEIN L13P / RIBOSOMAL PROTEIN L13 / HMAL13


Mass: 16249.214 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P29198
#15: Protein 50S RIBOSOMAL PROTEIN L14P / RIBOSOMAL PROTEIN L14 / HMAL14 / HL27


Mass: 14216.233 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P22450
#16: Protein 50S RIBOSOMAL PROTEIN L15P / RIBOSOMAL PROTEIN L15 / HMAL15 / HL9


Mass: 17874.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P12737
#17: Protein 50S RIBOSOMAL PROTEIN L15E


Mass: 22856.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P60618
#18: Protein 50S RIBOSOMAL PROTEIN L18P / RIBOSOMAL PROTEIN L18 / HMAL18 / HL12


Mass: 20509.740 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P14123
#19: Protein 50S RIBOSOMAL PROTEIN L18E / HL29 / L19 / RIBOSOMAL PROTEIN L18E


Mass: 12307.720 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P12733
#20: Protein 50S RIBOSOMAL PROTEIN L19E / HMAL19 / HL24 / RIBOSOMAL PROTEIN L19E


Mass: 16631.322 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P14119
#21: Protein 50S RIBOSOMAL PROTEIN L21E / HL31 / RIBOSOMAL PROTEIN L21E


Mass: 10436.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P12734
#22: Protein 50S RIBOSOMAL PROTEIN L22P HMAL22, HL23, RIBOSOMAL PROTEIN L22


Mass: 16835.746 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P10970
#23: Protein 50S RIBOSOMAL PROTEIN L23P / HMAL23 / HL25 / L21 / RIBOSOMAL PROTEIN L23


Mass: 9481.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P12732
#25: Protein 50S RIBOSOMAL PROTEIN L24P / HMAL24 / HL16 / HL15 / RIBOSOMAL PROTEIN L24P


Mass: 7233.720 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P14116
#26: Protein 50S RIBOSOMAL PROTEIN L24E / RIBOSOMAL PROTEIN L24E / HL21/HL22


Mass: 7758.667 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P10971
#27: Protein 50S RIBOSOMAL PROTEIN L30P / HMAL30 / HL20 / HL16 RIBOSOMAL PROTEIN L29


Mass: 17062.885 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P14121
#28: Protein 50S RIBOSOMAL PROTEIN L31E / RIBOSOMAL PROTEIN L31E / L34 / HL30


Mass: 10253.417 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P18138
#29: Protein 50S RIBOSOMAL PROTEIN L32E / RIBOSOMAL PROTEIN L32E / HL5


Mass: 26324.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P12736
#30: Protein 50S RIBOSOMAL PROTEIN L37AE


Mass: 8097.830 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P60619

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Protein , 1 types, 1 molecules 5

#4: Protein TRIGGER FACTOR


Mass: 15837.027 Da / Num. of mol.: 1
Fragment: N-TERMINAL RIBOSOME BINDING FRAGMENT, RESIDUES 1-144
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / References: GenBank: 147989, UniProt: P0A850*PLUS

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RIBOSOMAL PROTEIN ... , 2 types, 2 molecules SZ

#24: Protein RIBOSOMAL PROTEIN L24


Mass: 13539.759 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P10972
#31: Protein RIBOSOMAL PROTEIN L37E / L35E


Mass: 6199.007 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P32410

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Non-polymers , 6 types, 8119 molecules

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


Mass: 24.305 Da / Num. of mol.: 117 / Source method: obtained synthetically / Formula: Mg
#33: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#34: Chemical...
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 86 / Source method: obtained synthetically / Formula: Na
#35: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: Cl
#36: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cd
#37: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7887 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsNUMBERING OF L23P DIFFERS FROM THE GENE DERIVED SEQUENCE BY 1 BECAUSE OF THE MISSING INITIAL ...NUMBERING OF L23P DIFFERS FROM THE GENE DERIVED SEQUENCE BY 1 BECAUSE OF THE MISSING INITIAL METHIONINE (BASED ON PDB ENTRY 1JJ2). ONLY RESIDUES 25-59 OF THE TRIGGER FACTOR FRAGMENT 1-144 HAVE WELL DEFINED ELECTRON DENSITY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 55 %
Crystal growDetails: PEG 6000, KCL, NH4CL, MGCL2, CDCL2, POTASSIUM ACETATE, TRIS-MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 6, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 241873 / % possible obs: 96.8 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.258 / Net I/σ(I): 25.4
Reflection shellResolution: 3.5→3.63 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.691 / Mean I/σ(I) obs: 2 / % possible all: 94.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JJ2

1jj2


Resolution: 3.5→30 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.268 1775 0.8 %
Rwork0.192 --
obs0.192 181663 80.3 %
Displacement parametersBiso mean: 41.8 Å2
Baniso -1Baniso -2Baniso -3
1--2.13 Å20 Å20 Å2
2--2.73 Å20 Å2
3----0.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.52 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.73 Å0.64 Å
Refinement stepCycle: LAST / Resolution: 3.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29123 61617 232 7887 98859
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.52
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.5→3.72 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.386 191 1 %
Rwork0.307 18513 -
obs--49.9 %

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