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- PDB-2zjp: Thiopeptide antibiotic Nosiheptide bound to the large ribosomal s... -

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Basic information

Entry
Database: PDB / ID: 2zjp
TitleThiopeptide antibiotic Nosiheptide bound to the large ribosomal subunit of Deinococcus radiodurans
Components
  • (50S RIBOSOMAL PROTEIN ...) x 28
  • NOSIHEPTIDE
  • RIBOSOMAL 23S RNA
  • RIBOSOMAL 5S RNA
KeywordsRIBOSOME/ANTIBIOTIC / NOSIHEPTIDE / THIOPEPTIDE / THIAZOLE / ANTIBIOTIC / L11 / S50 / ANTIBACTERIAL / RIBOSOME-ANTIBIOTIC COMPLEX / RIBOSOME / ZINC-FINGER / TRANSLATION REGULATION / RNA-BINDING
Function / homology
Function and homology information


negative regulation of translational elongation / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / large ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / transferase activity / defense response to Gram-negative bacterium / tRNA binding ...negative regulation of translational elongation / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / large ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / transferase activity / defense response to Gram-negative bacterium / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / defense response to Gram-positive bacterium / translation / ribonucleoprotein complex / mRNA binding / RNA binding / metal ion binding / cytoplasm
Similarity search - Function
Thiazolylpeptide-type bacteriocin precursor / Ribosomal protein L25, C-terminal domain / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12, N-terminal domain / Ribosomal protein L17 / 50s Ribosomal Protein L17; Chain: A, / Ribosomal Protein L25; Chain P / Ribosomal Protein L13p; Chain: A; / Ribosomal protein L13 / Ribosomal protein L11/L12, C-terminal domain ...Thiazolylpeptide-type bacteriocin precursor / Ribosomal protein L25, C-terminal domain / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12, N-terminal domain / Ribosomal protein L17 / 50s Ribosomal Protein L17; Chain: A, / Ribosomal Protein L25; Chain P / Ribosomal Protein L13p; Chain: A; / Ribosomal protein L13 / Ribosomal protein L11/L12, C-terminal domain / Ribosomal protein L6 / Ribosomal Protein L25; Chain P / 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 L22; Chain A / Ribosomal Protein L30; Chain: A, / Aldehyde Oxidoreductase; domain 3 / RNA Polymerase Alpha Subunit; Chain A, domain 2 / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / RRM (RNA recognition motif) domain / Ribosomal protein L11, bacterial-type / Ribosomal protein L11, conserved site / Nucleic acid-binding proteins / Ribosomal protein L11 signature. / Ribosomal protein L16 signature 1. / : / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L11, N-terminal / Ribosomal protein L17 signature. / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11, RNA binding domain / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L28/L24 superfamily / Ribosomal protein L36 signature. / Beta Complex / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L32p, bacterial type / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L28 / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L20 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L33 superfamily / : / Ribosomal protein L30, bacterial-type / Ribosomal protein L16 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / L28p-like / Ribosomal protein L20 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L21 / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L19
Similarity search - Domain/homology
Nosiheptide / Chem-NO1 / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Nosiheptide precursor / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL28 ...Nosiheptide / Chem-NO1 / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Nosiheptide precursor / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL27
Similarity search - Component
Biological speciesDEINOCOCCUS RADIODURANS (radioresistant)
STREPTOMYCES ACTUOSUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å
Model type detailsCA ATOMS ONLY, CHAIN 1, 2, 3
AuthorsHarms, J.M. / Wilson, D.N. / Schluenzen, F. / Connell, S.R. / Stachelhaus, T. / Zaborowska, Z. / Spahn, C.M.T. / Fucini, P.
CitationJournal: Mol.Cell / Year: 2008
Title: Translational Regulation Via L11: Molecular Switches on the Ribosome Turned on and Off by Thiostrepton and Micrococcin.
Authors: Harms, J.M. / Wilson, D.N. / Schluenzen, F. / Connell, S.R. / Stachelhaus, T. / Zaborowska, Z. / Spahn, C.M. / Fucini, P.
History
DepositionMar 7, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 17, 2008Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary
Revision 1.4Nov 30, 2011Group: Database references
Revision 1.5Dec 28, 2011Group: Atomic model / Derived calculations
Revision 1.6Dec 12, 2012Group: Other
Revision 2.0Oct 16, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Polymer sequence / Structure summary
Category: entity / entity_poly / struct_conn
Item: _entity.src_method / _entity_poly.pdbx_seq_one_letter_code_can / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Nov 1, 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_conn_type / struct_ref_seq_dif / struct_sheet / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.2Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "HA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "HA" 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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: 50S RIBOSOMAL PROTEIN L33
2: 50S RIBOSOMAL PROTEIN L34
3: 50S RIBOSOMAL PROTEIN L35
4: 50S RIBOSOMAL PROTEIN L36
5: NOSIHEPTIDE
A: 50S RIBOSOMAL PROTEIN L2
B: 50S RIBOSOMAL PROTEIN L3
C: 50S RIBOSOMAL PROTEIN L4
D: 50S RIBOSOMAL PROTEIN L5
E: 50S RIBOSOMAL PROTEIN L6
F: 50S RIBOSOMAL PROTEIN L11
G: 50S RIBOSOMAL PROTEIN L13
H: 50S RIBOSOMAL PROTEIN L14
I: 50S RIBOSOMAL PROTEIN L15
J: 50S RIBOSOMAL PROTEIN L16
K: 50S RIBOSOMAL PROTEIN L17
L: 50S RIBOSOMAL PROTEIN L18
M: 50S RIBOSOMAL PROTEIN L19
N: 50S RIBOSOMAL PROTEIN L20
O: 50S RIBOSOMAL PROTEIN L21
P: 50S RIBOSOMAL PROTEIN L22
Q: 50S RIBOSOMAL PROTEIN L23
R: 50S RIBOSOMAL PROTEIN L24
S: 50S RIBOSOMAL PROTEIN L25
T: 50S RIBOSOMAL PROTEIN L27
U: 50S RIBOSOMAL PROTEIN L28
V: 50S RIBOSOMAL PROTEIN L29
W: 50S RIBOSOMAL PROTEIN L30
X: RIBOSOMAL 23S RNA
Y: 50S RIBOSOMAL PROTEIN L32
Z: RIBOSOMAL 5S RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,366,82169
Polymers1,365,63431
Non-polymers1,18738
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)169.900, 408.900, 694.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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50S RIBOSOMAL PROTEIN ... , 28 types, 28 molecules 1234ABCDEFGHIJKLMNOPQRSTUVWY

#1: Protein 50S RIBOSOMAL PROTEIN L33 / / Coordinate model: Cα atoms only


Mass: 6374.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DEINOCOCCUS RADIODURANS (radioresistant) / References: UniProt: Q9RSS4
#2: Protein/peptide 50S RIBOSOMAL PROTEIN L34 / / Coordinate model: Cα atoms only


Mass: 5626.587 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DEINOCOCCUS RADIODURANS (radioresistant) / References: UniProt: Q9RSH2
#3: Protein 50S RIBOSOMAL PROTEIN L35 / / Coordinate model: Cα atoms only


Mass: 7448.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DEINOCOCCUS RADIODURANS (radioresistant) / References: UniProt: Q9RSW6
#4: Protein/peptide 50S RIBOSOMAL PROTEIN L36 /


Mass: 4322.295 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DEINOCOCCUS RADIODURANS (radioresistant) / References: UniProt: Q9RSK0
#6: Protein 50S RIBOSOMAL PROTEIN L2 /


Mass: 29976.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DEINOCOCCUS RADIODURANS (radioresistant) / References: UniProt: Q9RXJ9
#7: Protein 50S RIBOSOMAL PROTEIN L3 /


Mass: 22477.150 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DEINOCOCCUS RADIODURANS (radioresistant) / References: UniProt: Q9RXK2
#8: Protein 50S RIBOSOMAL PROTEIN L4 /


Mass: 22308.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DEINOCOCCUS RADIODURANS (radioresistant) / References: UniProt: Q9RXK1
#9: Protein 50S RIBOSOMAL PROTEIN L5 /


Mass: 20379.908 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DEINOCOCCUS RADIODURANS (radioresistant) / References: UniProt: Q9RXJ0
#10: Protein 50S RIBOSOMAL PROTEIN L6 /


Mass: 19613.637 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DEINOCOCCUS RADIODURANS (radioresistant) / References: UniProt: Q9RSL3
#11: Protein 50S RIBOSOMAL PROTEIN L11 /


Mass: 14889.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DEINOCOCCUS RADIODURANS (radioresistant) / References: UniProt: Q9RSS7
#12: Protein 50S RIBOSOMAL PROTEIN L13 /


Mass: 19223.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DEINOCOCCUS RADIODURANS (radioresistant) / References: UniProt: Q9RXY1
#13: Protein 50S RIBOSOMAL PROTEIN L14 /


Mass: 14256.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DEINOCOCCUS RADIODURANS (radioresistant) / References: UniProt: Q9RXJ2
#14: Protein 50S RIBOSOMAL PROTEIN L15 /


Mass: 16894.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DEINOCOCCUS RADIODURANS (radioresistant) / References: UniProt: Q9RSK9
#15: Protein 50S RIBOSOMAL PROTEIN L16 /


Mass: 16257.194 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DEINOCOCCUS RADIODURANS (radioresistant) / References: UniProt: Q9RXJ5
#16: Protein 50S RIBOSOMAL PROTEIN L17 /


Mass: 12926.067 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DEINOCOCCUS RADIODURANS (radioresistant) / References: UniProt: Q9RSJ5
#17: Protein 50S RIBOSOMAL PROTEIN L18 /


Mass: 12163.936 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DEINOCOCCUS RADIODURANS (radioresistant) / References: UniProt: Q9RSL2
#18: Protein 50S RIBOSOMAL PROTEIN L19 /


Mass: 18347.818 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DEINOCOCCUS RADIODURANS (radioresistant) / References: UniProt: Q9RWB4
#19: Protein 50S RIBOSOMAL PROTEIN L20 /


Mass: 13991.274 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DEINOCOCCUS RADIODURANS (radioresistant) / References: UniProt: Q9RSW7
#20: Protein 50S RIBOSOMAL PROTEIN L21 /


Mass: 11165.743 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DEINOCOCCUS RADIODURANS (radioresistant) / References: UniProt: Q9RY64
#21: Protein 50S RIBOSOMAL PROTEIN L22 /


Mass: 15190.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DEINOCOCCUS RADIODURANS (radioresistant) / References: UniProt: Q9RXJ7
#22: Protein 50S RIBOSOMAL PROTEIN L23 /


Mass: 10539.210 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DEINOCOCCUS RADIODURANS (radioresistant) / References: UniProt: Q9RXK0
#23: Protein 50S RIBOSOMAL PROTEIN L24 /


Mass: 12384.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DEINOCOCCUS RADIODURANS (radioresistant) / References: UniProt: Q9RXJ1
#24: Protein 50S RIBOSOMAL PROTEIN L25 / / GENERAL STRESS PROTEIN CTC


Mass: 25415.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DEINOCOCCUS RADIODURANS (radioresistant) / References: UniProt: Q9RX88
#25: Protein 50S RIBOSOMAL PROTEIN L27 /


Mass: 9609.091 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DEINOCOCCUS RADIODURANS (radioresistant) / References: UniProt: Q9RY65
#26: Protein 50S RIBOSOMAL PROTEIN L28 /


Mass: 8982.592 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DEINOCOCCUS RADIODURANS (radioresistant) / References: UniProt: Q9RRG8
#27: Protein 50S RIBOSOMAL PROTEIN L29 /


Mass: 7774.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DEINOCOCCUS RADIODURANS (radioresistant) / References: UniProt: Q9RXJ4
#28: Protein 50S RIBOSOMAL PROTEIN L30 /


Mass: 6079.235 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DEINOCOCCUS RADIODURANS (radioresistant) / References: UniProt: Q9RSL0
#30: Protein 50S RIBOSOMAL PROTEIN L32 /


Mass: 6810.017 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DEINOCOCCUS RADIODURANS (radioresistant) / References: UniProt: P49228

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Protein/peptide , 1 types, 1 molecules 5

#5: Protein/peptide NOSIHEPTIDE / /


Type: Thiopeptide / Class: Antibiotic / Mass: 1195.308 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: NOSIHEPTIDE IS A HETROCYCLIC THIOPEPTIDE, CONSISTING OF FIVE THIAZOLES AND ONE 3-HYDROXYPYRIDINE RINGS. A MODIFIED INDOLE RING NO1(14) IS LINKED VIA THE SIDE CHAINS OF 3-HYDROXY 3GL(6) AND ...Details: NOSIHEPTIDE IS A HETROCYCLIC THIOPEPTIDE, CONSISTING OF FIVE THIAZOLES AND ONE 3-HYDROXYPYRIDINE RINGS. A MODIFIED INDOLE RING NO1(14) IS LINKED VIA THE SIDE CHAINS OF 3-HYDROXY 3GL(6) AND CYS(8). THE OBSERVED C-TERMINAL AMINO GROUP NH2(13) IS LIKELY TO BE A POST-TRANSLATIONAL DECARBOXYLATED REMNANT OF A SER C-TERMINAL RESIDUE
Source: (natural) STREPTOMYCES ACTUOSUS (bacteria) / References: UniProt: C6FX52, Nosiheptide

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RNA chain , 2 types, 2 molecules XZ

#29: RNA chain RIBOSOMAL 23S RNA


Mass: 933405.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DEINOCOCCUS RADIODURANS (radioresistant) / References: GenBank: AE000513
#31: RNA chain RIBOSOMAL 5S RNA


Mass: 39605.695 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DEINOCOCCUS RADIODURANS (radioresistant) / References: GenBank: AE000513

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Non-polymers , 3 types, 38 molecules

#32: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#33: Chemical ChemComp-NO1 / 4-(hydroxymethyl)-3-methyl-1H-indole-2-carboxylic acid /


Type: Thiopeptide / Class: Antibiotic / Mass: 205.210 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H11NO3
Details: NOSIHEPTIDE IS A HETROCYCLIC THIOPEPTIDE, CONSISTING OF FIVE THIAZOLES AND ONE 3-HYDROXYPYRIDINE RINGS. A MODIFIED INDOLE RING NO1(14) IS LINKED VIA THE SIDE CHAINS OF 3-HYDROXY 3GL(6) AND ...Details: NOSIHEPTIDE IS A HETROCYCLIC THIOPEPTIDE, CONSISTING OF FIVE THIAZOLES AND ONE 3-HYDROXYPYRIDINE RINGS. A MODIFIED INDOLE RING NO1(14) IS LINKED VIA THE SIDE CHAINS OF 3-HYDROXY 3GL(6) AND CYS(8). THE OBSERVED C-TERMINAL AMINO GROUP NH2(13) IS LIKELY TO BE A POST-TRANSLATIONAL DECARBOXYLATED REMNANT OF A SER C-TERMINAL RESIDUE
References: Nosiheptide
#34: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 35 / Source method: obtained synthetically / Formula: Mg

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Details

Compound detailsNosiheptide is a member of a sulphur-rich heterocyclic peptides class. All share a macrocylic core, ...Nosiheptide is a member of a sulphur-rich heterocyclic peptides class. All share a macrocylic core, consisting of a nitrogen containing, six-membered ring central to dehydroamino acids and a subset of five member ring structures including thiazoles, thiazolines and oxazoles. The main characteristic of the nosiheptide structure is a general tendency to be more oxidized than the thiostrepton one. No thiazoline, or hydrogenated quinaldic precursor nor tetrahydropyridine rings are present in nosiheptide. All the corresponding rings are unsaturated. Nosiheptide possess an indolic acid ring system that is appended to the side chains of the Ser/Cys and a central 6-membered nitrogen heterocycle produced by cyclization between two corresponding dehydroalanine acids with incorporation of an adjacent carbonyl group. Thiazole formation is by nucleophilic addition of each Cys side chain to the proceeding carbonyl group followed by dehydration and dehydrogenation. HERE, NOSIHEPTIDE IS REPRESENTED BY GROUPING TOGETHER THE SEQUENCE (SEQRES) AND THE ONE LIGAND (HET) NO1.
Nonpolymer detailsTHE CHIRALITY OF THE 4-HYDROXY GLUTAMIC ACID (3GL) IS NOT SATTELED. IN THE CURRENT ENTRY THE ...THE CHIRALITY OF THE 4-HYDROXY GLUTAMIC ACID (3GL) IS NOT SATTELED. IN THE CURRENT ENTRY THE DIASTEREOMER IS SHOWN TO BE (2S,4S), WHILES CCDC 15794 NOSHEP10 ENTRY SHOWS IT TO BE (2S,4R) (DOI 10.1021/JA00461A039).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 7

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Sample preparation

CrystalDensity Matthews: 4 Å3/Da / Density % sol: 66 %
Crystal growDetails: VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONSLS X06SA11
SYNCHROTRONESRF ID2920.97
Detector
TypeIDDetectorDate
MARRESEARCH1CCDFeb 1, 2006
ADSC QUANTUM 3152CCDDec 3, 2007
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.971
ReflectionResolution: 3.7→30 Å / Num. obs: 216249 / % possible obs: 85.6 % / Observed criterion σ(I): 1 / Rsym value: 0.14 / Net I/σ(I): 6.1
Reflection shellResolution: 3.7→3.76 Å / Mean I/σ(I) obs: 1.2 / Rsym value: 0.63 / % possible all: 75.2

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Processing

Software
NameClassification
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZJR

2zjr


Resolution: 3.7→30 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.34 --
Rwork0.3 --
obs0.3 216249 85.6 %
Refinement stepCycle: LAST / Resolution: 3.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24145 60249 50 0 84444
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
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_deg
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.38
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: 3.3→3.76 Å / % reflection obs: 63 %

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