[English] 日本語
Yorodumi
- PDB-1n8r: Structure of large ribosomal subunit in complex with virginiamycin M -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1n8r
TitleStructure of large ribosomal subunit in complex with virginiamycin M
Components
  • (50S ribosomal protein ...) x 27
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • Acidic ribosomal protein P0 homolog
KeywordsRibosome/Antibiotic / ribosome-antibiotic complex / virginiamycin M / streptogramin / antibiotic
Function / homology
Function and homology information


ribonuclease P activity / tRNA 5'-leader removal / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosome biogenesis / large ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation ...ribonuclease P activity / tRNA 5'-leader removal / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosome biogenesis / large ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / large 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 / DNA repair / nucleotide binding / mRNA binding / DNA binding / zinc ion binding / cytoplasm
Similarity search - Function
Single Heli x bin / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A - #60 / Ribosomal protein L30/L7, central domain / Ribosomal protein L39 / N-terminal domain of TfIIb - #30 / Ribosomal protein L21 / 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 ...Single Heli x bin / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A - #60 / Ribosomal protein L30/L7, central domain / Ribosomal protein L39 / N-terminal domain of TfIIb - #30 / Ribosomal protein L21 / 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 L31e; Chain: W; / Ribosomal protein L31 / Ribosomal protein L24 / Ribosomal protein L3; domain 3 / Ribosomal protein L3, domain 3 / 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 - #10 / Helix Hairpins - #310 / Ribosomal Protein L4; Chain: A; / Ribosomal protein L4/L1 / 50S ribosomal protein L10, archaea / 50s Ribosomal Protein L19e, Chain O, domain 1 / Ribosomal protein L15e / Ribosomal protein L15 / Ribosomal Protein L13p; Chain: A; / Ribosomal protein L13 / Atp Synthase Epsilon Chain; Chain: I; / Ribosomal Protein L24e; Chain: T; / Ribosomal protein L2; domain 3 / Ribosomal protein L2, domain 3 / Ribosomal protein L15e, archaeal / Ribosomal protein L19e, 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 / 50s Ribosomal Protein L5; Chain: A, / Ribosomal protein L5 / Ribosomal protein L30/L7 / Nucleotidyltransferase; domain 5 - #100 / Ribosomal protein L16/L10 / Ribosomal Protein L14 / Ribosomal protein L14/L23 / Ribosomal Protein L15; Chain: K; domain 2 - #10 / Ribosomal protein L6 / Ribosomal protein L22/L17 / Ribosomal Protein L15; Chain: K; domain 2 / Ribosomal Protein L15; Chain: K; domain 2 / Ribosomal Protein L30; Chain: A, / SH3 type barrels. - #30 / Ribosomal protein L7Ae, archaea / Ribosomal protein L30/S12 / Ribosomal Protein L22; Chain A / Outer Surface Protein A; domain 3 / Aldehyde Oxidoreductase; domain 3 / DNA repair Rad51/transcription factor NusA, alpha-helical / : / N-terminal domain of TfIIb / Helix-hairpin-helix domain / Ribosomal protein L2, archaeal-type / Translation factors / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Ribosomal L15/L27a, N-terminal / 50S ribosomal protein L10, insertion domain superfamily / Ribosomal protein L23 / : / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / metallochaperone-like domain / TRASH domain / RRM (RNA recognition motif) domain / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / Ribosomal protein L10e, conserved site / Ribosomal protein L44e signature. / Ribosomal protein L10e signature. / Ribosomal protein L10e / 60s Ribosomal Protein L30; Chain: A; / Ribosomal protein L19/L19e conserved site / : / Ribosomal protein L19e signature. / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature. / 60S ribosomal protein L19 / Ribosomal protein L13, eukaryotic/archaeal
Similarity search - Domain/homology
: / : / VIRGINIAMYCIN M1 / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL29 ...: / : / VIRGINIAMYCIN M1 / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 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 speciesHaloarcula marismortui (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsHansen, J.L. / Moore, P.B. / Steitz, T.A.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: Structures of Five Antibiotics Bound at the Peptidyl Transferase Center of the Large Ribosomal Subunit
Authors: Hansen, J. / Moore, P.B. / Steitz, T.A.
#1: Journal: Science / Year: 2000
Title: The complete atomic structure of the large ribosomal subunit at 2.4 A resolution
Authors: Ban, N. / Nissen, P. / Hansen, J. / Moore, P.B. / Steitz, T.A.
#2: Journal: Science / Year: 2000
Title: The structural basis of ribosome activity in peptide bond synthesis
Authors: Nissen, P. / Hansen, J. / Ban, N. / Moore, P.B. / Steitz, T.A.
History
DepositionNov 21, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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 / 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_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Mar 13, 2024Group: Source and taxonomy / Category: entity_src_nat

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 23S ribosomal RNA
B: 5S ribosomal RNA
C: 50S ribosomal protein L2P
D: 50S ribosomal protein L3P
E: 50S ribosomal protein L4E
F: 50S ribosomal protein L5P
G: 50S ribosomal protein L6P
H: 50S ribosomal protein L7Ae
I: Acidic ribosomal protein P0 homolog
J: 50S ribosomal protein L10e
K: 50S ribosomal protein L13P
L: 50S ribosomal protein L14P
M: 50S ribosomal protein L15P
N: 50S ribosomal protein L15E
O: 50S ribosomal protein L18P
P: 50S ribosomal protein L18E
Q: 50S ribosomal protein L19E
R: 50S ribosomal protein L21e
S: 50S ribosomal protein L22P
T: 50S ribosomal protein L23P
U: 50S ribosomal protein L24P
V: 50S ribosomal protein L24E
W: 50S ribosomal protein L29P
X: 50S ribosomal protein L30P
Y: 50S ribosomal protein L31E
Z: 50S ribosomal protein L32E
1: 50S ribosomal protein L37AE
2: 50S ribosomal protein L37e
3: 50S ribosomal protein L39e
4: 50S ribosomal protein L44E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,458,642262
Polymers1,451,91430
Non-polymers6,728232
Water141,9947882
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)212.902, 300.474, 575.176
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Cell settingorthorhombic
Space group name H-MC2221

-
Components

-
RNA chain , 2 types, 2 molecules AB

#1: RNA chain 23S ribosomal RNA


Mass: 946034.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cultured cells / Source: (natural) Haloarcula marismortui (Halophile) / References: GenBank: 3377779
#2: RNA chain 5S ribosomal RNA


Mass: 39318.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cultured cells / Source: (natural) Haloarcula marismortui (Halophile) / References: GenBank: 3377779

+
50S ribosomal protein ... , 27 types, 27 molecules CDEFGHJKLMNOPQRSTUVWXYZ1234

#3: Protein 50S ribosomal protein L2P / Hmal2 / HL4


Mass: 25237.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cultured cells / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P20276
#4: Protein 50S ribosomal protein L3P / Hmal3 / HL1


Mass: 37265.195 Da / Num. of mol.: 1 / Mutation: R310P, 311F insertion / Source method: isolated from a natural source / Details: cultured cells / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P20279
#5: Protein 50S ribosomal protein L4E / Hmal4 / HL6


Mass: 26442.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cultured cells / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P12735
#6: Protein 50S ribosomal protein L5P / Hmal5 / HL13


Mass: 19420.498 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cultured cells / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P14124
#7: Protein 50S ribosomal protein L6P / Hmal6 / HL10


Mass: 19830.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cultured cells / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P14135
#8: Protein 50S ribosomal protein L7Ae / HS6


Mass: 12600.822 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cultured cells / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P12743
#10: Protein 50S ribosomal protein L10e


Mass: 18022.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cultured cells / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P60617*PLUS
#11: Protein 50S ribosomal protein L13P / Hmal13


Mass: 16249.214 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cultured cells / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P29198
#12: Protein 50S ribosomal protein L14P / Hmal14 / HL27


Mass: 14216.233 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cultured cells / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P22450
#13: Protein 50S ribosomal protein L15P / Hmal15 / HL9


Mass: 17874.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cultured cells / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P12737
#14: Protein 50S ribosomal protein L15E


Mass: 22856.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cultured cells / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P60618*PLUS
#15: Protein 50S ribosomal protein L18P / Hmal18 / HL12


Mass: 20509.740 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cultured cells / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P14123
#16: Protein 50S ribosomal protein L18E / HL29 / L19


Mass: 12307.720 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cultured cells / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P12733
#17: Protein 50S ribosomal protein L19E / Hmal19 / HL24


Mass: 16631.322 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cultured cells / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P14119
#18: Protein 50S ribosomal protein L21e / HL31


Mass: 10436.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cultured cells / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P12734
#19: Protein 50S ribosomal protein L22P / Hmal22 / HL23


Mass: 16835.746 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cultured cells / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P10970
#20: Protein 50S ribosomal protein L23P / Hmal23 / HL25 / L21


Mass: 9481.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cultured cells / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P12732
#21: Protein 50S ribosomal protein L24P / Hmal24 / HL16 / HL15


Mass: 13539.759 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cultured cells / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P10972
#22: Protein 50S ribosomal protein L24E / HL21/HL22


Mass: 7233.720 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cultured cells / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P14116
#23: Protein 50S ribosomal protein L29P / Hmal29 / HL33


Mass: 7758.667 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cultured cells / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P10971
#24: Protein 50S ribosomal protein L30P / Hmal30 / HL20 / HL16


Mass: 17062.885 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cultured cells / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P14121
#25: Protein 50S ribosomal protein L31E / L34 / HL30


Mass: 10253.417 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cultured cells / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P18138
#26: Protein 50S ribosomal protein L32E / HL5


Mass: 26324.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cultured cells / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P12736
#27: Protein 50S ribosomal protein L37AE


Mass: 8097.830 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cultured cells / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P60619*PLUS
#28: Protein 50S ribosomal protein L37e / L35e


Mass: 6199.007 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cultured cells / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P32410
#29: Protein/peptide 50S ribosomal protein L39e / HL39e / HL46e


Mass: 5844.700 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cultured cells / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P22452
#30: Protein 50S ribosomal protein L44E / LA / HLA


Mass: 10815.245 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cultured cells / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P32411

-
Protein , 1 types, 1 molecules I

#9: Protein Acidic ribosomal protein P0 homolog / L10E / HMaL10


Mass: 37213.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cultured cells / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P15825

-
Non-polymers , 7 types, 8114 molecules

#31: Chemical ChemComp-VIR / VIRGINIAMYCIN M1


Mass: 525.593 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H35N3O7 / Comment: antibiotic*YM
#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.: 1 / 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.: 7882 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.17 Å3/Da / Density % sol: 61.17 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 1.2M KCl, 0.5M (NH4)Cl, 30mM MgCl2, 8% PEG, pH 5.80, VAPOR DIFFUSION, SITTING DROP at 292K
Components of the solutions
IDNameCrystal-IDSol-ID
1KCl11
2NH4Cl11
3MgCl211
4PEG 600011
5KCl12
6NH4Cl12
7MgCl212
8PEG 600012
Crystal grow
*PLUS
pH: 7.1 / Method: back-extraction, vapor diffusion / Details: Ban, N., (2000) Science, 289, 905.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.2 M1reservoirKCl
20.5 M1reservoirNH4Cl
3100 mMpotassium acetate1reservoir
430 mM1reservoirMgCl2
57 %PEG60001reservoir
615 mMTris1reservoir
715 mMMES1reservoir
81 mM1reservoirCdCl2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.0332 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 5, 2000
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 344322 / Num. obs: 339727 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 33.1 Å2 / Rmerge(I) obs: 0.144 / Rsym value: 0.144 / Net I/σ(I): 7.7
Reflection shellResolution: 3→3.05 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 1.7 / Num. unique all: 16729 / Rsym value: 0.49 / % possible all: 97.7
Reflection
*PLUS
Highest resolution: 3 Å / % possible obs: 94.6 % / Redundancy: 4 %
Reflection shell
*PLUS
Highest resolution: 3 Å / Lowest resolution: 3.1 Å / % possible obs: 37.7 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.9

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JJ2

1jj2


Resolution: 3→20 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.242 3203 1 %same reflections as 1JJ2
Rwork0.201 ---
obs0.2011 327972 94.6 %-
all-346861 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.7669 Å2 / ksol: 0.329291 e/Å3
Displacement parametersBiso mean: 43.9 Å2
Baniso -1Baniso -2Baniso -3
1-5.14 Å20 Å20 Å2
2--1.7 Å20 Å2
3----6.84 Å2
Refine analyzeLuzzati coordinate error free: 0.4 Å / Luzzati sigma a free: 0.54 Å
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28801 61617 269 7882 98569
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d15.6
X-RAY DIFFRACTIONc_improper_angle_d1.57
X-RAY DIFFRACTIONc_mcbond_it1.121.5
X-RAY DIFFRACTIONc_mcangle_it1.842
X-RAY DIFFRACTIONc_scbond_it1.32
X-RAY DIFFRACTIONc_scangle_it2.022.5
LS refinement shellResolution: 3→3.11 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.346 131 1 %
Rwork0.338 13488 -
obs--37.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1RNA.PARRNA.TOP
X-RAY DIFFRACTION2PROT.PARPROT.TOP
X-RAY DIFFRACTION3ION.PARION.TOP
Refinement
*PLUS
Highest resolution: 3 Å / Rfactor obs: 0.201
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg15.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.57
LS refinement shell
*PLUS
Highest resolution: 3 Å / Lowest resolution: 3.1 Å

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

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

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more