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- PDB-3pio: Crystal structure of the synergistic antibiotic pair lankamycin a... -

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Basic information

Entry
Database: PDB / ID: 3pio
TitleCrystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit
Components
  • (50S ribosomal protein ...) x 28
  • 5S ribosomal RNA
  • RIBOSOMAL 23S RNA
KeywordsRIBOSOME/ANTIBIOTIC / RIBOSOME / LARGE RIBOSOMAL SUBUNIT / 50S / RIBONUCLEOPROTEIN / RIBOSOMAL PROTEIN / RNA-BINDING / RRNA-BINDING / TRNA-BINDING / LANKAMYCIN / LANKACIDIN / MACROLIDE / RIBOSOME-ANTIBIOTIC complex
Function / homology
Function and homology information


ribosomal large subunit assembly / large ribosomal subunit rRNA binding / large ribosomal subunit / 5S rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / transferase activity / negative regulation of translation / tRNA binding / rRNA binding ...ribosomal large subunit assembly / large ribosomal subunit rRNA binding / large ribosomal subunit / 5S rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / transferase activity / negative regulation of translation / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / RNA binding / metal ion binding / cytoplasm
Similarity search - Function
Factor Xa Inhibitor - #60 / Ribosomal protein L25, C-terminal domain / Ribosomal protein L33 / Helix Hairpins - #3980 / Ribosomal protein L17 / 50s Ribosomal Protein L17; Chain: A, / Ribosomal Protein L25; Chain P / Ribosomal Protein L13p; Chain: A; / Ribosomal protein L13 / Ribosomal protein L2; domain 3 ...Factor Xa Inhibitor - #60 / Ribosomal protein L25, C-terminal domain / Ribosomal protein L33 / Helix Hairpins - #3980 / Ribosomal protein L17 / 50s Ribosomal Protein L17; Chain: A, / Ribosomal Protein L25; Chain P / Ribosomal Protein L13p; Chain: A; / Ribosomal protein L13 / Ribosomal protein L2; domain 3 / Ribosomal protein L2, domain 3 / 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, / SH3 type barrels. - #30 / Factor Xa Inhibitor / Aldehyde Oxidoreductase; domain 3 / RNA Polymerase Alpha Subunit; Chain A, domain 2 / Rubrerythrin, 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 / Single Sheet / 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
Similarity search - Domain/homology
: / Lankamycin / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL34 ...: / Lankamycin / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 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 R1 (radioresistant)
Deinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / ISOMORPHOUS REPLACEMENT / Resolution: 3.2473 Å
AuthorsBelousoff, M.J. / Shapira, T. / Bashan, A. / Zimmerman, E. / Arakawa, K. / Kinashi, H. / Rozenberg, H. / Yonath, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Crystal structure of the synergistic antibiotic pair, lankamycin and lankacidin, in complex with the large ribosomal subunit.
Authors: Belousoff, M.J. / Shapira, T. / Bashan, A. / Zimmerman, E. / Rozenberg, H. / Arakawa, K. / Kinashi, H. / Yonath, A.
History
DepositionNov 7, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 4, 2015Group: Structure summary
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: RIBOSOMAL 23S RNA
Y: 5S ribosomal RNA
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
Z: 50S ribosomal protein L32
1: 50S ribosomal protein L33
2: 50S ribosomal protein L34
3: 50S ribosomal protein L35
4: 50S ribosomal protein L36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,370,433242
Polymers1,364,30730
Non-polymers6,126212
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)170.590, 410.204, 695.078
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
DetailsBIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA. COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. BIOMOLECULE: 1 AUTHOR DETERMINED BIOLOGICAL UNIT: 30-MERIC APPLY THE FOLLOWING TO CHAINS: X, Y, A, B, C, D, E, F, G, AND CHAINS: H, I, J, K, L, M, N, O, P, AND CHAINS: Q, R, S, T, U, V, W, Z, 1, AND CHAINS: 2, 3, 4, 5, 6 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 BIOMT3 1 0.000000 0.000000 1.000000 0.00000

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Components

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RNA chain , 2 types, 2 molecules XY

#1: RNA chain RIBOSOMAL 23S RNA


Mass: 933405.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Deinococcus radiodurans R1 (radioresistant)
References: GenBank: AE000513.1
#2: RNA chain 5S ribosomal RNA /


Mass: 39605.695 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Deinococcus radiodurans R1 (radioresistant)
References: GenBank: AE000513.1

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50S ribosomal protein ... , 28 types, 28 molecules ABCDEFGHIJKLMNOPQRSTUVWZ1234

#3: 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
#4: 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
#5: 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
#6: 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
#7: 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
#8: 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
#9: 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
#10: 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
#11: 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
#12: Protein 50S ribosomal protein L16 /


Mass: 16125.997 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RXJ5
#13: 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
#14: 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
#15: 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
#16: 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
#17: 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
#18: 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
#19: 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
#20: 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
#21: 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
#22: 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
#23: 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
#24: 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
#25: 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
#26: 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
#27: Protein 50S ribosomal protein L33 /


Mass: 6374.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RSS4
#28: Protein/peptide 50S ribosomal protein L34 /


Mass: 5626.587 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RSH2
#29: Protein 50S ribosomal protein L35 /


Mass: 7448.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RSW6
#30: 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

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Non-polymers , 4 types, 212 molecules

#31: Chemical ChemComp-LMA / Lankamycin / [(2S,3R,4R,6R)-6-[[(1S,2R,3S,4S,6S,8R,9S,10S,11R,14R)-9-acetyloxy-6-hydroxy-11-[(2R,3R)-3-hydroxybutan-2-yl]-3-[(2S,3R, 4S,6R)-4-methoxy-3,6-dimethyl-oxan-2-yl]oxy-2,4,6,8,10,14-hexamethyl-7,13-dioxo-12-oxacyclotetradec-1-yl]oxy]-4-methoxy- 2,4-dimethyl-oxan-3-yl] ethanoate


Mass: 831.039 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C43H74O15
#32: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 154 / Source method: obtained synthetically / Formula: Mg
#33: Chemical...
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 42 / Source method: obtained synthetically / Formula: Na
#34: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: K

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

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Sample preparation

CrystalDensity Matthews: 4.46 Å3/Da / Density % sol: 72.4 %
Crystal growDetails: VAPOR DIFFUSION, HANGING DROP. 15% 2:1 ethanol:methylpentanediol was diffused to a hanging drop of 180 AU/ml solution of D50S.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Details: MICROFOCUS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 3.2473→19.995 Å / Num. obs: 353603 / % possible obs: 93.3 % / Observed criterion σ(I): 0.1 / Redundancy: 3.7 % / Rmerge(I) obs: 0.178 / Net I/σ(I): 6.1
Reflection shellResolution: 3.2473→3.36 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 1.2 / % possible all: 34

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Processing

Software
NameVersionClassification
PHENIXmodel building
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: ISOMORPHOUS REPLACEMENT
Starting model: PDB ENTRY 2ZJR

2zjr


Resolution: 3.2473→19.995 Å / SU ML: 0.41 / σ(F): 0.61 / Phase error: 32.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.294 3564 1.01 %
Rwork0.252 --
obs0.253 353603 93.3 %
Solvent computationShrinkage radii: 0.04 Å / VDW probe radii: 0.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42 Å2 / ksol: 0.24 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--13.881 Å20 Å2-0 Å2
2--13.1054 Å2-0 Å2
3----12.1603 Å2
Refinement stepCycle: LAST / Resolution: 3.2473→19.995 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24518 59596 269 0 84383
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00891726
X-RAY DIFFRACTIONf_angle_d1.016137620
X-RAY DIFFRACTIONf_dihedral_angle_d14.92743011
X-RAY DIFFRACTIONf_chiral_restr0.07517611
X-RAY DIFFRACTIONf_plane_restr0.0057124
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2473-3.36290.36842960.34628609X-RAY DIFFRACTION77
3.3629-3.49680.37253750.328135229X-RAY DIFFRACTION95
3.4968-3.6550.3353630.303335498X-RAY DIFFRACTION95
3.655-3.84650.35843380.281935693X-RAY DIFFRACTION96
3.8465-4.08550.30553730.262935818X-RAY DIFFRACTION96
4.0855-4.39790.29893600.247335854X-RAY DIFFRACTION96
4.3979-4.83480.25953690.2335876X-RAY DIFFRACTION96
4.8348-5.52150.26683590.213735970X-RAY DIFFRACTION96
5.5215-6.90850.26743670.224735993X-RAY DIFFRACTION95
6.9085-19.99510.2643640.231535499X-RAY DIFFRACTION93
Refinement TLS params.Method: refined / Origin x: 44.3174 Å / Origin y: 127.3391 Å / Origin z: 109.4249 Å
111213212223313233
T-0.2322 Å2-0.1608 Å2-0.0615 Å2-0.4204 Å20.2111 Å2---0.067 Å2
L0.3083 °20.0429 °20.0067 °2-0.0701 °2-0.0942 °2--0.5099 °2
S0.0385 Å °0.365 Å °0.0217 Å °-0.4228 Å °-0.0193 Å °0.0567 Å °-0.1261 Å °0.1375 Å °0.1083 Å °
Refinement TLS groupSelection details: ALL

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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

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