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- PDB-1yhq: Crystal Structure Of Azithromycin Bound To The G2099A Mutant 50S ... -

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Basic information

Entry
Database: PDB / ID: 1yhq
TitleCrystal Structure Of Azithromycin Bound To The G2099A Mutant 50S Ribosomal Subunit Of Haloarcula Marismortui
Components
  • (50S RIBOSOMAL PROTEIN ...) x 28
  • 23S Ribosomal RNA
  • 5S Ribosomal RNA
  • ACIDIC RIBOSOMAL PROTEIN P0 HOMOLOG
KeywordsRIBOSOME / azithromycin / antibiotic complexes / mutated 50S subunits
Function / homology
Function and homology information


ribonuclease P activity / tRNA 5'-leader removal / cytosolic ribosome / large ribosomal subunit / ribosome biogenesis / large ribosomal subunit rRNA binding / 5S rRNA binding / ribosomal large subunit assembly / cytosolic large ribosomal subunit / tRNA binding ...ribonuclease P activity / tRNA 5'-leader removal / cytosolic ribosome / large ribosomal subunit / ribosome biogenesis / large ribosomal subunit rRNA binding / 5S rRNA binding / ribosomal large subunit assembly / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / DNA repair / nucleotide 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 / 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 ...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 L2; domain 3 / Ribosomal protein L2, domain 3 / Ribosomal protein L11/L12, C-terminal domain / 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 L6 / 50s Ribosomal Protein L5; Chain: A, / Ribosomal protein L5 / Ribosomal protein L3, archaeal / Ribosomal protein L4, archaea / Ribosomal protein L5, archaeal / 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 / Helix-hairpin-helix domain / Ribosomal protein L2, archaeal-type / Translation factors / 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 / 60s Ribosomal Protein L30; Chain: A; / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / Ribosomal protein L44e signature. / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L10e / : / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein L44e / Ribosomal protein L24e, conserved site / Ribosomal protein L44 / Ribosomal protein L24e signature. / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature.
Similarity search - Domain/homology
: / : / STRONTIUM ION / AZITHROMYCIN / : / : / : / : / : / : ...: / : / STRONTIUM ION / AZITHROMYCIN / : / : / : / : / : / : / : / 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 uL11 / 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: 2.4 Å
AuthorsTu, D. / Blaha, G. / Moore, P.B. / Steitz, T.A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2005
Title: Structures of MLSBK antibiotics bound to mutated large ribosomal subunits provide a structural explanation for resistance.
Authors: Tu, D. / Blaha, G. / Moore, P.B. / Steitz, T.A.
History
DepositionJan 10, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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 / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999SEQUENCE Sequence reference for this ribosome: Baliga, N.S., Bonneau, R., Facciotti, M.T., Pan, M., ...SEQUENCE Sequence reference for this ribosome: Baliga, N.S., Bonneau, R., Facciotti, M.T., Pan, M., Glusman, G., Deutsch, E.W., Shannon, P., Chiu, Y., Weng, R.S., Gan, R.R., et al.(2004). Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea.Genome Res. 14, 2221-2234.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
0: 23S Ribosomal RNA
9: 5S Ribosomal RNA
A: 50S ribosomal protein L2P
B: 50S ribosomal protein L3P
C: 50S ribosomal protein L4E
D: 50S ribosomal protein L5P
E: 50S ribosomal protein L6P
F: 50S ribosomal protein L7AE
G: ACIDIC RIBOSOMAL PROTEIN P0 HOMOLOG
H: 50S RIBOSOMAL PROTEIN L10E
I: 50S RIBOSOMAL PROTEIN L11P
J: 50S ribosomal protein L13P
K: 50S ribosomal protein L14P
L: 50S ribosomal protein L15P
M: 50S Ribosomal Protein L15E
N: 50S ribosomal protein L18P
O: 50S ribosomal protein L18e
P: 50S ribosomal protein L19E
Q: 50S ribosomal protein L21e
R: 50S ribosomal protein L22P
S: 50S ribosomal protein L23P
T: 50S ribosomal protein L24P
U: 50S ribosomal protein L24E
V: 50S ribosomal protein L29P
W: 50S ribosomal protein L30P
X: 50S ribosomal protein L31e
Y: 50S ribosomal protein L32E
Z: 50S ribosomal protein L37Ae
1: 50S ribosomal protein L37e
2: 50S ribosomal protein L39e
3: 50S ribosomal protein L44E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,489,813337
Polymers1,474,19631
Non-polymers15,617306
Water139,8507763
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)212.081, 298.910, 574.815
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 Ribosomal RNA


Mass: 946141.375 Da / Num. of mol.: 1 / Mutation: G2099A / Source method: isolated from a natural source / Details: encoded by rrnA operon / Source: (natural) Haloarcula marismortui (Halophile) / Strain: DT41 / References: GenBank: 55229667
#2: RNA chain 5S Ribosomal RNA


Mass: 39303.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / Strain: DT41 / References: GenBank: 3377778

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50S RIBOSOMAL PROTEIN ... , 28 types, 28 molecules ABCDEFHIJKLMNOPQRSTUVWXYZ123

#3: Protein 50S ribosomal protein L2P


Mass: 25354.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / Strain: DT41 / References: UniProt: P20276
#4: Protein 50S ribosomal protein L3P


Mass: 37396.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / Strain: DT41 / References: GenBank: 55378384, UniProt: P20279*PLUS
#5: Protein 50S ribosomal protein L4E


Mass: 26442.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / Strain: DT41 / References: UniProt: P12735
#6: Protein 50S ribosomal protein L5P


Mass: 19551.693 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / Strain: DT41 / References: UniProt: P14124
#7: Protein 50S ribosomal protein L6P


Mass: 19961.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / Strain: DT41 / References: UniProt: P14135
#8: Protein 50S ribosomal protein L7AE


Mass: 12791.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / Strain: DT41 / References: UniProt: P12743
#10: Protein 50S RIBOSOMAL PROTEIN L10E


Mass: 19942.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / Strain: DT41 / References: GenBank: 55231756, UniProt: P60617*PLUS
#11: Protein 50S RIBOSOMAL PROTEIN L11P


Mass: 17097.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / Strain: DT41 / References: GenBank: 132647, UniProt: P14122*PLUS
#12: Protein 50S ribosomal protein L13P


Mass: 16249.214 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / Strain: DT41 / References: UniProt: P29198
#13: Protein 50S ribosomal protein L14P


Mass: 14191.243 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / Strain: DT41 / References: UniProt: P22450
#14: Protein 50S ribosomal protein L15P


Mass: 18005.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / Strain: DT41 / References: UniProt: P12737
#15: Protein 50S Ribosomal Protein L15E


Mass: 22143.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / Strain: DT41 / References: GenBank: 55231501, UniProt: P60618*PLUS
#16: Protein 50S ribosomal protein L18P


Mass: 20640.939 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / Strain: DT41 / References: UniProt: P14123
#17: Protein 50S ribosomal protein L18e


Mass: 12438.915 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / Strain: DT41 / References: UniProt: P12733
#18: Protein 50S ribosomal protein L19E


Mass: 16796.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / Strain: DT41 / References: UniProt: P14119
#19: Protein 50S ribosomal protein L21e


Mass: 10567.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / Strain: DT41 / References: UniProt: P12734
#20: Protein 50S ribosomal protein L22P


Mass: 16966.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / Strain: DT41 / References: UniProt: P10970
#21: Protein 50S ribosomal protein L23P


Mass: 9612.537 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / Strain: DT41 / References: UniProt: P12732
#22: Protein 50S ribosomal protein L24P


Mass: 13670.955 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / Strain: DT41 / References: UniProt: P10972
#23: Protein 50S ribosomal protein L24E


Mass: 7233.720 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / Strain: DT41 / References: UniProt: P14116
#24: Protein 50S ribosomal protein L29P


Mass: 7889.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / Strain: DT41 / References: UniProt: P10971
#25: Protein 50S ribosomal protein L30P


Mass: 17062.885 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / Strain: DT41 / References: UniProt: P14121
#26: Protein 50S ribosomal protein L31e


Mass: 10384.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / Strain: DT41 / References: UniProt: P18138
#27: Protein 50S ribosomal protein L32E


Mass: 26455.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / Strain: DT41 / References: UniProt: P12736
#28: Protein 50S ribosomal protein L37Ae


Mass: 9409.338 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / Strain: DT41 / References: GenBank: 55231162, UniProt: P60619*PLUS
#29: Protein 50S ribosomal protein L37e


Mass: 6330.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / Strain: DT41 / References: UniProt: P32410
#30: Protein/peptide 50S ribosomal protein L39e


Mass: 6133.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / Strain: DT41 / References: UniProt: P22452
#31: Protein 50S ribosomal protein L44E


Mass: 10815.245 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / Strain: DT41 / References: UniProt: P32411

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Protein , 1 types, 1 molecules G

#9: Protein ACIDIC RIBOSOMAL PROTEIN P0 HOMOLOG


Mass: 37213.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / Strain: DT41 / References: UniProt: P15825

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Non-polymers , 8 types, 8069 molecules

#32: Chemical ChemComp-ZIT / AZITHROMYCIN


Mass: 748.984 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C38H72N2O12 / Comment: medication, antibiotic*YM
#33: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 93 / Source method: obtained synthetically / Formula: Mg
#34: Chemical ChemComp-K / POTASSIUM ION


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


Mass: 22.990 Da / Num. of mol.: 75 / Source method: obtained synthetically / Formula: Na
#36: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: Cl
#37: Chemical...
ChemComp-SR / STRONTIUM ION


Mass: 87.620 Da / Num. of mol.: 108 / Source method: obtained synthetically / Formula: Sr
#38: Chemical
ChemComp-CD / CADMIUM ION


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


Mass: 18.015 Da / Num. of mol.: 7763 / Source method: isolated from a natural source / Formula: H2O

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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: 3.1 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: PEG 6000, KCl, NH4Cl, MgCl2, Kacetate, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 600011
2KCl11
3NH4Cl11
4MgCl211
5Kacetate11
6H2O11
7PEG 600012
8KCl12
9NH4Cl12
10MgCl212
11Kacetate12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 9, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 672764 / Redundancy: 4.8 % / Biso Wilson estimate: 41.9 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 22.6
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 1.8 / Num. unique all: 50400 / % possible all: 72.1

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Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→29.96 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 359492.31 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.229 6149 1 %RANDOM
Rwork0.19 ---
obs0.19 633741 90.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.2122 Å2 / ksol: 0.336224 e/Å3
Displacement parametersBiso mean: 47.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20 Å2
2--3.74 Å20 Å2
3----3.59 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.4→29.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29377 61619 357 7763 99116
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d15.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.35
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.221.5
X-RAY DIFFRACTIONc_mcangle_it2.082
X-RAY DIFFRACTIONc_scbond_it1.642
X-RAY DIFFRACTIONc_scangle_it2.392.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.383 687 0.9 %
Rwork0.341 73885 -
obs--64 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2RNA_RIBO_MODNTS.PARAMRNA_RIBO_MODNTS_DRUGS.T
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION5QUC.PAQUC.TO

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  • 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

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