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- PDB-3cce: Structure of Anisomycin resistant 50S Ribosomal Subunit: 23S rRNA... -

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Basic information

Entry
Database: PDB / ID: 3cce
TitleStructure of Anisomycin resistant 50S Ribosomal Subunit: 23S rRNA mutation U2535A
Components
  • (50S ribosomal protein ...) x 29
  • 23S RIBOSOMAL RNA
  • 5S RIBOSOMAL RNA
KeywordsRIBOSOME / 23S rRNA mutation U2535A
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 / structural constituent of ribosome / 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 / 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 L19e, domain 2 / Ribosomal protein L19e, domain 3 / 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 L11/L12, C-terminal domain / 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 L3, archaeal / Ribosomal protein L4, archaea / Ribosomal protein L5, archaeal / Ribosomal protein L32e, 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 L30/S12 / Ribosomal Protein L22; Chain A / Ribosomal protein L7Ae, archaea / Outer Surface Protein A; domain 3 / Aldehyde Oxidoreductase; domain 3 / DNA repair Rad51/transcription factor NusA, alpha-helical / : / N-terminal domain of TfIIb / Translation factors / Helix-hairpin-helix domain / 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 / : / Ribosomal protein L2, archaeal-type / 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 / 60s Ribosomal Protein L30; Chain: A; / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L10e / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L44e signature. / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / : / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / Single Sheet / Ribosomal protein L39e, conserved site
Similarity search - Domain/homology
: / : / STRONTIUM ION / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL29 ...: / : / STRONTIUM ION / : / 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 / Resolution: 2.75 Å
AuthorsBlaha, G. / Gurel, G.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Mutations outside the anisomycin-binding site can make ribosomes drug-resistant.
Authors: Blaha, G. / Gurel, G. / Schroeder, S.J. / Moore, P.B. / Steitz, T.A.
History
DepositionFeb 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2May 27, 2015Group: Source and taxonomy
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 50S ribosomal protein L2P
B: 50S ribosomal protein L3P
C: 50S ribosomal protein L4P
D: 50S ribosomal protein L5P
E: 50S ribosomal protein L6P
F: 50S ribosomal protein L7Ae
G: 50S ribosomal protein L10E
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
0: 23S RIBOSOMAL RNA
9: 5S RIBOSOMAL RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,493,272336
Polymers1,478,40431
Non-polymers14,868305
Water140,9317823
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)212.832, 299.896, 576.013
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221

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Components

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50S ribosomal protein ... , 29 types, 29 molecules ABCDEFGHIJKLMNOPQRSTUVWXYZ123

#1: Protein 50S ribosomal protein L2P / Hmal2 / Hl4


Mass: 25354.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P20276
#2: Protein 50S ribosomal protein L3P / Hmal3 / Hl1


Mass: 37396.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P20279
#3: Protein 50S ribosomal protein L4P / Hmal4 / Hl6


Mass: 26457.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P12735
#4: Protein 50S ribosomal protein L5P / Hmal5 / Hl13


Mass: 19551.693 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P14124
#5: Protein 50S ribosomal protein L6P / Hmal6 / Hl10


Mass: 19961.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P14135
#6: Protein 50S ribosomal protein L7Ae / Hs6


Mass: 12791.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P12743
#7: Protein 50S ribosomal protein L10E / Ribosomal protein L10 / Acidic ribosomal protein P0 homolog / L10E / HMal10


Mass: 37169.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P15825
#8: 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) / References: UniProt: P60617
#9: Protein 50S ribosomal protein L11P / Hmal11


Mass: 17097.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P14122
#10: Protein 50S ribosomal protein L13P / Hmal13


Mass: 16249.214 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P29198
#11: Protein 50S ribosomal protein L14P / Hmal14 / Hl27


Mass: 14216.233 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P22450
#12: Protein 50S ribosomal protein L15P / Hmal15 / Hl9


Mass: 18005.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P12737
#13: Protein 50S ribosomal protein L15e / 50S ribosomal protein LC12


Mass: 22404.301 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P60618
#14: Protein 50S ribosomal protein L18P / Hmal18 / Hl12


Mass: 20640.939 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P14123
#15: Protein 50S ribosomal protein L18e / Hl29 / L19


Mass: 12438.915 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P12733
#16: Protein 50S ribosomal protein L19e / Hmal19 / Hl24


Mass: 16796.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P14119
#17: Protein 50S ribosomal protein L21e / Hl31


Mass: 10567.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P12734
#18: Protein 50S ribosomal protein L22P / Hmal22 / Hl23


Mass: 16966.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P10970
#19: Protein 50S ribosomal protein L23P / Hmal23 / Hl25 / L21


Mass: 9612.537 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P12732
#20: Protein 50S ribosomal protein L24P / Hmal24 / Hl16 / Hl15


Mass: 13670.955 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P10972
#21: Protein 50S ribosomal protein L24e / Hl21/Hl22


Mass: 7364.915 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P14116
#22: Protein 50S ribosomal protein L29P / Hmal29 / Hl33


Mass: 7889.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P10971
#23: Protein 50S ribosomal protein L30P / Hmal30 / Hl20 / Hl16


Mass: 17062.885 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P14121
#24: Protein 50S ribosomal protein L31e / L34 / Hl30


Mass: 10384.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P18138
#25: Protein 50S ribosomal protein L32e / Hl5


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


Mass: 12900.325 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P60619*PLUS
#27: Protein 50S ribosomal protein L37e / L35e


Mass: 6330.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P32410
#28: Protein/peptide 50S ribosomal protein L39e / Hl39e / Hl46e


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


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

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RNA chain , 2 types, 2 molecules 09

#30: RNA chain 23S RIBOSOMAL RNA


Mass: 946470.562 Da / Num. of mol.: 1 / Mutation: G2099A, U2535A / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile)
#31: 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) / References: GenBank: 6468293

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Non-polymers , 7 types, 8128 molecules

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


Mass: 24.305 Da / Num. of mol.: 93 / Source method: obtained synthetically / Formula: Mg
#33: Chemical...
ChemComp-CL / CHLORIDE ION


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


Mass: 87.620 Da / Num. of mol.: 108 / Source method: obtained synthetically / Formula: Sr
#35: Chemical...
ChemComp-NA / SODIUM ION


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


Mass: 112.411 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cd
#37: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#38: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7823 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE SEQUENCE OF CHAIN 0 MATCHES TO GB ENTRY AY596297 BETWEEN 2634210 AND 2637132, WITH G2099A AND ...THE SEQUENCE OF CHAIN 0 MATCHES TO GB ENTRY AY596297 BETWEEN 2634210 AND 2637132, WITH G2099A AND U2535A MUTATIONS. THE SEQUENCE OF CHAIN Z MATCHES TO REFSEQ ENTRY YP_136287.

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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: 3.11 Å3/Da / Density % sol: 60.43 %
Crystal growTemperature: 292 K / Method: sitting drop / pH: 5.8
Details: PEG6000, KCL, NH4CL, MGCl2, pH 5.80, sitting drop, temperature 292K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG600011
2KCL11
3NH4CL11
4MGCl211
5PEG600012
6KCL12
7NH4CL12
8MGCl212

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1 Å
DetectorType: ADSC / Detector: CCD / Date: Sep 18, 2005
Details: 54-pole harmonic emission undulator, a vertically focusing mirror and a horizontally focusing monochromator
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 462394 / % possible obs: 99.1 % / Redundancy: 4.8 % / Biso Wilson estimate: 55.1 Å2 / Rmerge(I) obs: 0.107
Reflection shellResolution: 2.75→2.96 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.747 / Mean I/σ(I) obs: 1.74 / % possible all: 90.3

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Processing

Software
NameVersionClassificationNB
CNS1refinement
PDB_EXTRACT3.004data extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementResolution: 2.75→49.33 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 173653.03 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.232 3745 1 %RANDOM
Rwork0.183 ---
obs0.183 379835 81.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.47 Å2 / ksol: 0.308367 e/Å3
Displacement parametersBiso mean: 53.5 Å2
Baniso -1Baniso -2Baniso -3
1-1.41 Å20 Å20 Å2
2--4.01 Å20 Å2
3----5.43 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.51 Å
Refinement stepCycle: LAST / Resolution: 2.75→49.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29375 61621 305 7823 99124
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_d16
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.31
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.161.5
X-RAY DIFFRACTIONc_mcangle_it2.032
X-RAY DIFFRACTIONc_scbond_it1.422
X-RAY DIFFRACTIONc_scangle_it2.22.5
LS refinement shellResolution: 2.75→2.92 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.371 589 1.1 %
Rwork0.326 54500 -
obs--71.2 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein.param
X-RAY DIFFRACTION2dna-rna-joe-martin_comb_mnt.par
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4water.param

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

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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

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