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- PDB-5jvh: The crystal structure large ribosomal subunit (50S) of Deinococcu... -

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Basic information

Entry
Database: PDB / ID: 5jvh
TitleThe crystal structure large ribosomal subunit (50S) of Deinococcus radiodurans in complex with evernimicin
Components
  • (50S ribosomal protein ...) x 26
  • 23S ribosomal RNA
  • 5S ribosomal RNA
KeywordsRIBOSOME / Antibiotics
Function / homology
Function and homology information


large ribosomal subunit / transferase activity / 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 ...large ribosomal subunit / transferase activity / 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 / mRNA binding / RNA binding / zinc 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 L25; Chain P / 50s Ribosomal Protein L5; Chain: A, / Ribosomal protein L5 ...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 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 L14 / Ribosomal protein L14/L23 / Ribosomal protein L6 / Ribosomal protein L22/L17 / Ribosomal Protein L30; Chain: A, / Ribosomal Protein L22; Chain A / Outer Surface Protein A; domain 3 / Factor Xa Inhibitor / Aldehyde Oxidoreductase; domain 3 / Rubrerythrin, domain 2 / RNA Polymerase Alpha Subunit; Chain A, domain 2 / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / : / RRM (RNA recognition motif) domain / Single Sheet / Ribosomal protein L16 signature 1. / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / : / Beta Complex / Ribosomal protein L17 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L32p, bacterial type / Ribosomal protein L28/L24 superfamily / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / : / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L28 / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L18, bacterial-type / : / Ribosomal protein L6, bacterial-type / Ribosomal protein L5, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L20 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 / Ribosomal L28 family / Ribosomal protein L33 superfamily / Ribosomal protein L16 / Ribosomal protein L28/L24 / Ribosomal protein L30, bacterial-type / L28p-like / : / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L20 / Ribosomal L32p protein family / Ribosomal protein L19 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L21 / Ribosomal protein L32p / Large ribosomal subunit protein uL24, C-terminal domain / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L24 / Few Secondary Structures
Similarity search - Domain/homology
Evernimicin / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL34 ...Evernimicin / : / : / 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 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 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.58 Å
AuthorsYonath, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Avilamycin and evernimicin induce structural changes in rProteins uL16 and CTC that enhance the inhibition of A-site tRNA binding.
Authors: Krupkin, M. / Wekselman, I. / Matzov, D. / Eyal, Z. / Diskin Posner, Y. / Rozenberg, H. / Zimmerman, E. / Bashan, A. / Yonath, A.
History
DepositionMay 11, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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 / struct_conn
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.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
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: 23S ribosomal 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
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,349,717152
Polymers1,345,09628
Non-polymers4,621124
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area145570 Å2
ΔGint-1285 kcal/mol
Surface area451650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.475, 407.380, 692.552
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

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RNA chain , 2 types, 2 molecules XY

#1: RNA chain 23S ribosomal RNA


Mass: 933405.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Deinococcus radiodurans R1 (radioresistant)
References: GenBank: 1026245073
#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: 11612676

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50S ribosomal protein ... , 26 types, 26 molecules ABCDEGHIJKLMNOPQRSTUVWZ123

#3: Protein 50S ribosomal protein L2


Mass: 30107.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Deinococcus radiodurans R1 (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 / Details: deinococcus
Source: (natural) Deinococcus radiodurans R1 (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 R1 (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 R1 (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 R1 (radioresistant)
References: UniProt: Q9RSL3
#8: Protein 50S ribosomal protein L13


Mass: 19223.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Deinococcus radiodurans R1 (radioresistant)
References: UniProt: Q9RXY1
#9: Protein 50S ribosomal protein L14


Mass: 14256.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Deinococcus radiodurans R1 (radioresistant)
References: UniProt: Q9RXJ2
#10: Protein 50S ribosomal protein L15


Mass: 16894.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Deinococcus radiodurans R1 (radioresistant)
References: UniProt: Q9RSK9
#11: Protein 50S ribosomal protein L16


Mass: 16125.997 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Deinococcus radiodurans R1 (radioresistant)
References: UniProt: Q9RXJ5
#12: Protein 50S ribosomal protein L17


Mass: 12926.067 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Deinococcus radiodurans R1 (radioresistant)
References: UniProt: Q9RSJ5
#13: Protein 50S ribosomal protein L18


Mass: 12163.936 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Deinococcus radiodurans R1 (radioresistant)
References: UniProt: Q9RSL2
#14: Protein 50S ribosomal protein L19


Mass: 18347.818 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Deinococcus radiodurans R1 (radioresistant)
References: UniProt: Q9RWB4
#15: Protein 50S ribosomal protein L20


Mass: 13991.274 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Deinococcus radiodurans R1 (radioresistant)
References: UniProt: Q9RSW7
#16: Protein 50S ribosomal protein L21


Mass: 11165.743 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Deinococcus radiodurans R1 (radioresistant)
References: UniProt: Q9RY64
#17: Protein 50S ribosomal protein L22


Mass: 15190.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Deinococcus radiodurans R1 (radioresistant)
References: UniProt: Q9RXJ7
#18: Protein 50S ribosomal protein L23


Mass: 10539.210 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Deinococcus radiodurans R1 (radioresistant)
References: UniProt: Q9RXK0
#19: Protein 50S ribosomal protein L24


Mass: 12384.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Deinococcus radiodurans R1 (radioresistant)
References: UniProt: Q9RXJ1
#20: 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 R1 (radioresistant)
References: UniProt: Q9RX88
#21: Protein 50S ribosomal protein L27


Mass: 9609.091 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Deinococcus radiodurans R1 (radioresistant)
References: UniProt: Q9RY65
#22: Protein 50S ribosomal protein L28


Mass: 8982.592 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Deinococcus radiodurans R1 (radioresistant)
References: UniProt: Q9RRG8
#23: Protein 50S ribosomal protein L29


Mass: 7774.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Deinococcus radiodurans R1 (radioresistant)
References: UniProt: Q9RXJ4
#24: Protein 50S ribosomal protein L30


Mass: 6079.235 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Deinococcus radiodurans R1 (radioresistant)
References: UniProt: Q9RSL0
#25: Protein 50S ribosomal protein L32


Mass: 6810.017 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Deinococcus radiodurans R1 (radioresistant)
References: UniProt: P49228
#26: Protein 50S ribosomal protein L33


Mass: 6243.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Deinococcus radiodurans R1 (radioresistant)
References: UniProt: Q9RSS4
#27: 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 R1 (radioresistant)
References: UniProt: Q9RSH2
#28: Protein 50S ribosomal protein L35


Mass: 7448.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Deinococcus radiodurans R1 (radioresistant)
References: UniProt: Q9RSW6

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Non-polymers , 2 types, 124 molecules

#29: Chemical ChemComp-6O1 / Evernimicin


Mass: 1631.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C70H97Cl2NO38
#30: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 123 / Source method: obtained synthetically / Formula: Mg

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Details

Has protein modificationY

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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: 4.82 Å3/Da / Density % sol: 74.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: Magnesium chloride, HEPES, ammonium chloride, ethanol, 2-ethyl-1,3-hexandiol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.033 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 12, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3.58→30 Å / Num. obs: 264969 / % possible obs: 94.4 % / Redundancy: 3.7 % / Biso Wilson estimate: 112.24 Å2 / Rmerge(I) obs: 0.121 / Χ2: 1.256 / Net I/av σ(I): 9.752 / Net I/σ(I): 7.4 / Num. measured all: 982811
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3.58-3.643.40.84130171.17293.5
3.64-3.713.40.697130831.19293.9
3.71-3.783.40.633132001.22694.7
3.78-3.863.40.521132121.24294.9
3.86-3.943.40.452132501.30295.1
3.94-4.033.50.399132751.3295.1
4.03-4.133.50.356132731.27995.2
4.13-4.243.60.297133361.32295.3
4.24-4.373.60.264133141.32895.4
4.37-4.513.70.229132961.33995.4
4.51-4.673.80.191133661.35795.5
4.67-4.853.80.167133941.29995.3
4.85-5.073.90.143133121.35395.4
5.07-5.3440.124133841.28195.2
5.34-5.6740.111133751.36595.1
5.67-6.1140.103133511.16795
6.11-6.7240.097133271.28394.4
6.72-7.6740.081132541.08593.6
7.67-9.623.90.06130931.00791.9
9.62-304.10.037128571.21388.1

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PDB_EXTRACT3.2data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZJR

2zjr


Resolution: 3.58→29.845 Å / FOM work R set: 0.8126 / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2471 13326 5.06 %
Rwork0.2037 250181 -
obs0.2059 263507 94.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 340.53 Å2 / Biso mean: 96.69 Å2 / Biso min: 29.4 Å2
Refinement stepCycle: final / Resolution: 3.58→29.845 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23837 59613 234 0 83684
Biso mean--81.22 --
Num. residues----5856
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00891066
X-RAY DIFFRACTIONf_angle_d1.299136767
X-RAY DIFFRACTIONf_chiral_restr0.06917520
X-RAY DIFFRACTIONf_plane_restr0.0077005
X-RAY DIFFRACTIONf_dihedral_angle_d17.41542770
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.58-3.62060.33834300.31618200863093
3.6206-3.66310.34984650.29888192865793
3.6631-3.70770.3324150.29038256867194
3.7077-3.75460.31954700.28188281875195
3.7546-3.80390.32544300.26418342877295
3.8039-3.85590.29984350.25138335877095
3.8559-3.91090.27834430.24728342878595
3.9109-3.96910.26934540.23918321877595
3.9691-4.0310.2764510.22858408885995
4.031-4.09690.27494260.23328356878295
4.0969-4.16740.28114240.22268376880095
4.1674-4.24290.24944780.20498387886595
4.2429-4.32430.23914670.19788366883395
4.3243-4.41230.21574290.19228394882395
4.4123-4.50790.23444580.19038390884895
4.5079-4.61240.22834500.18558435888595
4.6124-4.72730.23754190.18388420883995
4.7273-4.85460.23094840.18178400888495
4.8546-4.99680.20954900.17348350884095
4.9968-5.15730.22624740.1678374884895
5.1573-5.34070.21864100.17348466887695
5.3407-5.55320.2284430.17268416885995
5.5532-5.80420.21824390.17448439887895
5.8042-6.10770.23814440.17828408885295
6.1077-6.48670.24064300.1838434886495
6.4867-6.98160.26384560.18928363881994
6.9816-7.67340.2414640.1848334879893
7.6734-8.75910.22424310.19028260869192
8.7591-10.94430.22833900.19218228861891
10.9443-29.84580.23864270.22367908833585
Refinement TLS params.Method: refined / Origin x: 212.6279 Å / Origin y: 534.8714 Å / Origin z: 109.1717 Å
111213212223313233
T0.0936 Å2-0.1789 Å2-0.1213 Å2-1.0206 Å20.1556 Å2--0.2506 Å2
L0.4621 °20.0113 °2-0.0265 °2-0.2585 °2-0.1305 °2--0.8283 °2
S-0.0047 Å °0.2711 Å °0.0917 Å °-0.297 Å °0.0393 Å °0.0603 Å °-0.1386 Å °0.1315 Å °0.0204 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allX1 - 2877
2X-RAY DIFFRACTION1allY3 - 122
3X-RAY DIFFRACTION1allA14 - 272
4X-RAY DIFFRACTION1allB1 - 205
5X-RAY DIFFRACTION1allC2 - 195
6X-RAY DIFFRACTION1allD3 - 179
7X-RAY DIFFRACTION1allE5 - 175
8X-RAY DIFFRACTION1allG30 - 171
9X-RAY DIFFRACTION1allH1 - 134
10X-RAY DIFFRACTION1allI11 - 144
11X-RAY DIFFRACTION1allJ6 - 141
12X-RAY DIFFRACTION1allK3 - 115
13X-RAY DIFFRACTION1allL8 - 111
14X-RAY DIFFRACTION1allM2 - 109
15X-RAY DIFFRACTION1allN2 - 118
16X-RAY DIFFRACTION1allO5 - 98
17X-RAY DIFFRACTION1allP8 - 134
18X-RAY DIFFRACTION1allQ2 - 94
19X-RAY DIFFRACTION1allR4 - 113
20X-RAY DIFFRACTION1allS1 - 179
21X-RAY DIFFRACTION1allT12 - 85
22X-RAY DIFFRACTION1allU8 - 79
23X-RAY DIFFRACTION1allV2 - 66
24X-RAY DIFFRACTION1allW1 - 55
25X-RAY DIFFRACTION1allZ3 - 59
26X-RAY DIFFRACTION1all12 - 54
27X-RAY DIFFRACTION1all21 - 46
28X-RAY DIFFRACTION1all36 - 64
29X-RAY DIFFRACTION1all81
30X-RAY DIFFRACTION1all51 - 123

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  • 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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