[English] 日本語
Yorodumi
- PDB-1zev: Crystal Structure of a Pathogenic RNA: CUG Repeats -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1zev
TitleCrystal Structure of a Pathogenic RNA: CUG Repeats
Components5'-R(*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*G)-3'
KeywordsRNA / UU mismatches / triplet repeats / causitive agent of myotonic dystrophy type I
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.58 Å
AuthorsMooers, B.H. / Logue, J.S. / Berglund, J.A.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: The structural basis of myotonic dystrophy from the crystal structure of CUG repeats.
Authors: Mooers, B.H. / Logue, J.S. / Berglund, J.A.
History
DepositionApr 19, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 7 TLS DETAILS NUMBER OF TLS GROUPS : 18 TLS GROUP : 19 NUMBER OF COMPONENTS GROUP : 2 COMPONENTS C ... TLS DETAILS NUMBER OF TLS GROUPS : 18 TLS GROUP : 19 NUMBER OF COMPONENTS GROUP : 2 COMPONENTS C SSSEQI TO C SSSEQI RESIDUE RANGE : A 1 A 1 RESIDUE RANGE : B 18 B 18 ORIGIN FOR THE GROUP (A): -8.8200 7.1830 18.5870 T TENSOR T11: -0.0519 T22: -0.0267 T33: 0.0385 T12: 0.0394 T13: -0.0319 T23: 0.0779 L TENSOR L11: 14.1366 L22: 11.7182 L33: 4.2157 L12: -1.4888 L13: -6.4616 L23: 1.1182 S TENSOR S11: -0.4483 S12: -1.2562 S13: -0.2132 S21: -0.5346 S22: 0.7290 S23: 0.6125 S31: -0.0260 S32: 0.5428 S33: -0.2808 TLS GROUP : 20 NUMBER OF COMPONENTS GROUP : 2 COMPONENTS C SSSEQI TO C SSSEQI RESIDUE RANGE : A 2 A 2 RESIDUE RANGE : B 17 B 17 ORIGIN FOR THE GROUP (A): -9.8510 10.0160 16.1620 T TENSOR T11: 0.0618 T22: 0.0150 T33: 0.0336 T12: 0.0005 T13: -0.0092 T23: 0.1532 L TENSOR L11: 15.9283 L22: 27.8775 L33: 9.9726 L12: -11.0879 L13: -9.0205 L23: 14.3390 S TENSOR S11: 0.3958 S12: -0.4326 S13: -0.3760 S21: -0.6098 S22: 0.1489 S23: 0.6202 S31: -0.1389 S32: -0.2975 S33: -0.5447 TLS GROUP : 21 NUMBER OF COMPONENTS GROUP : 2 COMPONENTS C SSSEQI TO C SSSEQI RESIDUE RANGE : A 3 A 3 RESIDUE RANGE : B 16 B 16 ORIGIN FOR THE GROUP (A): -10.1910 12.9460 13.7150 T TENSOR T11: -0.0179 T22: -0.0258 T33: 0.0665 T12: -0.0341 T13: 0.0043 T23: 0.0581 L TENSOR L11: 8.0179 L22: 4.2885 L33: 13.7466 L12: 1.9119 L13: 2.0030 L23: 2.7726 S TENSOR S11: 0.2204 S12: -0.1382 S13: -0.3021 S21: 0.0477 S22: -0.0126 S23: 0.4627 S31: 0.9454 S32: -0.3193 S33: -0.2078 TLS GROUP : 22 NUMBER OF COMPONENTS GROUP : 2 COMPONENTS C SSSEQI TO C SSSEQI RESIDUE RANGE : A 4 A 4 RESIDUE RANGE : B 15 B 15 ORIGIN FOR THE GROUP (A): -8.6980 15.8100 11.4540 T TENSOR T11: -0.1034 T22: -0.1096 T33: 0.0163 T12: -0.0867 T13: -0.0150 T23: 0.0586 L TENSOR L11: 14.2712 L22: 9.1272 L33: 13.0762 L12: 8.1245 L13: 8.3756 L23: 4.4191 S TENSOR S11: -0.0699 S12: 0.2076 S13: -0.4628 S21: -0.0698 S22: 0.3285 S23: 0.1541 S31: 0.6432 S32: 0.0607 S33: -0.2587 TLS GROUP : 23 NUMBER OF COMPONENTS GROUP : 2 COMPONENTS C SSSEQI TO C SSSEQI RESIDUE RANGE : A 5 A 5 RESIDUE RANGE : B 14 B 14 ORIGIN FOR THE GROUP (A): -5.9030 17.0960 8.8580 T TENSOR T11: -0.1003 T22: -0.0312 T33: 0.0165 T12: -0.0099 T13: -0.0097 T23: 0.0419 L TENSOR L11: 10.4040 L22: 0.4045 L33: 2.0592 L12: -0.6052 L13: 2.1545 L23: -0.8971 S TENSOR S11: 0.0810 S12: 0.1737 S13: -0.0476 S21: 0.0359 S22: 0.1777 S23: 0.1903 S31: 0.2348 S32: 0.0430 S33: -0.2587 TLS GROUP : 24 NUMBER OF COMPONENTS GROUP : 2 COMPONENTS C SSSEQI TO C SSSEQI RESIDUE RANGE : A 6 A 6 RESIDUE RANGE : B 13 B 13 ORIGIN FOR THE GROUP (A): -3.2100 16.9620 5.8750 T TENSOR T11: -0.1161 T22: -0.0992 T33: -0.0105 T12: -0.0165 T13: -0.0078 T23: -0.0219 L TENSOR L11: 2.4593 L22: 5.5141 L33: 3.9213 L12: -3.0189 L13: -1.5248 L23: -0.4479 S TENSOR S11: -0.0587 S12: -0.0207 S13: -0.1416 S21: 0.2278 S22: 0.1527 S23: 0.0541 S31: 0.0852 S32: -0.1081 S33: -0.0940 TLS GROUP : 25 NUMBER OF COMPONENTS GROUP : 2 COMPONENTS C SSSEQI TO C SSSEQI RESIDUE RANGE : A 7 A 7 RESIDUE RANGE : B 12 B 12 ORIGIN FOR THE GROUP (A): -1.5120 14.7440 3.2050 T TENSOR T11: -0.0158 T22: -0.0849 T33: -0.0189 T12: -0.0105 T13: -0.0475 T23: -0.0454 L TENSOR L11: 7.8751 L22: 6.5666 L33: 3.6804 L12: -6.7783 L13: 2.4894 L23: -3.5984 S TENSOR S11: 0.0417 S12: -0.0303 S13: -0.1646 S21: -0.0313 S22: 0.2035 S23: 0.1687 S31: 0.0968 S32: 0.0260 S33: -0.2452 TLS GROUP : 26 NUMBER OF COMPONENTS GROUP : 2 COMPONENTS C SSSEQI TO C SSSEQI RESIDUE RANGE : A 8 A 8 RESIDUE RANGE : B 11 B 11 ORIGIN FOR THE GROUP (A): -1.4640 11.9480 0.4300 T TENSOR T11: 0.0450 T22: -0.0649 T33: 0.0035 T12: -0.0415 T13: -0.0712 T23: -0.0422 L TENSOR L11: 4.4328 L22: 13.0940 L33: 12.9403 L12: -2.5463 L13: 0.6691 L23: -12.6048 S TENSOR S11: 0.3532 S12: -0.0516 S13: -0.2391 S21: -0.4567 S22: -0.0446 S23: 0.2498 S31: 1.0755 S32: 0.2924 S33: -0.3085 TLS GROUP : 27 NUMBER OF COMPONENTS GROUP : 2 COMPONENTS C SSSEQI TO C SSSEQI RESIDUE RANGE : A 9 A 9 RESIDUE RANGE : B 10 B 10 ORIGIN FOR THE GROUP (A): -3.4650 9.2410 -1.7830 T TENSOR T11: 0.0051 T22: -0.0719 T33: 0.0921 T12: -0.0603 T13: -0.0885 T23: -0.0627 L TENSOR L11: 6.9740 L22: 14.3431 L33: 1.2275 L12: -2.9973 L13: 2.5501 L23: -3.0588 S TENSOR S11: 0.3202 S12: 0.1617 S13: -0.6944 S21: 0.4586 S22: 0.3253 S23: -0.0135 S31: 0.2834 S32: 0.3436 S33: -0.6455 TLS GROUP : 28 NUMBER OF COMPONENTS GROUP : 2 COMPONENTS C SSSEQI TO C SSSEQI RESIDUE RANGE : A 10 A 10 RESIDUE RANGE : B 9 B 9 ORIGIN FOR THE GROUP (A): -6.1240 7.6550 -4.1420 T TENSOR T11: -0.0803 T22: 0.0836 T33: 0.0494 T12: -0.0595 T13: -0.1002 T23: 0.0253 L TENSOR L11: 7.1459 L22: 9.2674 L33: 0.9937 L12: 0.0008 L13: 1.4810 L23: 2.5229 S TENSOR S11: 0.3680 S12: -0.1839 S13: -0.6079 S21: 0.3513 S22: -0.2671 S23: -0.3854 S31: -0.3182 S32: 0.5033 S33: -0.1009 TLS GROUP : 29 NUMBER OF COMPONENTS GROUP : 2 COMPONENTS C SSSEQI TO C SSSEQI RESIDUE RANGE : A 11 A 11 RESIDUE RANGE : B 8 B 8 ORIGIN FOR THE GROUP (A): -9.2880 7.5890 -6.5580 T TENSOR T11: -0.1326 T22: 0.0042 T33: 0.0594 T12: 0.0242 T13: -0.0717 T23: -0.0629 L TENSOR L11: 7.4564 L22: 11.8118 L33: 3.0967 L12: -3.3750 L13: -0.6497 L23: -2.0931 S TENSOR S11: 0.7084 S12: 0.5031 S13: 0.1893 S21: -0.1568 S22: -0.4749 S23: -0.9273 S31: -0.2426 S32: 0.6932 S33: -0.2335 TLS GROUP : 30 NUMBER OF COMPONENTS GROUP : 2 COMPONENTS C SSSEQI TO C SSSEQI RESIDUE RANGE : A 12 A 12 RESIDUE RANGE : B 7 B 7 ORIGIN FOR THE GROUP (A): -11.9940 8.9350 -8.9040 T TENSOR T11: -0.1174 T22: -0.0779 T33: 0.0132 T12: 0.0421 T13: -0.0327 T23: -0.0281 L TENSOR L11: 1.4856 L22: 12.4331 L33: 0.6545 L12: 0.0722 L13: -0.4493 L23: 0.5355 S TENSOR S11: -0.0167 S12: -0.1062 S13: -0.0815 S21: 0.4470 S22: 0.3990 S23: 0.1298 S31: -0.0564 S32: 0.1336 S33: -0.3823 TLS GROUP : 31 NUMBER OF COMPONENTS GROUP : 2 COMPONENTS C SSSEQI TO C SSSEQI RESIDUE RANGE : A 13 A 13 RESIDUE RANGE : B 6 B 6 ORIGIN FOR THE GROUP (A): -13.1080 11.3590 -12.0290 T TENSOR T11: -0.1811 T22: -0.1171 T33: -0.0058 T12: -0.0654 T13: 0.0121 T23: -0.0111 L TENSOR L11: 5.8744 L22: 5.7272 L33: 3.3770 L12: -0.7151 L13: 1.4720 L23: 2.8566 S TENSOR S11: 0.2693 S12: -0.0225 S13: -0.0459 S21: 0.5660 S22: -0.0530 S23: 0.0215 S31: 0.2608 S32: -0.2357 S33: -0.2163 TLS GROUP : 32 NUMBER OF COMPONENTS GROUP : 2 COMPONENTS C SSSEQI TO C SSSEQI RESIDUE RANGE : A 14 A 14 RESIDUE RANGE : B 5 B 5 ORIGIN FOR THE GROUP (A): -11.6110 13.7960 -14.6430 T TENSOR T11: 0.0377 T22: 0.0045 T33: 0.0462 T12: -0.0653 T13: -0.0615 T23: 0.0191 L TENSOR L11: 23.2118 L22: 24.3718 L33: 6.2589 L12: 22.3271 L13: 11.1429 L23: 12.3412 S TENSOR S11: 0.2578 S12: 0.5855 S13: -0.0770 S21: 0.9721 S22: 0.1334 S23: 0.4012 S31: 0.3259 S32: 1.0778 S33: -0.3912 TLS GROUP : 33 NUMBER OF COMPONENTS GROUP : 2 COMPONENTS C SSSEQI TO C SSSEQI RESIDUE RANGE : A 15 A 15 RESIDUE RANGE : B 4 B 4 ORIGIN FOR THE GROUP (A): -9.4020 16.0510 -17.2890 T TENSOR T11: -0.1586 T22: -0.1379 T33: -0.0735 T12: 0.0012 T13: 0.0218 T23: 0.0441 L TENSOR L11: 18.4991 L22: 9.4699 L33: 7.8384 L12: 9.9666 L13: 9.9360 L23: 6.1890 S TENSOR S11: 0.3094 S12: 0.7188 S13: -0.2308 S21: 0.4228 S22: -0.0059 S23: -0.0318 S31: 0.4375 S32: 0.7723 S33: -0.3035 TLS GROUP : 34 NUMBER OF COMPONENTS GROUP : 2 COMPONENTS C SSSEQI TO C SSSEQI RESIDUE RANGE : A 16 A 16 RESIDUE RANGE : B 3 B 3 ORIGIN FOR THE GROUP (A): -6.1200 17.5310 -19.9960 T TENSOR T11: -0.1111 T22: -0.0378 T33: -0.0072 T12: 0.0165 T13: 0.0025 T23: 0.0168 L TENSOR L11: 31.0036 L22: 0.2921 L33: 1.0800 L12: 2.0370 L13: 5.7447 L23: 0.3278 S TENSOR S11: 0.0224 S12: 0.2153 S13: -0.2586 S21: -0.0283 S22: 0.2254 S23: -0.0834 S31: 0.4199 S32: -0.0954 S33: -0.2478 TLS GROUP : 35 NUMBER OF COMPONENTS GROUP : 2 COMPONENTS C SSSEQI TO C SSSEQI RESIDUE RANGE : A 17 A 17 RESIDUE RANGE : B 2 B 2 ORIGIN FOR THE GROUP (A): -3.3970 16.9530 -23.2680 T TENSOR T11: -0.0772 T22: 0.0305 T33: 0.0662 T12: 0.0132 T13: 0.0301 T23: 0.0003 L TENSOR L11: 6.1503 L22: 4.8385 L33: 0.4192 L12: -2.6607 L13: -1.6028 L23: 0.7660 S TENSOR S11: -0.2331 S12: -0.0752 S13: 0.6094 S21: 0.1883 S22: 0.5087 S23: -0.4581 S31: 0.1606 S32: -0.5986 S33: -0.2756 TLS GROUP : 36 NUMBER OF COMPONENTS GROUP : 2 COMPONENTS C SSSEQI TO C SSSEQI RESIDUE RANGE : A 18 A 18 RESIDUE RANGE : B 1 B 1 ORIGIN FOR THE GROUP (A): -2.1650 15.3180 -26.1940 T TENSOR T11: -0.0191 T22: -0.0692 T33: 0.0706 T12: -0.0071 T13: -0.0324 T23: -0.0525 L TENSOR L11: 5.0650 L22: 1.0127 L33: 4.7334 L12: 1.6469 L13: -2.7360 L23: -2.1360 S TENSOR S11: 0.3081 S12: -0.0535 S13: 0.3060 S21: -0.5620 S22: 0.1701 S23: 0.0099 S31: 0.1114 S32: -0.2038 S33: -0.4782

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 5'-R(*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*G)-3'
B: 5'-R(*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*G)-3'


Theoretical massNumber of molelcules
Total (without water)11,3892
Polymers11,3892
Non-polymers00
Water73941
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.102, 39.102, 141.277
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Number of models2
Components on special symmetry positions
IDModelComponents
11A-35-

HOH

21B-23-

HOH

31B-25-

HOH

41B-31-

HOH

52A-110-

HOH

62A-113-

HOH

72A-124-

HOH

82A-127-

HOH

92A-134-

HOH

-
Components

#1: RNA chain 5'-R(*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*G)-3'


Mass: 5694.363 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 1.81 Å3/Da / Density % sol: 52.6 %
Description: DETERMINED BY MODEL BUILDING IN MAD MAP BUT REFINED AGAINST ONLY THE NATIVE DATA.
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: MOPS, NaCl, MgCL2, MPD, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1MOPS11
2NaCl11
3MgCL211
4MPD11
5H2O11
6NaCl12
7MgCL212
8MPD12
9H2O12

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONALS 8.2.110.886
SYNCHROTRONALS 8.2.220.9198, 0.9204, 0.8856
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDJul 25, 2004
ADSC QUANTUM 42CCDApr 5, 2004
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.8861
20.91981
30.92041
40.88561
ReflectionResolution: 1.58→19.55 Å / Num. obs: 11050 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 6.2 % / Biso Wilson estimate: 23.5 Å2 / Rsym value: 0.051 / Net I/σ(I): 40.5
Reflection shellResolution: 1.58→1.62 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 5.1 / Rsym value: 0.365 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
Blu-Icedata collection
SCALEPACKdata scaling
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.58→19.55 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.956 / SU B: 8.17 / SU ML: 0.14 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.236 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS BUT WERE NOT ADDED TO COORDINATES. THERE ARE TWO OVERLAPPED DUPLEXES IN THE ASU, EACH WITH AN OCCUPANCY OF O.5. REMARK 3 CONTAINS TLS ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS BUT WERE NOT ADDED TO COORDINATES. THERE ARE TWO OVERLAPPED DUPLEXES IN THE ASU, EACH WITH AN OCCUPANCY OF O.5. REMARK 3 CONTAINS TLS DETAILS FOR MODEL 1 IN THE COORDINATES, REMARK 7 CONTAINS TLS DETAILS FOR MODEL 2 IN THE COORDINATES.
RfactorNum. reflection% reflectionSelection details
Rfree0.279 1085 9.8 %RANDOM
Rwork0.218 ---
obs0.224 9965 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.437 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å20.29 Å20 Å2
2--0.57 Å20 Å2
3----0.86 Å2
Refinement stepCycle: LAST / Resolution: 1.58→19.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 750 0 41 791
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0211664
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0632584
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0820.2356
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02720
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2120.5221
X-RAY DIFFRACTIONr_nbd_other0.2120.5443
X-RAY DIFFRACTIONr_nbtor_refined0.3150.5576
X-RAY DIFFRACTIONr_nbtor_other0.0650.5313
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3580.536
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1320.1512
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1740.28
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3110.528
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it1.55632308
X-RAY DIFFRACTIONr_scangle_it1.8954.52584
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.58→1.62 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 77 -
Rwork0.229 753 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.0853-0.6834-0.25826.23581.9160.81160.278-0.42680.11550.3089-0.05930.04140.1959-0.3656-0.21860.0174-0.05760.0346-0.01090.04190.044-5.12717.14337.871
23.22840.8538-3.943711.24570.55285.0486-0.2607-0.72120.40780.60060.3722-0.36320.066-1.0109-0.11140.07160.04020.0484-0.0121-0.0780.0653-3.2116.68835.127
38.6496-11.97032.898721.9246-7.15763.2549-0.0416-0.04930.19810.03620.21620.0748-0.0781-0.4224-0.1745-0.14350.0314-0.0156-0.2058-0.0217-0.0115-1.25714.67732.076
43.38152.78960.747744.8823-17.66778.0168-0.3288-0.08990.1030.49670.56730.4785-0.3803-1.07-0.2385-0.12440.0176-0.0014-0.1632-0.0565-0.0697-0.94911.17329.134
54.32279.5071-2.327521.6477-4.88431.56570.3604-0.11510.06370.0135-0.21710.38890.0523-0.0361-0.1433-0.0674-0.0474-0.0152-0.22030.0168-0.0362-1.4527.89426.494
60.1256-0.5517-0.0042.4735-0.47995.00360.2710.4166-0.3937-0.00140.0456-0.14270.4899-0.1734-0.3166-0.0103-0.0037-0.0423-0.2121-0.00890.0307-2.9535.59523.842
715.02746.6071-2.60025.8902-2.49721.0640.05340.4135-0.6314-0.07610.115-0.1289-0.1419-0.1736-0.1684-0.12090.0347-0.0001-0.06830.0087-0.0044-5.8055.30820.823
821.5328-10.8356-11.94816.05917.44557.00750.0127-0.43830.0869-0.15430.30920.6183-0.9698-0.0247-0.32190.02180.0451-0.03930.2170.07410.0045-8.5176.83218.411
910.73-0.16752.11892.0198-2.132.59820.1201-0.0288-0.13810.51220.61530.33240.20770.1005-0.73540.19640.0459-0.04530.00860.09780.0985-10.0769.70716.091
107.87622.12244.760112.69722.06382.92720.6257-0.1859-0.28980.26240.06540.80430.408-0.241-0.69110.1645-0.12990.0079-0.06530.09480.1345-10.03813.0413.914
1124.108810.70115.122715.559910.786212.2080.1609-0.5703-0.5117-0.229-0.11910.58220.4328-0.7744-0.04170.0211-0.065-0.0054-0.01940.0709-0.0192-8.60116.08411.593
123.572-1.7604-2.87042.00470.79442.6448-0.03670.588-0.17910.09540.3550.3052-0.10110.0445-0.3183-0.03810.00540.0048-0.0450.0683-0.0149-6.07317.4738.791
131.415-0.3091-1.80490.50480.7592.60620.2636-0.0773-0.0205-0.12850.19590.12490.0888-0.1441-0.4596-0.088-0.00410.0006-0.1225-0.00320.0034-3.2316.9595.981
1410.1674-9.1385.92149.0432-6.29144.58040.13880.0262-0.1249-0.25520.07370.21920.2458-0.0769-0.2125-0.01250.025-0.0297-0.0766-0.03130.0089-1.58614.7372.867
155.13990.5073-0.87410.7444-3.06418.1106-0.14310.1596-0.2832-0.13760.2645-0.00330.5095-0.5938-0.1214-0.0348-0.0288-0.0795-0.1569-0.04150.0249-1.25411.4240.263
1614.06246.5339-9.254223.9506-12.36919.2033-0.64630.3203-1.1699-0.92670.8437-0.4620.0893-0.9255-0.19730.0684-0.0325-0.0904-0.0642-0.00290.0559-3.0368.854-1.972
170.922-2.2651.344710.44880.64515.15220.60970.5309-0.2655-0.84350.35960.0129-0.5373-1.0224-0.96920.23790.0137-0.13820.1994-0.05230.0758-5.8487.542-4.498
1831.3412-16.8754-5.546213.25661.80423.79031.28260.284-1.5743-0.2232-0.8458-0.2558-1.1018-1.2678-0.43670.04660.021-0.13880.1193-0.03290.0523-8.3147.221-7.079
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA11
2X-RAY DIFFRACTION1BB1818
3X-RAY DIFFRACTION2AA22
4X-RAY DIFFRACTION2BB1717
5X-RAY DIFFRACTION3AA33
6X-RAY DIFFRACTION3BB1616
7X-RAY DIFFRACTION4AA44
8X-RAY DIFFRACTION4BB1515
9X-RAY DIFFRACTION5AA55
10X-RAY DIFFRACTION5BB1414
11X-RAY DIFFRACTION6AA66
12X-RAY DIFFRACTION6BB1313
13X-RAY DIFFRACTION7AA77
14X-RAY DIFFRACTION7BB1212
15X-RAY DIFFRACTION8AA88
16X-RAY DIFFRACTION8BB1111
17X-RAY DIFFRACTION9AA99
18X-RAY DIFFRACTION9BB1010
19X-RAY DIFFRACTION10AA1010
20X-RAY DIFFRACTION10BB99
21X-RAY DIFFRACTION11AA1111
22X-RAY DIFFRACTION11BB88
23X-RAY DIFFRACTION12AA1212
24X-RAY DIFFRACTION12BB77
25X-RAY DIFFRACTION13AA1313
26X-RAY DIFFRACTION13BB66
27X-RAY DIFFRACTION14AA1414
28X-RAY DIFFRACTION14BB55
29X-RAY DIFFRACTION15AA1515
30X-RAY DIFFRACTION15BB44
31X-RAY DIFFRACTION16AA1616
32X-RAY DIFFRACTION16BB33
33X-RAY DIFFRACTION17AA1717
34X-RAY DIFFRACTION17BB22
35X-RAY DIFFRACTION18AA1818
36X-RAY DIFFRACTION18BB11

+
About Yorodumi

-
News

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

New format data for meta-information of EMDB entries

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

Related info.:EMDB header

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

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

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

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

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

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

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

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

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

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

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

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

+
Jul 12, 2017. Major update of PDB

Major update of PDB

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

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

-
Yorodumi

Thousand views of thousand structures

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

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

Read more