[English] 日本語
Yorodumi
- PDB-3e76: Crystal structure of Wild-type GroEL with bound Thallium ions -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3.0E+76
TitleCrystal structure of Wild-type GroEL with bound Thallium ions
Components60 kDa chaperonin
KeywordsCHAPERONE / GroEL / HSP60 / chaperonin / thallium / ATP-binding / Nucleotide-binding
Function / homology
Function and homology information


chaperonin ATPase / isomerase activity / ATP-dependent protein folding chaperone / unfolded protein binding / protein refolding / ATP binding / cytoplasm
Similarity search - Function
GROEL; domain 2 / TCP-1-like chaperonin intermediate domain / GROEL; domain 1 / GroEL-like equatorial domain / GroEL / GroEL / Chaperonin Cpn60, conserved site / Chaperonins cpn60 signature. / Chaperonin Cpn60/GroEL / GroEL-like equatorial domain superfamily ...GROEL; domain 2 / TCP-1-like chaperonin intermediate domain / GROEL; domain 1 / GroEL-like equatorial domain / GroEL / GroEL / Chaperonin Cpn60, conserved site / Chaperonins cpn60 signature. / Chaperonin Cpn60/GroEL / GroEL-like equatorial domain superfamily / TCP-1-like chaperonin intermediate domain superfamily / GroEL-like apical domain superfamily / TCP-1/cpn60 chaperonin family / Chaperonin Cpn60/GroEL/TCP-1 family / 3-Layer(bba) Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / THALLIUM (I) ION / Chaperonin GroEL
Similarity search - Component
Biological speciesEscherichia coli UTI89 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.94 Å
AuthorsKiser, P.D. / Lorimer, G.H. / Palczewski, K.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Use of thallium to identify monovalent cation binding sites in GroEL.
Authors: Kiser, P.D. / Lorimer, G.H. / Palczewski, K.
History
DepositionAug 17, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 30, 2023Group: 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 / struct_ncs_dom_lim / 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.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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 60 kDa chaperonin
B: 60 kDa chaperonin
C: 60 kDa chaperonin
D: 60 kDa chaperonin
E: 60 kDa chaperonin
F: 60 kDa chaperonin
G: 60 kDa chaperonin
H: 60 kDa chaperonin
I: 60 kDa chaperonin
J: 60 kDa chaperonin
K: 60 kDa chaperonin
L: 60 kDa chaperonin
M: 60 kDa chaperonin
N: 60 kDa chaperonin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)818,71488
Polymers801,64714
Non-polymers17,06774
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)135.676, 260.954, 287.872
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21C
31A
41D
51E
61F
71G
81H
91I
101J
111K
121L
131M
141N
12A
22B
32C
42D
52E
62F
72G
82H
92I
102J
112K
122L
132M
142N

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ALAALAVALVAL1BB2 - 391 - 38
211ALAALAVALVAL1CC2 - 391 - 38
311ALAALAVALVAL1AA2 - 391 - 38
411ALAALAVALVAL1DD2 - 391 - 38
511ALAALAVALVAL1EE2 - 391 - 38
611ALAALAVALVAL1FF2 - 391 - 38
711ALAALAVALVAL1GG2 - 391 - 38
811ALAALAVALVAL1HH2 - 391 - 38
911ALAALAVALVAL1II2 - 391 - 38
1011ALAALAVALVAL1JJ2 - 391 - 38
1111ALAALAVALVAL1KK2 - 391 - 38
1211ALAALAVALVAL1LL2 - 391 - 38
1311ALAALAVALVAL1MM2 - 391 - 38
1411ALAALAVALVAL1NN2 - 391 - 38
121PROPROPHEPHE1BB47 - 19546 - 194
221PROPROPHEPHE1CC47 - 19546 - 194
321PROPROPHEPHE1AA47 - 19546 - 194
421PROPROPHEPHE1DD47 - 19546 - 194
521PROPROPHEPHE1EE47 - 19546 - 194
621PROPROPHEPHE1FF47 - 19546 - 194
721PROPROPHEPHE1GG47 - 19546 - 194
821PROPROPHEPHE1HH47 - 19546 - 194
921PROPROPHEPHE1II47 - 19546 - 194
1021PROPROPHEPHE1JJ47 - 19546 - 194
1121PROPROPHEPHE1KK47 - 19546 - 194
1221PROPROPHEPHE1LL47 - 19546 - 194
1321PROPROPHEPHE1MM47 - 19546 - 194
1421PROPROPHEPHE1NN47 - 19546 - 194
131HISHISPROPRO1BB401 - 525400 - 524
231HISHISPROPRO1CC401 - 525400 - 524
331HISHISPROPRO1AA401 - 525400 - 524
431HISHISPROPRO1DD401 - 525400 - 524
531HISHISPROPRO1EE401 - 525400 - 524
631HISHISPROPRO1FF401 - 525400 - 524
731HISHISPROPRO1GG401 - 525400 - 524
831HISHISPROPRO1HH401 - 525400 - 524
931HISHISPROPRO1II401 - 525400 - 524
1031HISHISPROPRO1JJ401 - 525400 - 524
1131HISHISPROPRO1KK401 - 525400 - 524
1231HISHISPROPRO1LL401 - 525400 - 524
1331HISHISPROPRO1MM401 - 525400 - 524
1431HISHISPROPRO1NN401 - 525400 - 524
141LEULEUALAALA1BB40 - 4639 - 45
241LEULEUALAALA1CC40 - 4639 - 45
341LEULEUALAALA1AA40 - 4639 - 45
441LEULEUALAALA1DD40 - 4639 - 45
541LEULEUALAALA1EE40 - 4639 - 45
641LEULEUALAALA1FF40 - 4639 - 45
741LEULEUALAALA1GG40 - 4639 - 45
841LEULEUALAALA1HH40 - 4639 - 45
941LEULEUALAALA1II40 - 4639 - 45
1041LEULEUALAALA1JJ40 - 4639 - 45
1141LEULEUALAALA1KK40 - 4639 - 45
1241LEULEUALAALA1LL40 - 4639 - 45
1341LEULEUALAALA1MM40 - 4639 - 45
1441LEULEUALAALA1NN40 - 4639 - 45
151ASPASPLEULEU6BB196 - 400195 - 399
251ASPASPLEULEU6CC196 - 400195 - 399
351ASPASPLEULEU6AA196 - 400195 - 399
451ASPASPLEULEU6DD196 - 400195 - 399
551ASPASPLEULEU6EE196 - 400195 - 399
651ASPASPLEULEU6FF196 - 400195 - 399
751ASPASPLEULEU6GG196 - 400195 - 399
851ASPASPLEULEU6HH196 - 400195 - 399
951ASPASPLEULEU6II196 - 400195 - 399
1051ASPASPLEULEU6JJ196 - 400195 - 399
1151ASPASPLEULEU6KK196 - 400195 - 399
1251ASPASPLEULEU6LL196 - 400195 - 399
1351ASPASPLEULEU6MM196 - 400195 - 399
1451ASPASPLEULEU6NN196 - 400195 - 399
112AGSAGSAGSAGS1AO549
212AGSAGSAGSAGS1BU549
312AGSAGSAGSAGS1CAA549
412AGSAGSAGSAGS1DFA549
512AGSAGSAGSAGS1ELA549
612AGSAGSAGSAGS1FQA549
712AGSAGSAGSAGS1GWA549
812AGSAGSAGSAGS1HBB549
912AGSAGSAGSAGS1IHB549
1012AGSAGSAGSAGS1JMB549
1112AGSAGSAGSAGS1KRB549
1212AGSAGSAGSAGS1LWB549
1312AGSAGSAGSAGS1MBC549
1412AGSAGSAGSAGS1NGC549

NCS ensembles :
ID
1
2

-
Components

#1: Protein
60 kDa chaperonin / Protein Cpn60 / groEL protein


Mass: 57260.504 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli UTI89 (bacteria) / Gene: groL, groEL, UTI89_C4741 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1R3B6, EC: 3.6.4.9
#2: Chemical
ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#3: Chemical...
ChemComp-TL / THALLIUM (I) ION / Thallium


Mass: 204.383 Da / Num. of mol.: 46 / Source method: obtained synthetically / Formula: Tl
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Mg

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.27 Å3/Da / Density % sol: 62.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97741 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 9, 2008
RadiationMonochromator: KOHZU double crystal monochromator with a sagittally focused second crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 3.94→50 Å / Num. obs: 90513 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.3 % / Rmerge(I) obs: 0.189 / Net I/σ(I): 12.8
Reflection shellResolution: 3.94→4.08 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.96 / Mean I/σ(I) obs: 2.1 / % possible all: 88

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry: 1XCK
Resolution: 3.94→49.39 Å / Cor.coef. Fo:Fc: 0.897 / Cor.coef. Fo:Fc free: 0.857 / SU B: 129.239 / SU ML: 0.842 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Overall temperature factor/TLS / Cross valid method: THROUGHOUT / ESU R Free: 0.952 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.293 4456 5 %RANDOM
Rwork0.261 ---
obs0.262 84364 97.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 125.21 Å2
Baniso -1Baniso -2Baniso -3
1--3.53 Å20 Å20 Å2
2---1.48 Å20 Å2
3---5.01 Å2
Refinement stepCycle: LAST / Resolution: 3.94→49.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms53970 0 494 0 54464
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02254824
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9191.99874130
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1657322
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.54226.0672100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.5261510080
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.58715308
X-RAY DIFFRACTIONr_chiral_restr0.0580.29030
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0239648
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1810.223119
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2850.237743
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.21094
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1810.218
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3220.270
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2310.29
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_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11B2308tight positional0.020.05
12C2308tight positional0.040.05
13A2308tight positional0.040.05
14D2308tight positional0.020.05
15E2308tight positional0.030.05
16F2308tight positional0.020.05
17G2308tight positional0.030.05
18H2308tight positional0.020.05
19I2308tight positional0.040.05
110J2308tight positional0.050.05
111K2308tight positional0.040.05
112L2308tight positional0.020.05
113M2308tight positional0.050.05
114N2308tight positional0.020.05
21A31tight positional0.020.05
22B31tight positional0.010.05
23C31tight positional0.020.05
24D31tight positional0.020.05
25E31tight positional0.010.05
26F31tight positional0.020.05
27G31tight positional0.020.05
28H31tight positional0.020.05
29I31tight positional0.010.05
210J31tight positional0.020.05
211K31tight positional0.020.05
212L31tight positional0.020.05
213M31tight positional0.110.05
214N31tight positional0.020.05
11B1547loose positional1.115
12C1547loose positional15
13A1547loose positional0.955
14D1547loose positional1.045
15E1547loose positional1.045
16F1547loose positional1.215
17G1547loose positional0.795
18H1547loose positional1.095
19I1547loose positional0.895
110J1547loose positional1.065
111K1547loose positional1.125
112L1547loose positional0.965
113M1547loose positional1.345
114N1547loose positional1.635
LS refinement shellResolution: 3.94→4.04 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 287 -
Rwork0.334 5357 -
obs--85.19 %
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)
18.2251-2.5856-1.19856.4610.52611.11050.15760.2223-0.08840.215-0.0477-0.2035-0.2537-0.0144-0.1099-0.8297-0.0296-0.1095-0.8776-0.0624-0.6398-4.604445.926962.2561
24.44554.1434-2.17966.2984-4.546713.78940.1299-0.10330.5198-0.47440.04121.15340.8742-0.5934-0.171-0.08460.116-0.0829-0.81150.0338-0.0712-23.457347.922286.5107
38.37970.42020.38988.83861.5663.9325-0.1189-0.4511-0.28480.37570.1849-0.22470.22460.3547-0.066-0.17620.0633-0.1537-0.6940.1457-0.3619-1.469643.8057101.5075
49.6151.5484-0.13034.71830.95211.11570.05540.05070.08550.01030.0535-0.41010.0361-0.4542-0.1089-0.8376-0.0052-0.0801-0.8038-0.0597-0.4885-29.63214.970961.6097
50.7324-1.3772.61916.7618-6.575711.75340.0511-0.3221-0.872-0.07560.13351.18070.9008-0.0316-0.1846-0.11250.0562-0.09740.1445-0.05830.1093-43.41821.751285.7884
610.29830.4158-0.66565.8698-0.21215.09640.4998-0.6072-0.16170.9872-0.628-0.951-0.0653-0.16290.12830.388-0.1827-0.2689-0.48510.09010.1326-27.117516.9516100.8691
75.20181.05290.69899.8003-0.3761.34960.0451-0.3813-0.00770.08280.07890.19980.1837-0.3603-0.1241-0.77-0.0150.0018-0.7126-0.0348-0.5449-21.1754-23.966861.7482
813.8182-5.16114.12082.3613-3.42869.46110.24511.296-0.79210.12250.34040.00490.84870.2404-0.58550.505-0.30680.0061-0.1526-0.12530.3623-19.7285-42.353886.3652
95.2235-1.4660.50755.1104-1.55945.575-0.7388-0.03530.80061.28370.8094-0.5841-0.5345-0.41-0.07061.13850.2472-0.1278-0.1763-0.11350.4748-21.2889-19.718100.6885
106.3509-1.91520.94127.7613-0.69941.62280.2296-0.1590.31270.1002-0.00920.19450.266-0.1819-0.2204-0.7357-0.08640.0307-0.83080.0094-0.82614.7232-41.516462.269
117.16644.52576.1553.09282.580612.55640.0121-0.5634-0.07750.03510.4906-1.0171-0.68260.8752-0.5026-0.1062-0.03960.0128-0.6215-0.2273-0.13829.9087-51.275687.0989
1212.8220.2116-1.5437.2163-0.49083.55060.1849-0.54091.15730.3493-0.12850.0659-0.529-0.3753-0.05640.1356-0.14850.1426-0.6199-0.0829-0.333711.1403-37.6563100.7731
139.8402-0.14940.08625.0238-0.32262.04820.2572-0.16410.23490.14210.1677-0.08740.34710.4509-0.4249-0.7782-0.0118-0.0309-0.7151-0.0056-0.69750.7812-24.441563.1923
140.08760.92440.868214.08839.65738.66150.28090.43161.1459-0.89620.6414-1.5647-0.03790.8243-0.92230.130.1828-0.0410.8002-0.10880.175167.7545-18.360388.2125
1514.0094-3.439-1.6597.691-2.0863.99320.5246-1.50590.92460.5336-0.3980.23170.08350.2761-0.12650.2802-0.51210.04650.0153-0.381-0.239645.5602-24.9212101.8886
166.68881.3804-0.46996.71440.80652.1889-0.0630.04040.19330.14290.3351-0.1260.04230.2609-0.2721-0.8438-0.0048-0.0574-0.71660.0877-0.689459.827814.252463.4272
176.623-1.38253.81754.97314.14387.41130.25710.62011.2793-0.4423-0.029-0.8322-0.42980.0777-0.2281-0.0197-0.21420.21360.58510.01620.050465.371231.763988.178
1813.6361-2.24380.53138.6983-0.27993.1880.0419-0.3184-0.84360.24280.1164-0.02930.62450.4232-0.15820.0318-0.0021-0.0235-0.0919-0.1179-0.770955.592610.7277102.319
194.9520.7514-0.32099.0999-0.05951.85680.2271-0.17740.14610.0338-0.0857-0.1052-0.43230.2366-0.1414-0.8088-0.0171-0.0527-0.70890.0429-0.551735.285545.709763.0117
2012.42594.201-0.82422.04012.06568.92240.43431.30361.6216-0.38730.1336-0.403-0.5857-0.1848-0.56790.5044-0.0998-0.0721-0.42520.21740.475724.803361.402987.4304
218.06911.30430.208411.418-0.60184.3381-0.49740.15880.1709-0.20860.421-0.5496-0.13120.53280.0763-0.2638-0.0264-0.118-0.2902-0.0511-0.772635.394741.4378101.7482
228.9433-1.95221.46087.24370.34532.2694-0.0890.34030.1394-0.19720.20740.01690.2020.5769-0.1184-0.86180.0328-0.0341-0.49050.0122-0.838359.4428-8.968530.0868
237.10134.24582.14633.07962.65284.11520.4952-0.4661-0.82670.55090.3112-0.71381.140.5932-0.80640.24680.1365-0.23860.7599-0.08820.356564.1353-26.68575.3785
2413.07830.6320.13046.5106-0.89312.3675-0.2001-0.5981.2606-0.8236-0.09710.4382-0.6301-0.02260.29720.08310.0341-0.19350.5691-0.2838-0.491856.7327-4.8061-8.6428
256.94571.64060.5759.1150.36911.67870.23180.1328-0.4295-0.2898-0.1682-0.19840.45290.3062-0.0636-0.74390.07030.0343-0.63260.0732-0.91232.2107-38.185329.3725
264.9224-1.70024.76285.8135-1.15184.68450.4689-0.5771-1.29420.7628-0.1295-0.12051.065-0.5175-0.33940.72870.1530.05680.23960.0887-0.092420.9571-52.70274.5163
277.4727-4.0606-0.73469.56390.73165.2952-0.2963-0.52030.35460.3360.1677-0.76480.39740.70040.1286-0.045-0.0133-0.07560.1481-0.0963-0.670433.5935-33.546-9.3298
288.4992.64380.19247.0017-0.91792.11620.25390.1068-0.1602-0.28630.01030.15980.3178-0.2346-0.2642-0.7961-0.00540.0427-0.59690.0203-0.8192-7.5613-35.064328.6424
292.392-4.38483.48558.3142-5.61877.2247-0.0374-0.2866-0.34450.8150.790.76470.844-1.7357-0.75260.5399-0.3893-0.00650.80260.09790.232-25.9705-35.32373.7945
305.7305-0.644-0.338710.44060.93734.71450.01240.3654-0.2886-0.4006-0.03290.15960.53760.08830.0204-0.05660.07020.06610.5970.1309-0.4485-3.3811-33.6062-10.2272
3111.0133-2.5562-0.87695.3194-0.36862.08110.10440.31990.0872-0.2392-0.1239-0.1539-0.1195-0.44360.0195-0.85020.0260.0451-0.605-0.114-0.7373-29.9373-2.148728.0229
320.4227-0.49361.22920.5764-1.43553.5750.3703-0.231.15881.3779-0.01861.1079-1.5092-1.2406-0.35170.26550.087-0.01381.335-0.2260.6484-41.544412.08473.2384
337.40630.80060.73444.12382.18796.16770.3334-0.0611-0.2424-1.0611-0.669-0.4377-0.1873-0.05970.33550.35150.2320.23570.56870.1311-0.1132-26.0504-4.4821-11.1576
346.41120.1957-1.51819.83490.33311.3235-0.01790.26780.1639-0.4478-0.13990.5155-0.4098-0.3210.1578-0.56940.1435-0.1294-0.6119-0.1151-0.5353-18.132335.938428.5034
352.7772-1.25490.68121.1022-1.30612.02920.0947-0.24332.3457-0.45880.26160.08710.45240.7741-0.35631.34980.5159-0.0250.9594-0.11760.9847-14.147554.50054.2438
360.77350.38280.27785.3063-1.1462.6571-0.64510.361-0.7663-0.7890.489-0.34790.1602-0.1550.15610.9636-0.02320.05160.7294-0.05450.4627-17.215732.0663-10.6798
376.41452.4536-0.03699.69671.42651.65780.03810.37240.4271-0.63330.07140.1114-0.49680.2557-0.1096-0.60680.0322-0.0216-0.6081-0.0182-0.455519.102850.422829.264
382.984-3.3462-3.77238.35742.13785.71970.21530.93860.92310.56930.0277-0.7404-0.34570.3746-0.2431.0706-0.1170.20550.66430.11040.919835.912959.22025.0111
393.64532.3160.60851.544-0.00392.2048-0.16591.069-0.25730.29040.31660.6422-0.07790.5755-0.15071.36750.18780.0131.1288-0.15890.470216.261448.0937-9.9434
408.66081.07180.8966.64051.19472.07060.10720.19940.3751-0.5249-0.11230.2183-0.29370.39580.0051-0.6888-0.0412-0.0106-0.58190.1236-0.545153.553430.457930.0582
413.556-5.045-5.71417.15748.10669.18181.5702-0.1509-0.5866-0.5373-0.2-1.9788-0.1635-1.0405-1.37020.8042-0.2377-0.29951.3985-0.09440.637170.57422.965.624
426.652-1.4465-1.50643.9327-0.96280.80131.25451.6381-0.3378-0.3488-0.73690.4878-0.574-0.4169-0.51761.76610.4339-0.12861.23620.00360.262348.869930.9828-8.6739
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 135
2X-RAY DIFFRACTION1A410 - 525
3X-RAY DIFFRACTION2A136 - 190
4X-RAY DIFFRACTION2A375 - 409
5X-RAY DIFFRACTION3A191 - 374
6X-RAY DIFFRACTION4B2 - 135
7X-RAY DIFFRACTION4B410 - 525
8X-RAY DIFFRACTION5B136 - 190
9X-RAY DIFFRACTION5B375 - 409
10X-RAY DIFFRACTION6B191 - 374
11X-RAY DIFFRACTION7C2 - 135
12X-RAY DIFFRACTION7C410 - 525
13X-RAY DIFFRACTION8C136 - 190
14X-RAY DIFFRACTION8C375 - 409
15X-RAY DIFFRACTION9C191 - 374
16X-RAY DIFFRACTION10D2 - 135
17X-RAY DIFFRACTION10D410 - 525
18X-RAY DIFFRACTION11D136 - 190
19X-RAY DIFFRACTION11D375 - 409
20X-RAY DIFFRACTION12D191 - 374
21X-RAY DIFFRACTION13E2 - 135
22X-RAY DIFFRACTION13E410 - 525
23X-RAY DIFFRACTION14E136 - 190
24X-RAY DIFFRACTION14E375 - 409
25X-RAY DIFFRACTION15E191 - 374
26X-RAY DIFFRACTION16F2 - 135
27X-RAY DIFFRACTION16F410 - 525
28X-RAY DIFFRACTION17F136 - 190
29X-RAY DIFFRACTION17F375 - 409
30X-RAY DIFFRACTION18F191 - 374
31X-RAY DIFFRACTION19G2 - 135
32X-RAY DIFFRACTION19G410 - 525
33X-RAY DIFFRACTION20G136 - 190
34X-RAY DIFFRACTION20G375 - 409
35X-RAY DIFFRACTION21G191 - 374
36X-RAY DIFFRACTION22H2 - 135
37X-RAY DIFFRACTION22H410 - 525
38X-RAY DIFFRACTION23H136 - 190
39X-RAY DIFFRACTION23H375 - 409
40X-RAY DIFFRACTION24H191 - 374
41X-RAY DIFFRACTION25I2 - 135
42X-RAY DIFFRACTION25I410 - 525
43X-RAY DIFFRACTION26I136 - 190
44X-RAY DIFFRACTION26I375 - 409
45X-RAY DIFFRACTION27I191 - 374
46X-RAY DIFFRACTION28J2 - 135
47X-RAY DIFFRACTION28J410 - 525
48X-RAY DIFFRACTION29J136 - 190
49X-RAY DIFFRACTION29J375 - 409
50X-RAY DIFFRACTION30J191 - 374
51X-RAY DIFFRACTION31K2 - 135
52X-RAY DIFFRACTION31K410 - 525
53X-RAY DIFFRACTION32K136 - 190
54X-RAY DIFFRACTION32K375 - 409
55X-RAY DIFFRACTION33K191 - 374
56X-RAY DIFFRACTION34L2 - 135
57X-RAY DIFFRACTION34L410 - 525
58X-RAY DIFFRACTION35L136 - 190
59X-RAY DIFFRACTION35L375 - 409
60X-RAY DIFFRACTION36L191 - 374
61X-RAY DIFFRACTION37M2 - 135
62X-RAY DIFFRACTION37M410 - 525
63X-RAY DIFFRACTION38M136 - 190
64X-RAY DIFFRACTION38M375 - 409
65X-RAY DIFFRACTION39M191 - 374
66X-RAY DIFFRACTION40N2 - 135
67X-RAY DIFFRACTION40N410 - 525
68X-RAY DIFFRACTION41N136 - 190
69X-RAY DIFFRACTION41N375 - 409
70X-RAY DIFFRACTION42N191 - 374

+
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://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