[English] 日本語
Yorodumi
- PDB-5opw: Crystal structure of the GroEL mutant A109C -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5opw
TitleCrystal structure of the GroEL mutant A109C
Components60 kDa chaperonin
KeywordsCHAPERONE / chaperonin
Function / homology
Function and homology information


GroEL-GroES complex / chaperonin ATPase / virion assembly / chaperone cofactor-dependent protein refolding / isomerase activity / ATP-dependent protein folding chaperone / response to radiation / unfolded protein binding / protein folding / response to heat ...GroEL-GroES complex / chaperonin ATPase / virion assembly / chaperone cofactor-dependent protein refolding / isomerase activity / ATP-dependent protein folding chaperone / response to radiation / unfolded protein binding / protein folding / response to heat / protein refolding / magnesium ion binding / ATP hydrolysis activity / ATP binding / membrane / identical protein binding / cytosol
Similarity search - Function
GROEL; domain 2 / TCP-1-like chaperonin intermediate domain / GROEL; domain 1 / GroEL-like equatorial domain / 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 ...GROEL; domain 2 / TCP-1-like chaperonin intermediate domain / GROEL; domain 1 / GroEL-like equatorial domain / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.19 Å
AuthorsYan, X. / Shi, Q. / Bracher, A. / Milicic, G. / Singh, A.K. / Hartl, F.U. / Hayer-Hartl, M.
CitationJournal: Cell / Year: 2018
Title: GroEL Ring Separation and Exchange in the Chaperonin Reaction.
Authors: Yan, X. / Shi, Q. / Bracher, A. / Milicic, G. / Singh, A.K. / Hartl, F.U. / Hayer-Hartl, M.
History
DepositionAug 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 10, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

-
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


Theoretical massNumber of molelcules
Total (without water)802,09614
Polymers802,09614
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: Textbook
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area48690 Å2
ΔGint-223 kcal/mol
Surface area293870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.695, 262.047, 149.213
Angle α, β, γ (deg.)90.000, 100.810, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18A
28I
19A
29J
110A
210K
111A
211L
112A
212M
113A
213N
114B
214C
115B
215D
116B
216E
117B
217F
118B
218G
119B
219H
120B
220I
121B
221J
122B
222K
123B
223L
124B
224M
125B
225N
126C
226D
127C
227E
128C
228F
129C
229G
130C
230H
131C
231I
132C
232J
133C
233K
134C
234L
135C
235M
136C
236N
137D
237E
138D
238F
139D
239G
140D
240H
141D
241I
142D
242J
143D
243K
144D
244L
145D
245M
146D
246N
147E
247F
148E
248G
149E
249H
150E
250I
151E
251J
152E
252K
153E
253L
154E
254M
155E
255N
156F
256G
157F
257H
158F
258I
159F
259J
160F
260K
161F
261L
162F
262M
163F
263N
164G
264H
165G
265I
166G
266J
167G
267K
168G
268L
169G
269M
170G
270N
171H
271I
172H
272J
173H
273K
174H
274L
175H
275M
176H
276N
177I
277J
178I
278K
179I
279L
180I
280M
181I
281N
182J
282K
183J
283L
184J
284M
185J
285N
186K
286L
187K
287M
188K
288N
189L
289M
190L
290N
191M
291N

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 0 / Auth seq-ID: 2 - 525 / Label seq-ID: 1 - 524

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14AA
24EE
15AA
25FF
16AA
26GG
17AA
27HH
18AA
28II
19AA
29JJ
110AA
210KK
111AA
211LL
112AA
212MM
113AA
213NN
114BB
214CC
115BB
215DD
116BB
216EE
117BB
217FF
118BB
218GG
119BB
219HH
120BB
220II
121BB
221JJ
122BB
222KK
123BB
223LL
124BB
224MM
125BB
225NN
126CC
226DD
127CC
227EE
128CC
228FF
129CC
229GG
130CC
230HH
131CC
231II
132CC
232JJ
133CC
233KK
134CC
234LL
135CC
235MM
136CC
236NN
137DD
237EE
138DD
238FF
139DD
239GG
140DD
240HH
141DD
241II
142DD
242JJ
143DD
243KK
144DD
244LL
145DD
245MM
146DD
246NN
147EE
247FF
148EE
248GG
149EE
249HH
150EE
250II
151EE
251JJ
152EE
252KK
153EE
253LL
154EE
254MM
155EE
255NN
156FF
256GG
157FF
257HH
158FF
258II
159FF
259JJ
160FF
260KK
161FF
261LL
162FF
262MM
163FF
263NN
164GG
264HH
165GG
265II
166GG
266JJ
167GG
267KK
168GG
268LL
169GG
269MM
170GG
270NN
171HH
271II
172HH
272JJ
173HH
273KK
174HH
274LL
175HH
275MM
176HH
276NN
177II
277JJ
178II
278KK
179II
279LL
180II
280MM
181II
281NN
182JJ
282KK
183JJ
283LL
184JJ
284MM
185JJ
285NN
186KK
286LL
187KK
287MM
188KK
288NN
189LL
289MM
190LL
290NN
191MM
291NN

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91

-
Components

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


Mass: 57292.566 Da / Num. of mol.: 14 / Fragment: GroEL / Mutation: A109C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Gene: groL, groEL, mopA, b4143, JW4103 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A6F5

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.37 Å3/Da / Density % sol: 63.49 % / Mosaicity: 0.11 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M sodium citrate, pH 5.5, and 15 % PEG 6000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Aug 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 3.19→50 Å / Num. obs: 168385 / % possible obs: 99.5 % / Redundancy: 3.5 % / CC1/2: 0.987 / Rmerge(I) obs: 0.175 / Rpim(I) all: 0.109 / Rrim(I) all: 0.207 / Net I/σ(I): 6.3
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.1 %

Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
3.19-3.250.86178460.5750.571.03693.7
17.49-49.350.03910170.9990.0270.04894.7

-
Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.518
Highest resolutionLowest resolution
Rotation49.35 Å3.33 Å

-
Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
MOLREP11.2.08phasing
REFMAC5.8.0071refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 4WSC
Resolution: 3.19→50 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.891 / SU B: 62.815 / SU ML: 0.444 / SU R Cruickshank DPI: 0.4858 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.477
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2524 8289 4.9 %RANDOM
Rwork0.2446 ---
obs0.2449 160056 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 227.07 Å2 / Biso mean: 83.96 Å2 / Biso min: 33.13 Å2
Baniso -1Baniso -2Baniso -3
1--1.69 Å2-0 Å20.68 Å2
2---0.46 Å2-0 Å2
3---1.77 Å2
Refinement stepCycle: final / Resolution: 3.19→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms53984 0 0 0 53984
Num. residues----7336
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01954383
X-RAY DIFFRACTIONr_bond_other_d0.0030.0254866
X-RAY DIFFRACTIONr_angle_refined_deg0.8221.98873430
X-RAY DIFFRACTIONr_angle_other_deg0.9393126420
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.73357322
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.71326.0672100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.6211510094
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.96115308
X-RAY DIFFRACTIONr_chiral_restr0.0450.28932
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0261824
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0210248
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A323970.04
12B323970.04
21A324040.03
22C324040.03
31A324220.03
32D324220.03
41A323350.03
42E323350.03
51A322770.04
52F322770.04
61A324040.03
62G324040.03
71A323190.04
72H323190.04
81A323530.04
82I323530.04
91A323590.04
92J323590.04
101A323450.04
102K323450.04
111A321970.05
112L321970.05
121A322720.04
122M322720.04
131A323010.04
132N323010.04
141B325250.03
142C325250.03
151B325060.03
152D325060.03
161B324580.03
162E324580.03
171B323950.04
172F323950.04
181B324660.03
182G324660.03
191B324690.03
192H324690.03
201B324870.03
202I324870.03
211B324630.04
212J324630.04
221B324850.03
222K324850.03
231B323150.04
232L323150.04
241B323580.04
242M323580.04
251B324300.04
252N324300.04
261C324880.03
262D324880.03
271C324270.03
272E324270.03
281C324340.03
282F324340.03
291C325240.02
292G325240.02
301C324430.03
302H324430.03
311C324740.03
312I324740.03
321C324380.04
322J324380.04
331C323990.03
332K323990.03
341C323160.04
342L323160.04
351C323560.04
352M323560.04
361C324230.04
362N324230.04
371D323600.04
372E323600.04
381D323970.04
382F323970.04
391D324840.03
392G324840.03
401D323720.04
402H323720.04
411D324520.03
412I324520.03
421D324260.04
422J324260.04
431D323960.04
432K323960.04
441D323010.04
442L323010.04
451D323090.04
452M323090.04
461D323530.04
462N323530.04
471E323770.04
472F323770.04
481E323820.03
482G323820.03
491E324960.03
492H324960.03
501E324900.03
502I324900.03
511E323970.04
512J323970.04
521E323730.03
522K323730.03
531E323130.04
532L323130.04
541E324410.03
542M324410.03
551E324180.04
552N324180.04
561F323640.03
562G323640.03
571F324440.04
572H324440.04
581F325180.03
582I325180.03
591F323230.04
592J323230.04
601F322720.04
602K322720.04
611F323690.04
612L323690.04
621F322960.04
622M322960.04
631F324210.04
632N324210.04
641G323770.03
642H323770.03
651G324170.03
652I324170.03
661G324610.03
662J324610.03
671G324640.03
672K324640.03
681G322840.04
682L322840.04
691G323460.04
692M323460.04
701G323890.04
702N323890.04
711H325540.03
712I325540.03
721H324250.04
722J324250.04
731H323760.04
732K323760.04
741H324030.04
742L324030.04
751H323840.04
752M323840.04
761H324730.04
762N324730.04
771I324500.04
772J324500.04
781I324220.03
782K324220.03
791I324490.04
792L324490.04
801I324420.03
802M324420.03
811I325440.03
812N325440.03
821J324790.03
822K324790.03
831J322860.04
832L322860.04
841J323500.04
842M323500.04
851J323750.04
852N323750.04
861K322860.04
862L322860.04
871K323260.04
872M323260.04
881K323540.04
882N323540.04
891L322410.05
892M322410.05
901L323380.04
902N323380.04
911M323880.04
912N323880.04
LS refinement shellResolution: 3.193→3.276 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 614 -
Rwork0.348 11339 -
all-11953 -
obs--96.02 %
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)
13.0049-0.62590.12022.74020.27330.36840.02880.0793-0.03320.190.05540.0232-0.0157-0.0211-0.08430.03760.002-0.03740.04670.0240.337560.2456-9.60978.746
21.80021.61932.82612.24681.6896.47890.1984-0.048-0.3422-0.2105-0.0201-0.10020.5038-0.4164-0.17830.41720.0461-0.06750.421-0.12670.64466.1217-26.5463-15.8812
34.00070.63680.69755.9534-0.23113.06280.10150.33120.9183-0.73940.09381.0854-0.0937-0.2562-0.19530.771-0.0121-0.19250.77410.07011.165856.2228-5.6896-29.8703
42.21310.34460.20113.3067-0.04570.97640.14190.0382-0.13490.0434-0.0763-0.04920.14330.0572-0.06560.0367-0.0164-0.01250.1446-0.03580.440735.5946-41.10179.2913
54.5687-0.43962.13110.5617-1.02884.88130.15240.0293-0.271-0.07830.18780.36350.2336-0.22-0.34020.514-0.051-0.0760.3156-0.15930.868525.7192-56.7281-14.9408
63.54821.70460.20735.4733-0.66992.0751-0.30510.77030.8537-0.61360.50960.4513-0.05210.0296-0.20440.689-0.1827-0.09180.9010.0710.990436.2442-36.4352-29.1619
73.24280.29120.17432.58990.20280.8276-0.0372-0.1608-0.0271-0.05280.0051-0.03390.16550.02860.03210.04780.0204-0.03560.0227-0.04030.33-4.3588-41.18529.7848
81.5448-1.41941.32432.6059-3.70026.050.08490.184-0.10480.14320.17790.3644-0.3952-0.5204-0.26270.3453-0.043-0.05360.2479-0.01150.7102-22.8903-43.378-14.3212
94.1117-0.09660.06164.86190.15452.74790.10190.39891.0162-0.32010.1604-0.6766-0.52450.2477-0.26230.4571-0.00820.04860.29940.09380.964-0.6121-39.1668-28.8786
102.8728-0.306-0.19882.52130.35220.9995-0.04820.0196-0.06240.03910.04280.0277-0.0545-0.07570.00540.01670.0127-0.06110.0123-0.03920.3477-29.3526-10.344310.6928
111.84761.0348-0.30976.4379-4.56953.82470.4550.2140.41440.5289-0.16040.2138-0.67620.0516-0.29460.60920.03950.07730.43860.02970.6987-43.08512.4735-13.2668
124.9104-1.24410.49885.6339-0.12914.75240.33970.67760.0908-0.9023-0.2685-1.2446-0.01170.2594-0.07120.79270.16940.17240.51940.0921.0313-25.8948-12.1349-27.959
132.2762-0.0382-0.33083.58330.15770.98810.11520.04890.16770.1313-0.06890.119-0.1283-0.1584-0.04630.1166-0.014-0.06710.03790.02590.3916-21.017728.697610.8966
143.09431.5333-1.81741.1718-1.37686.0268-0.120.21750.4772-0.30920.16940.178-0.18680.4105-0.04940.7205-0.0305-0.12510.39940.19070.8533-20.181747.1596-13.3455
153.24510.0853-0.04265.56680.053.9209-0.29630.5017-0.9791-0.72430.4085-0.98920.21580.1719-0.11221.1887-0.2062-0.00210.6872-0.01311.2471-21.745524.4271-27.7046
162.37321.1137-0.26712.8954-0.07460.98190.0791-0.16320.06670.0343-0.0619-0.0138-0.0918-0.0543-0.01720.05340.0045-0.10460.02490.0220.42914.86946.089.9271
170.9968-0.8798-1.65091.16682.55456.25040.02460.03750.28920.020.2492-0.35440.16860.7489-0.27380.42190.0855-0.01550.2678-0.00450.722229.561256.1608-14.8209
185.2994-0.3284-0.22473.86050.50962.77160.010.3037-1.5188-0.21080.10240.26510.66920.046-0.11230.56970.0624-0.07350.3349-0.09831.054510.930642.4475-28.6423
193.6221-0.19990.15882.38630.13431.1448-0.1410.01490.04480.02980.1528-0.1105-0.14630.2258-0.01170.12330.0286-0.05330.10990.05620.331850.932629.06599.0607
200.6457-0.4145-0.10231.17482.16436.01070.27520.2083-0.1892-0.05120.0274-0.34540.43850.3489-0.30250.4550.0843-0.03610.70040.08640.855368.0523.8326-15.7332
216.6938-0.4617-0.28044.7481-0.03484.24770.20520.6244-0.6053-0.5105-0.24550.93750.0742-0.20110.04040.66960.2941-0.17630.7528-0.10920.973645.962730.1345-29.7837
223.2804-0.0039-0.06142.6072-0.2720.7432-0.1140.15820.09810.05160.14840.0812-0.1018-0.1268-0.03440.1568-0.0036-0.04220.12820.01350.4098-7.014739.916744.0013
232.41182.334-0.07344.9717-3.07264.91540.0767-0.104-0.0718-0.09880.32380.36670.1755-0.7583-0.40050.43750.1230.04460.5717-0.00170.7235-24.577840.359968.8946
244.9374-0.3329-0.59745.4153-0.0383.67760.2172-0.2145-0.32020.3141-0.0179-0.70210.01420.3329-0.19930.5980.046-0.05370.6176-0.05290.7974-1.39637.655982.3146
252.69320.12960.11182.20680.1981.06420.0019-0.07170.0041-0.1381-0.02310.02910.0438-0.18450.02120.0656-0.0086-0.04130.15160.00040.3778-29.39766.925744.1654
261.11780.72461.28254.936-2.28015.22410.0578-0.0757-0.41730.18310.11950.1750.538-0.1424-0.17730.4254-0.03960.00970.5790.00780.6622-40.9505-7.121368.6091
274.53711.9794-0.44434.4794-0.16433.29660.2737-0.4404-0.11250.6092-0.1302-0.87580.09370.1453-0.14350.8013-0.0578-0.11810.6287-0.01080.907-24.53278.976182.6079
282.2201-0.5262-0.00033.1226-0.04240.81670.0796-0.0085-0.1333-0.0261-0.09290.11950.189-0.10230.01320.1802-0.0178-0.00410.1655-0.02450.3669-17.7805-31.187543.6356
292.2543-0.55952.44290.4483-1.15695.78020.20740.1078-0.33770.2511-0.0764-0.23450.28960.3614-0.13090.8215-0.065-0.03780.46550.05020.9289-14.4273-49.648867.7303
303.54410.126-0.42393.93240.46623.74990.1005-0.30870.80130.45230.0963-0.4112-0.1829-0.0301-0.19680.96170.0467-0.02060.69890.03741.0264-16.8658-27.155782.3135
313.8005-1.12150.02192.41820.5270.85150.0376-0.0018-0.16880.1796-0.0068-0.14090.15380.1155-0.03080.1826-0.003-0.05650.19410.03170.43719.3085-45.835942.9683
323.92140.69881.10450.18490.09423.65390.3402-0.0667-0.21430.19550.1266-0.1427-0.14520.4817-0.46690.82820.1576-0.10160.82270.09341.028435.5012-55.393667.0693
333.2969-1.2206-0.50941.7179-0.55741.59470.1714-0.2520.48720.23870.16810.3544-0.4518-0.2266-0.33951.20050.07860.07091.20370.10851.187715.9839-44.145781.7781
343.26590.4834-0.22022.03570.10360.9967-0.0463-0.0108-0.0818-0.07590.0582-0.12630.09230.2223-0.01190.17090.0093-0.06740.24960.03340.389753.8079-25.945642.4951
350.56531.02941.33883.82313.15756.26680.1698-0.13270.11260.05080.1221-0.3456-0.5430.3327-0.2920.5524-0.0247-0.00390.87360.0390.852770.9645-19.339966.903
363.57691.32720.73732.75030.2612.48650.6598-0.86640.11140.631-0.73011.18870.0453-0.29360.07031.1304-0.30410.17041.3041-0.06471.407749.9241-27.515681.7111
372.9360.2869-0.33913.0010.08440.8507-0.0192-0.01030.0408-0.12140.07180.0476-0.08040.1458-0.05260.0764-0.0043-0.0880.21290.02570.366759.923113.44142.3687
382.3738-2.1909-2.09364.1380.38316.33140.2116-0.28860.34320.20090.24970.2194-0.7925-0.1816-0.46130.5071-0.03620.02720.6469-0.03940.724765.16830.875166.7892
391.6106-0.2225-0.42135.823-1.07163.3211-0.1363-0.2406-0.77850.53010.31631.4720.114-0.5399-0.180.63430.0670.24260.93890.08561.409457.57749.222380.9408
402.6558-0.3279-0.20963.2492-0.04291.08860.11170.06790.19470.0508-0.0329-0.1104-0.2750.1733-0.07880.1505-0.0211-0.06280.1761-0.00090.454932.841742.857342.9014
413.5482-1.1513-3.65821.51891.20313.9619-0.1069-0.10130.17660.18650.28380.24660.0349-0.2265-0.1770.7420.0855-0.12610.6746-0.03510.898922.927457.707867.6153
422.525-2.9293-0.01324.8915-0.21292.569-0.4545-1.0414-1.37520.50030.78040.73260.2233-0.1394-0.32590.92870.19490.01921.35840.35531.686735.807738.429781.2544
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