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- PDB-9bkx: Mycobacterium tuberculosis encapsulin in complex with DyP -

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Basic information

Entry
Database: PDB / ID: 9bkx
TitleMycobacterium tuberculosis encapsulin in complex with DyP
Components
  • Dye-decolorizing peroxidase
  • Type 1 encapsulin shell protein
KeywordsPROTEIN BINDING / Encapsulin / DyP
Function / homology
Function and homology information


encapsulin nanocompartment / peroxidase / peroxidase activity / heme binding / extracellular region / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Type 1 encapsulin shell protein / : / Encapsulating protein for peroxidase / : / : / Dyp-type peroxidase, C-terminal / Dyp-type peroxidase, N-terminal / DyP-type peroxidase family. / Dyp-type peroxidase / Dimeric alpha-beta barrel
Similarity search - Domain/homology
NICKEL (II) ION / Type 1 encapsulin shell protein / Dye-decolorizing peroxidase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsCuthbert, B.J. / Batot, G.O. / Contreras, H. / Chen, X. / Burley, K.H. / Goulding, C.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Microorganisms / Year: 2024
Title: Structural Characterization of Mycobacterium tuberculosis Encapsulin in Complex with Dye-Decolorizing Peroxide.
Authors: Cuthbert, B.J. / Chen, X. / Burley, K. / Batot, G. / Contreras, H. / Dixon, S. / Goulding, C.W.
History
DepositionApr 29, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2025Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Type 1 encapsulin shell protein
B: Type 1 encapsulin shell protein
C: Type 1 encapsulin shell protein
D: Type 1 encapsulin shell protein
E: Type 1 encapsulin shell protein
F: Type 1 encapsulin shell protein
G: Type 1 encapsulin shell protein
H: Type 1 encapsulin shell protein
I: Type 1 encapsulin shell protein
J: Type 1 encapsulin shell protein
K: Type 1 encapsulin shell protein
L: Type 1 encapsulin shell protein
M: Type 1 encapsulin shell protein
N: Type 1 encapsulin shell protein
O: Type 1 encapsulin shell protein
P: Type 1 encapsulin shell protein
Q: Type 1 encapsulin shell protein
R: Type 1 encapsulin shell protein
S: Type 1 encapsulin shell protein
T: Type 1 encapsulin shell protein
d: Dye-decolorizing peroxidase
g: Dye-decolorizing peroxidase
h: Dye-decolorizing peroxidase
i: Dye-decolorizing peroxidase
p: Dye-decolorizing peroxidase
q: Dye-decolorizing peroxidase
r: Dye-decolorizing peroxidase
s: Dye-decolorizing peroxidase
t: Dye-decolorizing peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)955,511187
Polymers934,00329
Non-polymers21,509158
Water7,062392
1
A: Type 1 encapsulin shell protein
B: Type 1 encapsulin shell protein
C: Type 1 encapsulin shell protein
D: Type 1 encapsulin shell protein
E: Type 1 encapsulin shell protein
F: Type 1 encapsulin shell protein
G: Type 1 encapsulin shell protein
H: Type 1 encapsulin shell protein
I: Type 1 encapsulin shell protein
J: Type 1 encapsulin shell protein
K: Type 1 encapsulin shell protein
L: Type 1 encapsulin shell protein
M: Type 1 encapsulin shell protein
N: Type 1 encapsulin shell protein
O: Type 1 encapsulin shell protein
P: Type 1 encapsulin shell protein
Q: Type 1 encapsulin shell protein
R: Type 1 encapsulin shell protein
S: Type 1 encapsulin shell protein
T: Type 1 encapsulin shell protein
d: Dye-decolorizing peroxidase
g: Dye-decolorizing peroxidase
h: Dye-decolorizing peroxidase
i: Dye-decolorizing peroxidase
p: Dye-decolorizing peroxidase
q: Dye-decolorizing peroxidase
r: Dye-decolorizing peroxidase
s: Dye-decolorizing peroxidase
t: Dye-decolorizing peroxidase
hetero molecules

A: Type 1 encapsulin shell protein
B: Type 1 encapsulin shell protein
C: Type 1 encapsulin shell protein
D: Type 1 encapsulin shell protein
E: Type 1 encapsulin shell protein
F: Type 1 encapsulin shell protein
G: Type 1 encapsulin shell protein
H: Type 1 encapsulin shell protein
I: Type 1 encapsulin shell protein
J: Type 1 encapsulin shell protein
K: Type 1 encapsulin shell protein
L: Type 1 encapsulin shell protein
M: Type 1 encapsulin shell protein
N: Type 1 encapsulin shell protein
O: Type 1 encapsulin shell protein
P: Type 1 encapsulin shell protein
Q: Type 1 encapsulin shell protein
R: Type 1 encapsulin shell protein
S: Type 1 encapsulin shell protein
T: Type 1 encapsulin shell protein
d: Dye-decolorizing peroxidase
g: Dye-decolorizing peroxidase
h: Dye-decolorizing peroxidase
i: Dye-decolorizing peroxidase
p: Dye-decolorizing peroxidase
q: Dye-decolorizing peroxidase
r: Dye-decolorizing peroxidase
s: Dye-decolorizing peroxidase
t: Dye-decolorizing peroxidase
hetero molecules

A: Type 1 encapsulin shell protein
B: Type 1 encapsulin shell protein
C: Type 1 encapsulin shell protein
D: Type 1 encapsulin shell protein
E: Type 1 encapsulin shell protein
F: Type 1 encapsulin shell protein
G: Type 1 encapsulin shell protein
H: Type 1 encapsulin shell protein
I: Type 1 encapsulin shell protein
J: Type 1 encapsulin shell protein
K: Type 1 encapsulin shell protein
L: Type 1 encapsulin shell protein
M: Type 1 encapsulin shell protein
N: Type 1 encapsulin shell protein
O: Type 1 encapsulin shell protein
P: Type 1 encapsulin shell protein
Q: Type 1 encapsulin shell protein
R: Type 1 encapsulin shell protein
S: Type 1 encapsulin shell protein
T: Type 1 encapsulin shell protein
d: Dye-decolorizing peroxidase
g: Dye-decolorizing peroxidase
h: Dye-decolorizing peroxidase
i: Dye-decolorizing peroxidase
p: Dye-decolorizing peroxidase
q: Dye-decolorizing peroxidase
r: Dye-decolorizing peroxidase
s: Dye-decolorizing peroxidase
t: Dye-decolorizing peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,866,534561
Polymers2,802,00887
Non-polymers64,526474
Water1,08160
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z+1/2,-x,y+1/21
crystal symmetry operation10_545-y,z-1/2,-x+1/21
Unit cell
Length a, b, c (Å)313.451, 313.451, 313.451
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Space group name HallP2ac2ab3
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y+1/2,-z,x+1/2
#5: z+1/2,-x+1/2,-y
#6: -y,z+1/2,-x+1/2
#7: -z+1/2,-x,y+1/2
#8: -z,x+1/2,-y+1/2
#9: y+1/2,-z+1/2,-x
#10: x+1/2,-y+1/2,-z
#11: -x,y+1/2,-z+1/2
#12: -x+1/2,-y,z+1/2
Components on special symmetry positions
IDModelComponents
11H-414-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 58 or (resid 59...
d_2ens_1(chain "B" and (resid 1 through 27 or (resid 28...
d_3ens_1(chain "C" and (resid 1 through 27 or (resid 28...
d_4ens_1(chain "D" and (resid 1 through 27 or (resid 28...
d_5ens_1(chain "E" and (resid 1 through 27 or (resid 28...
d_6ens_1(chain "F" and (resid 1 through 27 or (resid 28...
d_7ens_1(chain "G" and (resid 1 through 27 or (resid 28...
d_8ens_1(chain "H" and (resid 1 through 27 or (resid 28...
d_9ens_1(chain "I" and (resid 1 through 27 or (resid 28...
d_10ens_1(chain "J" and (resid 1 through 27 or (resid 28...
d_11ens_1(chain "K" and (resid 1 through 27 or (resid 28...
d_12ens_1(chain "L" and (resid 1 through 58 or (resid 59...
d_13ens_1(chain "M" and (resid 1 through 27 or (resid 28...
d_14ens_1(chain "N" and (resid 1 through 58 or (resid 59...
d_15ens_1(chain "O" and (resid 1 through 27 or (resid 28...
d_16ens_1(chain "P" and (resid 1 through 58 or (resid 59...
d_17ens_1(chain "Q" and (resid 1 through 58 or (resid 59...
d_18ens_1(chain "R" and (resid 1 through 27 or (resid 28...
d_19ens_1(chain "S" and (resid 1 through 27 or (resid 28...
d_20ens_1(chain "T" and (resid 1 through 27 or (resid 28...
d_1ens_2(chain "d" and (resid 323 through 328 or (resid 329...
d_2ens_2(chain "h" and ((resid 323 through 326 and (name N...
d_3ens_2(chain "s" and ((resid 323 through 326 and (name N...
d_1ens_3(chain "p" and ((resid 325 through 327 and (name N...
d_2ens_3(chain "q" and ((resid 325 through 327 and (name N...
d_3ens_3(chain "t" and ((resid 325 through 327 and (name N...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1METMETLEULEUAA1 - 691 - 69
d_12ens_1ALAALASERSERAA71 - 7271 - 72
d_13ens_1PROPROASPASPAA74 - 11674 - 116
d_14ens_1THRTHRSERSERAA118 - 154118 - 154
d_15ens_1ALAALAILEILEAA156 - 209156 - 209
d_16ens_1GLYGLYSERSERAA211 - 264211 - 264
d_21ens_1METMETLEULEUBB1 - 691 - 69
d_22ens_1ALAALASERSERBB71 - 7271 - 72
d_23ens_1PROPROASPASPBB74 - 11674 - 116
d_24ens_1THRTHRSERSERBB118 - 154118 - 154
d_25ens_1ALAALAILEILEBB156 - 209156 - 209
d_26ens_1GLYGLYSERSERBB211 - 264211 - 264
d_31ens_1METMETLEULEUCC1 - 691 - 69
d_32ens_1ALAALASERSERCC71 - 7271 - 72
d_33ens_1PROPROASPASPCC74 - 11674 - 116
d_34ens_1THRTHRSERSERCC118 - 154118 - 154
d_35ens_1ALAALAILEILECC156 - 209156 - 209
d_36ens_1GLYGLYSERSERCC211 - 264211 - 264
d_41ens_1METMETLEULEUDD1 - 691 - 69
d_42ens_1ALAALASERSERDD71 - 7271 - 72
d_43ens_1PROPROASPASPDD74 - 11674 - 116
d_44ens_1THRTHRSERSERDD118 - 154118 - 154
d_45ens_1ALAALAILEILEDD156 - 209156 - 209
d_46ens_1GLYGLYSERSERDD211 - 264211 - 264
d_51ens_1METMETLEULEUEE1 - 691 - 69
d_52ens_1ALAALASERSEREE71 - 7271 - 72
d_53ens_1PROPROASPASPEE74 - 11674 - 116
d_54ens_1THRTHRSERSEREE118 - 154118 - 154
d_55ens_1ALAALAILEILEEE156 - 209156 - 209
d_56ens_1GLYGLYSERSEREE211 - 264211 - 264
d_61ens_1METMETLEULEUFF1 - 691 - 69
d_62ens_1ALAALASERSERFF71 - 7271 - 72
d_63ens_1PROPROASPASPFF74 - 11674 - 116
d_64ens_1THRTHRSERSERFF118 - 154118 - 154
d_65ens_1ALAALAILEILEFF156 - 209156 - 209
d_66ens_1GLYGLYSERSERFF211 - 264211 - 264
d_71ens_1METMETLEULEUGG1 - 691 - 69
d_72ens_1ALAALASERSERGG71 - 7271 - 72
d_73ens_1PROPROASPASPGG74 - 11674 - 116
d_74ens_1THRTHRSERSERGG118 - 154118 - 154
d_75ens_1ALAALAILEILEGG156 - 209156 - 209
d_76ens_1GLYGLYSERSERGG211 - 264211 - 264
d_81ens_1METMETLEULEUHH1 - 691 - 69
d_82ens_1ALAALASERSERHH71 - 7271 - 72
d_83ens_1PROPROASPASPHH74 - 11674 - 116
d_84ens_1THRTHRSERSERHH118 - 154118 - 154
d_85ens_1ALAALAILEILEHH156 - 209156 - 209
d_86ens_1GLYGLYSERSERHH211 - 264211 - 264
d_91ens_1METMETLEULEUII1 - 691 - 69
d_92ens_1ALAALASERSERII71 - 7271 - 72
d_93ens_1PROPROASPASPII74 - 11674 - 116
d_94ens_1THRTHRSERSERII118 - 154118 - 154
d_95ens_1ALAALAILEILEII156 - 209156 - 209
d_96ens_1GLYGLYSERSERII211 - 264211 - 264
d_101ens_1METMETLEULEUJJ1 - 691 - 69
d_102ens_1ALAALASERSERJJ71 - 7271 - 72
d_103ens_1PROPROASPASPJJ74 - 11674 - 116
d_104ens_1THRTHRSERSERJJ118 - 154118 - 154
d_105ens_1ALAALAILEILEJJ156 - 209156 - 209
d_106ens_1GLYGLYSERSERJJ211 - 264211 - 264
d_111ens_1METMETLEULEUKK1 - 691 - 69
d_112ens_1ALAALASERSERKK71 - 7271 - 72
d_113ens_1PROPROASPASPKK74 - 11674 - 116
d_114ens_1THRTHRSERSERKK118 - 154118 - 154
d_115ens_1ALAALAILEILEKK156 - 209156 - 209
d_116ens_1GLYGLYSERSERKK211 - 264211 - 264
d_121ens_1METMETLEULEULL1 - 691 - 69
d_122ens_1ALAALASERSERLL71 - 7271 - 72
d_123ens_1PROPROASPASPLL74 - 11674 - 116
d_124ens_1THRTHRSERSERLL118 - 154118 - 154
d_125ens_1ALAALAILEILELL156 - 209156 - 209
d_126ens_1GLYGLYSERSERLL211 - 264211 - 264
d_131ens_1METMETLEULEUMM1 - 691 - 69
d_132ens_1ALAALASERSERMM71 - 7271 - 72
d_133ens_1PROPROASPASPMM74 - 11674 - 116
d_134ens_1THRTHRSERSERMM118 - 154118 - 154
d_135ens_1ALAALAILEILEMM156 - 209156 - 209
d_136ens_1GLYGLYSERSERMM211 - 264211 - 264
d_141ens_1METMETLEULEUNN1 - 691 - 69
d_142ens_1ALAALASERSERNN71 - 7271 - 72
d_143ens_1PROPROASPASPNN74 - 11674 - 116
d_144ens_1THRTHRSERSERNN118 - 154118 - 154
d_145ens_1ALAALAILEILENN156 - 209156 - 209
d_146ens_1GLYGLYSERSERNN211 - 264211 - 264
d_151ens_1METMETLEULEUOO1 - 691 - 69
d_152ens_1ALAALASERSEROO71 - 7271 - 72
d_153ens_1PROPROASPASPOO74 - 11674 - 116
d_154ens_1THRTHRSERSEROO118 - 154118 - 154
d_155ens_1ALAALAILEILEOO156 - 209156 - 209
d_156ens_1GLYGLYSERSEROO211 - 264211 - 264
d_161ens_1METMETLEULEUPP1 - 691 - 69
d_162ens_1ALAALASERSERPP71 - 7271 - 72
d_163ens_1PROPROASPASPPP74 - 11674 - 116
d_164ens_1THRTHRSERSERPP118 - 154118 - 154
d_165ens_1ALAALAILEILEPP156 - 209156 - 209
d_166ens_1GLYGLYSERSERPP211 - 264211 - 264
d_171ens_1METMETLEULEUQQ1 - 691 - 69
d_172ens_1ALAALASERSERQQ71 - 7271 - 72
d_173ens_1PROPROASPASPQQ74 - 11674 - 116
d_174ens_1THRTHRSERSERQQ118 - 154118 - 154
d_175ens_1ALAALAILEILEQQ156 - 209156 - 209
d_176ens_1GLYGLYSERSERQQ211 - 264211 - 264
d_181ens_1METMETLEULEURR1 - 691 - 69
d_182ens_1ALAALASERSERRR71 - 7271 - 72
d_183ens_1PROPROASPASPRR74 - 11674 - 116
d_184ens_1THRTHRSERSERRR118 - 154118 - 154
d_185ens_1ALAALAILEILERR156 - 209156 - 209
d_186ens_1GLYGLYSERSERRR211 - 264211 - 264
d_191ens_1METMETLEULEUSS1 - 691 - 69
d_192ens_1ALAALASERSERSS71 - 7271 - 72
d_193ens_1PROPROASPASPSS74 - 11674 - 116
d_194ens_1THRTHRSERSERSS118 - 154118 - 154
d_195ens_1ALAALAILEILESS156 - 209156 - 209
d_196ens_1GLYGLYSERSERSS211 - 264211 - 264
d_201ens_1METMETLEULEUTT1 - 691 - 69
d_202ens_1ALAALASERSERTT71 - 7271 - 72
d_203ens_1PROPROASPASPTT74 - 11674 - 116
d_204ens_1THRTHRSERSERTT118 - 154118 - 154
d_205ens_1ALAALAILEILETT156 - 209156 - 209
d_206ens_1GLYGLYSERSERTT211 - 264211 - 264
d_11ens_2GLYGLYLYSLYSdU323 - 331323 - 331
d_21ens_2GLYGLYLYSLYShW323 - 331323 - 331
d_31ens_2GLYGLYLYSLYSsBA323 - 331323 - 331
d_11ens_3LEULEULYSLYSpY325 - 331325 - 331
d_21ens_3LEULEULYSLYSqZ325 - 331325 - 331
d_31ens_3LEULEULYSLYStCA325 - 331325 - 331

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(0.452796390353, 0.747638971167, 0.48581004279), (-0.316977178559, 0.644251206959, -0.696035811295), (-0.833367204272, 0.161171806231, 0.528699112653)64.0334255436, 52.29089352, 116.230365538
2given(-0.994294807255, -0.0723375413923, 0.0783907926389), (-0.072611508193, -0.0793347096853, -0.994199966162), (0.0781370919804, -0.99421993741, 0.0736295518957)144.349608494, -0.988411505533, -11.6784716644
3given(0.356383312901, -0.336379865505, 0.871687742468), (0.0116346770282, 0.934470419955, 0.355850626695), (-0.934267396721, -0.116677419886, 0.336943335165)-44.5876039079, -33.0541980337, 116.867396232
4given(0.33429303132, -0.936395914374, 0.106821630555), (0.876262745149, 0.350537857671, 0.330585558976), (-0.347003992304, -0.016908633389, 0.937711217509)-29.7830026736, -145.826450659, 30.8027447742
5given(-0.495623031541, -0.778226307364, -0.385644428371), (0.819363706635, -0.271662220203, -0.504819526528), (0.288098814395, -0.566183232392, 0.772292444934)86.3652309872, -125.464972603, -49.7610336102
6given(-0.46810455043, 0.192801978504, 0.862383630962), (-0.577077156466, 0.672378054179, -0.46356197832), (-0.669223494321, -0.714657364996, -0.203481609255)63.3089165065, 56.7779784205, 90.4771844704
7given(0.17719968804, -0.508802374922, -0.842449057114), (0.748769006961, -0.485823180871, 0.450911090064), (-0.638705914152, -0.710701048404, 0.294887732916)89.1360119029, -210.606056558, 48.9994350263
8given(-0.706998388217, 0.201974104705, -0.677760828085), (0.201637266194, -0.861005739024, -0.466917048574), (-0.677861115524, -0.466771441282, 0.568004163421)202.388227556, -124.791050548, 49.7403198013
9given(-0.498717221038, 0.818366679033, 0.285582058413), (-0.777428195592, -0.27665141043, -0.564862282158), (-0.383257790707, -0.503726091993, 0.77419215322)160.151127021, 4.81326132784, 7.86856894837
10given(0.520792018147, 0.477980306504, 0.707326304069), (-0.83574905442, 0.454410778879, 0.308276437754), (-0.174066630548, -0.751695197958, 0.636125095793)20.0635147662, -1.1522007493, -17.4210821016
11given(0.939118112894, -0.343488665288, 0.0085268314277), (0.109282076027, 0.322127466356, 0.94036765325), (-0.325752356698, -0.882184466106, 0.34005289275)-23.838344346, -134.632690262, 7.21722759449
12given(-0.281187553991, 0.491728435153, 0.824097509729), (0.565323840692, 0.778800037452, -0.271807757082), (-0.775462774494, 0.389453010935, -0.496974685118)75.1236283001, -39.7541447612, 208.382115591
13given(0.636890267949, -0.178260716914, 0.750062599652), (0.707058903858, 0.522863454607, -0.476110821461), (-0.307308465661, 0.833568788188, 0.459047472807)-43.8713989536, -55.1526287678, 132.192824144
14given(0.523178528558, -0.833495628477, -0.177677417151), (0.479334723607, 0.460179755854, -0.747310387354), (0.70464349142, 0.305809793191, 0.640279564244)-14.5838610286, -21.0515898891, -3.06746157433
15given(-0.47030117029, -0.568049990726, -0.675378425226), (0.199682668115, 0.676951905478, -0.708422860814), (0.859618311391, -0.468033466437, -0.204941535605)123.179376106, 15.071590211, -10.2358076585
16given(-0.966916093381, 0.249551359057, -0.052890335158), (0.248849154253, 0.877148058549, -0.410713259843), (-0.0561013973766, -0.410286975879, -0.910229218733)178.503490737, 3.89540699507, 120.671727579
17given(0.453372175255, -0.304472103866, -0.837705442666), (0.747488371603, 0.641815404507, 0.171272066768), (0.48550469104, -0.703825066693, 0.518570603171)84.4895016809, -100.343726337, -56.2218174552
18given(-0.429580828242, 0.256655718913, -0.865787591709), (0.901451743355, 0.0652497891843, -0.427933662398), (-0.0533391639323, -0.964297831046, -0.259392803736)200.551352559, -111.223096409, 26.254656716
19given(-0.423430468548, 0.904146918826, -0.0567889732431), (0.25330897725, 0.0579780411517, -0.96564647195), (-0.869793768861, -0.423269294801, -0.253578200422)187.204248951, -17.9493923483, 133.033597353
20given(0.087737654351, -0.860423961856, 0.501968833567), (-0.449855594915, 0.415377694259, 0.790627165506), (-0.888781214773, -0.295181261221, -0.350622268676)46.7863832221, -126.381234275, 11.8028487085
21given(-0.945567267995, -0.220896348323, -0.238971431336), (0.277331774266, -0.162780328546, -0.94688418068), (0.170263409691, -0.961617058884, 0.215181326755)147.785473043, -8.69910838568, -16.0004339474
22given(0.234624712273, -0.136705285908, -0.962425534364), (-0.33955966322, 0.916169563435, -0.212914457353), (0.910851513423, 0.376755883618, 0.168536419371)138.34667166, 38.5658165379, 21.4283136217
23given(-0.207163774026, 0.483914303139, -0.850241211627), (0.403531901884, 0.833984504886, 0.376340071971), (0.891204339584, -0.265135423562, -0.368046236606)205.405173779, -78.8203162115, 14.3519387595

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Components

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Protein , 2 types, 29 molecules ABCDEFGHIJKLMNOPQRSTdghipqrst

#1: Protein
Type 1 encapsulin shell protein / Culture filtrate protein 29 / CFP29


Mass: 30461.139 Da / Num. of mol.: 20
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: enc, cfp29, Rv0798c / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: I6WZG6
#2: Protein
Dye-decolorizing peroxidase / DyP


Mass: 36086.637 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: dyp, Rv0799c / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: I6Y4U9, peroxidase

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Non-polymers , 6 types, 550 molecules

#3: Chemical...
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 41 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical
ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#5: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 78 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical...
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 33 / Source method: obtained synthetically / Formula: Ni
#7: Chemical ChemComp-12P / DODECAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 546.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H50O13 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 392 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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Experimental details

-
Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Trimethlyamine N-oxide (TMN), 0.1 M Tris-HCl pH 8.5, and 20% polyethylene glycol MME 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.15→54.56 Å / Num. obs: 174789 / % possible obs: 99.4 % / Redundancy: 4.5 % / Biso Wilson estimate: 52.51 Å2 / CC1/2: 0.957 / Rmerge(I) obs: 0.204 / Rpim(I) all: 0.155 / Rrim(I) all: 0.257 / Χ2: 0.98 / Net I/σ(I): 7.4
Reflection shellResolution: 3.15→3.2 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.887 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 8661 / CC1/2: 0.507 / Rpim(I) all: 0.683 / Rrim(I) all: 1.125 / Χ2: 0.99 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
MOSFLMdata reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.15→49.56 Å / SU ML: 0.3743 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.6013
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2327 8545 4.89 %
Rwork0.2011 166127 -
obs0.2026 174672 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.28 Å2
Refinement stepCycle: LAST / Resolution: 3.15→49.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms41211 0 1121 392 42724
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001943084
X-RAY DIFFRACTIONf_angle_d0.526758338
X-RAY DIFFRACTIONf_chiral_restr0.0426725
X-RAY DIFFRACTIONf_plane_restr0.00457499
X-RAY DIFFRACTIONf_dihedral_angle_d13.445515919
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.434159192948
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.402124405418
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.443445639405
ens_1d_5AAX-RAY DIFFRACTIONTorsion NCS0.394349372794
ens_1d_6AAX-RAY DIFFRACTIONTorsion NCS0.423298591817
ens_1d_7AAX-RAY DIFFRACTIONTorsion NCS0.424123721501
ens_1d_8AAX-RAY DIFFRACTIONTorsion NCS0.323031491438
ens_1d_9AAX-RAY DIFFRACTIONTorsion NCS0.434042873653
ens_1d_10AAX-RAY DIFFRACTIONTorsion NCS0.41138606353
ens_1d_11AAX-RAY DIFFRACTIONTorsion NCS0.405849841182
ens_1d_12AAX-RAY DIFFRACTIONTorsion NCS0.482798988958
ens_1d_13AAX-RAY DIFFRACTIONTorsion NCS0.464366891365
ens_1d_14AAX-RAY DIFFRACTIONTorsion NCS0.471742079765
ens_1d_15AAX-RAY DIFFRACTIONTorsion NCS0.472514472529
ens_1d_16AAX-RAY DIFFRACTIONTorsion NCS0.47439348018
ens_1d_17AAX-RAY DIFFRACTIONTorsion NCS0.481841015055
ens_1d_18AAX-RAY DIFFRACTIONTorsion NCS0.494460476541
ens_1d_19AAX-RAY DIFFRACTIONTorsion NCS0.441091913119
ens_1d_20AAX-RAY DIFFRACTIONTorsion NCS0.416220099788
ens_2d_2UdX-RAY DIFFRACTIONTorsion NCS2.36215675186
ens_2d_3UdX-RAY DIFFRACTIONTorsion NCS2.79262793053
ens_3d_2YpX-RAY DIFFRACTIONTorsion NCS1.85511178293
ens_3d_3YpX-RAY DIFFRACTIONTorsion NCS1.33737234588
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.15-3.190.32423080.29475537X-RAY DIFFRACTION99.76
3.19-3.220.34892870.28595466X-RAY DIFFRACTION99.72
3.22-3.260.31292620.26785589X-RAY DIFFRACTION99.66
3.26-3.30.30623210.25685509X-RAY DIFFRACTION99.85
3.3-3.350.29242520.24295516X-RAY DIFFRACTION99.9
3.35-3.390.29142850.24895525X-RAY DIFFRACTION99.95
3.39-3.440.25112730.25395572X-RAY DIFFRACTION99.64
3.44-3.490.29112860.24675472X-RAY DIFFRACTION99.72
3.49-3.550.27212510.22695582X-RAY DIFFRACTION99.91
3.55-3.610.25692960.23875560X-RAY DIFFRACTION99.83
3.61-3.670.28522560.22965529X-RAY DIFFRACTION99.79
3.67-3.730.26132910.21325541X-RAY DIFFRACTION99.79
3.74-3.810.22852800.19285539X-RAY DIFFRACTION99.71
3.81-3.880.23532940.19945516X-RAY DIFFRACTION99.9
3.88-3.970.24472810.18725550X-RAY DIFFRACTION99.76
3.97-4.060.21643400.1765489X-RAY DIFFRACTION99.79
4.06-4.160.22853190.18525469X-RAY DIFFRACTION99.81
4.16-4.280.20932810.17215611X-RAY DIFFRACTION99.75
4.28-4.40.20072620.16245529X-RAY DIFFRACTION99.5
4.4-4.540.19333420.16525488X-RAY DIFFRACTION99.61
4.54-4.70.17672780.14985525X-RAY DIFFRACTION99.28
4.71-4.890.1892940.15365556X-RAY DIFFRACTION99.2
4.89-5.120.19853180.16295476X-RAY DIFFRACTION99.04
5.12-5.380.20492350.19475567X-RAY DIFFRACTION98.84
5.39-5.720.2153190.20715476X-RAY DIFFRACTION98.27
5.72-6.160.24612340.21325487X-RAY DIFFRACTION97.49
6.16-6.780.23542860.21255559X-RAY DIFFRACTION98.83
6.78-7.760.24162720.20255594X-RAY DIFFRACTION98.8
7.76-9.760.18212660.16835597X-RAY DIFFRACTION98.49
9.77-49.560.20892760.21065701X-RAY DIFFRACTION97.47

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