[English] 日本語
Yorodumi
- PDB-7w7d: Heme exporter HrtBA in complex with heme -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7w7d
TitleHeme exporter HrtBA in complex with heme
Components
  • Putative ABC transport system integral membrane protein
  • Putative ABC transport system, ATP-binding protein
KeywordsMEMBRANE PROTEIN / Heme efflux / heme detoxification / heme extraction / ABC transporter / 4-helix TMD
Function / homology
Function and homology information


transmembrane transporter activity / ATP hydrolysis activity / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
: / MacB-like periplasmic core domain / MacB-like periplasmic core domain / ABC transporter, lipoprotein release, LolD / MacB, ATP-binding domain / ABC3 transporter permease protein domain / FtsX-like permease C-terminal / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter ...: / MacB-like periplasmic core domain / MacB-like periplasmic core domain / ABC transporter, lipoprotein release, LolD / MacB, ATP-binding domain / ABC3 transporter permease protein domain / FtsX-like permease C-terminal / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / ABC transport system integral membrane protein / ABC transport system, ATP-binding protein
Similarity search - Component
Biological speciesCorynebacterium diphtheriae NCTC 13129 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsHisano, T. / Nakamura, H. / Rahman, M.M. / Tosha, T. / Shiro, Y. / Shirouzu, M.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)26220807 Japan
Japan Society for the Promotion of Science (JSPS)16K07309 Japan
Japan Society for the Promotion of Science (JSPS)JP19H00926 Japan
Japan Society for the Promotion of Science (JSPS)JP19H05761 Japan
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Structural basis for heme detoxification by an ATP-binding cassette-type efflux pump in gram-positive pathogenic bacteria.
Authors: Nakamura, H. / Hisano, T. / Rahman, M.M. / Tosha, T. / Shirouzu, M. / Shiro, Y.
History
DepositionDec 4, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative ABC transport system, ATP-binding protein
B: Putative ABC transport system integral membrane protein
C: Putative ABC transport system, ATP-binding protein
D: Putative ABC transport system integral membrane protein
E: Putative ABC transport system, ATP-binding protein
F: Putative ABC transport system integral membrane protein
G: Putative ABC transport system, ATP-binding protein
H: Putative ABC transport system integral membrane protein
I: Putative ABC transport system, ATP-binding protein
J: Putative ABC transport system integral membrane protein
K: Putative ABC transport system, ATP-binding protein
L: Putative ABC transport system integral membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)365,53814
Polymers364,30512
Non-polymers1,2332
Water00
1
A: Putative ABC transport system, ATP-binding protein
B: Putative ABC transport system integral membrane protein
C: Putative ABC transport system, ATP-binding protein
D: Putative ABC transport system integral membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,0525
Polymers121,4354
Non-polymers6161
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Putative ABC transport system, ATP-binding protein
F: Putative ABC transport system integral membrane protein
G: Putative ABC transport system, ATP-binding protein
H: Putative ABC transport system integral membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,0525
Polymers121,4354
Non-polymers6161
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
I: Putative ABC transport system, ATP-binding protein
J: Putative ABC transport system integral membrane protein
K: Putative ABC transport system, ATP-binding protein
L: Putative ABC transport system integral membrane protein


Theoretical massNumber of molelcules
Total (without water)121,4354
Polymers121,4354
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.585, 135.026, 160.969
Angle α, β, γ (deg.)112.488, 100.412, 93.776
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 5 through 19 or resid 21...
d_2ens_1(chain "C" and (resid 5 through 19 or resid 21...
d_3ens_1(chain "E" and (resid 5 through 19 or resid 21...
d_4ens_1(chain "G" and (resid 5 through 19 or resid 21...
d_5ens_1(chain "I" and (resid 5 through 19 or resid 21...
d_6ens_1(chain "K" and (resid 5 through 19 or resid 21...
d_1ens_2(chain "B" and (resid 1 through 8 or resid 10...
d_2ens_2(chain "D" and (resid 1 through 8 or resid 10...
d_3ens_2(chain "F" and (resid 1 through 8 or resid 10...
d_4ens_2(chain "H" and (resid 1 through 8 or resid 10...
d_5ens_2(chain "J" and (resid 1 through 8 or resid 10...
d_6ens_2(chain "L" and (resid 1 through 8 or resid 10...
d_1ens_3(chain "A" and resid 5 through 218)
d_2ens_3(chain "C" and resid 5 through 218)
d_3ens_3(chain "E" and resid 5 through 218)
d_4ens_3(chain "G" and resid 5 through 218)
d_1ens_4(chain "I" and resid 5 through 218)
d_2ens_4(chain "K" and resid 5 through 218)
d_1ens_5(chain "B" and (resid 1 through 42 or resid 215 through 341))
d_2ens_5(chain "D" and (resid 1 through 42 or resid 215 through 341))
d_3ens_5(chain "F" and (resid 1 through 42 or resid 215 through 341))
d_4ens_5(chain "H" and (resid 1 through 42 or resid 215 through 341))
d_1ens_6(chain "B" and resid 43 through 214)
d_2ens_6(chain "D" and resid 43 through 214)
d_3ens_6(chain "F" and resid 43 through 214)
d_4ens_6(chain "H" and resid 43 through 214)
d_1ens_7(chain "J" and (resid 1 through 42 or resid 215 through 343))
d_2ens_7(chain "L" and (resid 1 through 42 or resid 215 through 343))
d_1ens_8(chain "J" and resid 43 through 214)
d_2ens_8(chain "L" and resid 43 through 214)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1PROGLYA3 - 17
d_12ens_1SERGLYA19 - 41
d_13ens_1SERLEUA43 - 108
d_14ens_1GLYGLYA110 - 132
d_15ens_1VALLEUA135 - 180
d_16ens_1ASPTHRA182 - 195
d_17ens_1ASPASPA197
d_18ens_1SERVALA199 - 208
d_19ens_1METALAA210 - 215
d_21ens_1PROGLYD3 - 17
d_22ens_1SERGLYD19 - 41
d_23ens_1SERLEUD43 - 108
d_24ens_1GLYGLYD110 - 132
d_25ens_1VALLEUD135 - 180
d_26ens_1ASPTHRD182 - 195
d_27ens_1ASPASPD197
d_28ens_1SERVALD199 - 208
d_29ens_1METALAD210 - 215
d_31ens_1PROGLYF1 - 15
d_32ens_1SERGLYF17 - 39
d_33ens_1SERLEUF41 - 106
d_34ens_1GLYGLYF108 - 130
d_35ens_1VALLEUF133 - 178
d_36ens_1ASPTHRF180 - 193
d_37ens_1ASPASPF195
d_38ens_1SERVALF197 - 206
d_39ens_1METALAF208 - 213
d_41ens_1PROGLYI3 - 17
d_42ens_1SERGLYI19 - 41
d_43ens_1SERLEUI43 - 108
d_44ens_1GLYGLYI110 - 132
d_45ens_1VALLEUI135 - 180
d_46ens_1ASPTHRI182 - 195
d_47ens_1ASPASPI197
d_48ens_1SERVALI199 - 208
d_49ens_1METALAI210 - 215
d_51ens_1PROGLYK3 - 17
d_52ens_1SERGLYK19 - 41
d_53ens_1SERLEUK43 - 108
d_54ens_1GLYGLYK110 - 132
d_55ens_1VALLEUK135 - 180
d_56ens_1ASPTHRK182 - 195
d_57ens_1ASPASPK197
d_58ens_1SERVALK199 - 208
d_59ens_1METALAK210 - 215
d_61ens_1PROGLYM3 - 17
d_62ens_1SERGLYM19 - 41
d_63ens_1SERLEUM43 - 108
d_64ens_1GLYGLYM110 - 132
d_65ens_1VALLEUM135 - 180
d_66ens_1ASPTHRM182 - 195
d_67ens_1ASPASPM197
d_68ens_1SERVALM199 - 208
d_69ens_1METALAM210 - 215
d_11ens_2METILEB1 - 8
d_12ens_2ALAGLYB10 - 40
d_13ens_2GLNSERB42 - 73
d_14ens_2GLNALAB76 - 77
d_15ens_2TRPTRPB80
d_16ens_2ASPTHRB82 - 91
d_17ens_2ILEASPB93 - 96
d_18ens_2ASNPROB98 - 108
d_19ens_2GLYGLYB110 - 119
d_110ens_2ILEGLUB121 - 122
d_111ens_2GLYLEUB124 - 135
d_112ens_2VALALAB137 - 148
d_113ens_2VALTHRB150 - 180
d_114ens_2ALAASNB182 - 190
d_115ens_2GLUPHEB192 - 210
d_116ens_2ALAGLUB212 - 219
d_117ens_2SERALAB221 - 240
d_118ens_2LEULYSB242 - 263
d_119ens_2TYRVALB265 - 334
d_120ens_2PROALAB336 - 339
d_121ens_2GLYGLYB341
d_21ens_2METILEE1 - 8
d_22ens_2ALAGLYE10 - 40
d_23ens_2GLNSERE42 - 73
d_24ens_2GLNALAE76 - 77
d_25ens_2TRPTRPE80
d_26ens_2ASPTHRE82 - 91
d_27ens_2ILEASPE93 - 96
d_28ens_2ASNPROE98 - 108
d_29ens_2GLYGLYE110 - 119
d_210ens_2ILEGLUE121 - 122
d_211ens_2GLYLEUE124 - 135
d_212ens_2VALALAE137 - 148
d_213ens_2VALTHRE150 - 180
d_214ens_2ALAASNE182 - 190
d_215ens_2GLUPHEE192 - 210
d_216ens_2ALAGLUE212 - 219
d_217ens_2SERALAE221 - 240
d_218ens_2LEULYSE242 - 263
d_219ens_2TYRVALE265 - 334
d_220ens_2PROALAE336 - 339
d_221ens_2GLYGLYE341
d_31ens_2METILEG1 - 8
d_32ens_2ALAGLYG10 - 40
d_33ens_2GLNSERG42 - 73
d_34ens_2GLNALAG76 - 77
d_35ens_2TRPTRPG80
d_36ens_2ASPTHRG82 - 91
d_37ens_2ILEASPG93 - 96
d_38ens_2ASNPROG98 - 108
d_39ens_2GLYGLYG110 - 119
d_310ens_2ILEGLUG121 - 122
d_311ens_2GLYLEUG124 - 135
d_312ens_2VALALAG137 - 148
d_313ens_2VALTHRG150 - 180
d_314ens_2ALAASNG182 - 190
d_315ens_2GLUPHEG192 - 210
d_316ens_2ALAGLUG212 - 219
d_317ens_2SERALAG221 - 240
d_318ens_2LEULYSG242 - 263
d_319ens_2TYRVALG265 - 334
d_320ens_2PROALAG336 - 339
d_321ens_2GLYGLYG341
d_41ens_2METILEJ1 - 8
d_42ens_2ALAGLYJ10 - 40
d_43ens_2GLNSERJ42 - 73
d_44ens_2GLNALAJ76 - 77
d_45ens_2TRPTRPJ80
d_46ens_2ASPTHRJ82 - 91
d_47ens_2ILEASPJ93 - 96
d_48ens_2ASNPROJ98 - 108
d_49ens_2GLYGLYJ110 - 119
d_410ens_2ILEGLUJ121 - 122
d_411ens_2GLYLEUJ124 - 135
d_412ens_2VALALAJ137 - 148
d_413ens_2VALTHRJ150 - 180
d_414ens_2ALAASNJ182 - 190
d_415ens_2GLUPHEJ192 - 210
d_416ens_2ALAGLUJ212 - 219
d_417ens_2SERALAJ221 - 240
d_418ens_2LEULYSJ242 - 263
d_419ens_2TYRVALJ265 - 334
d_420ens_2PROALAJ336 - 339
d_421ens_2GLYGLYJ341
d_51ens_2METILEL1 - 8
d_52ens_2ALAGLYL10 - 40
d_53ens_2GLNSERL42 - 73
d_54ens_2GLNALAL76 - 77
d_55ens_2TRPTRPL80
d_56ens_2ASPTHRL82 - 91
d_57ens_2ILEASPL93 - 96
d_58ens_2ASNPROL98 - 108
d_59ens_2GLYGLYL110 - 119
d_510ens_2ILEGLUL121 - 122
d_511ens_2GLYLEUL124 - 135
d_512ens_2VALALAL137 - 148
d_513ens_2VALTHRL150 - 180
d_514ens_2ALAASNL182 - 190
d_515ens_2GLUPHEL192 - 210
d_516ens_2ALAGLUL212 - 219
d_517ens_2SERALAL221 - 240
d_518ens_2LEULYSL242 - 263
d_519ens_2TYRVALL265 - 334
d_520ens_2PROALAL336 - 339
d_521ens_2GLYGLYL341
d_61ens_2METILEN1 - 8
d_62ens_2ALAGLYN10 - 40
d_63ens_2GLNSERN42 - 73
d_64ens_2GLNALAN76 - 77
d_65ens_2TRPTRPN80
d_66ens_2ASPTHRN82 - 91
d_67ens_2ILEASPN93 - 96
d_68ens_2ASNPRON98 - 108
d_69ens_2GLYGLYN110 - 119
d_610ens_2ILEGLUN121 - 122
d_611ens_2GLYLEUN124 - 135
d_612ens_2VALALAN137 - 148
d_613ens_2VALTHRN150 - 180
d_614ens_2ALAASNN182 - 190
d_615ens_2GLUPHEN192 - 210
d_616ens_2ALAGLUN212 - 219
d_617ens_2SERALAN221 - 240
d_618ens_2LEULYSN242 - 263
d_619ens_2TYRVALN265 - 334
d_620ens_2PROALAN336 - 339
d_621ens_2GLYGLYN341
d_11ens_3PROLEUA3 - 216
d_21ens_3PROLEUD3 - 216
d_31ens_3PROLEUF1 - 214
d_41ens_3PROLEUI3 - 216
d_11ens_4PROLEUK3 - 216
d_21ens_4PROLEUM3 - 216
d_11ens_5METGLNB1 - 42
d_12ens_5ALAGLYB215 - 341
d_21ens_5METGLNE1 - 42
d_22ens_5ALAGLYE215 - 341
d_31ens_5METGLNG1 - 42
d_32ens_5ALAGLYG215 - 341
d_41ens_5METGLNJ1 - 42
d_42ens_5ALAGLYJ215 - 341
d_11ens_6ASNPROB43 - 214
d_21ens_6ASNPROE43 - 214
d_31ens_6ASNPROG43 - 214
d_41ens_6ASNPROJ43 - 214
d_11ens_7METGLNL1 - 42
d_12ens_7ALATHRL215 - 343
d_21ens_7METGLNN1 - 42
d_22ens_7ALATHRN215 - 343
d_11ens_8ASNPROL43 - 214
d_21ens_8ASNPRON43 - 214

NCS ensembles :
ID
ens_1
ens_2
ens_3
ens_4
ens_5
ens_6
ens_7
ens_8

NCS oper:
IDCodeMatrixVector
1given(-0.645147486714, -0.231081799983, 0.728275993085), (-0.248395201175, -0.837958981035, -0.485926506928), (0.722554180958, -0.494394526485, 0.483207520389)32.4234953366, 91.3231905659, 14.3457449139
2given(0.583838253921, 0.630144998279, 0.51190836524), (0.694999817246, -0.0620038353862, -0.716331472452), (-0.419652412464, 0.773997936393, -0.474150869631)-19.9722021923, 46.3286784211, 110.473737669
3given(-0.260816797854, -0.921164177951, 0.288844517374), (-0.941564494059, 0.308786852682, 0.134562190596), (-0.213145259118, -0.2368696622, -0.947872281294)68.6480512674, 53.3581980011, 156.477573971
4given(-0.803254148804, -0.533232313515, -0.265416789695), (0.150759773822, -0.613101234093, 0.775485891136), (-0.57624149714, 0.582898084212, 0.572866092902)48.17703505, -16.134875321, 47.8786885689
5given(0.456323398776, 0.793555432716, -0.402540346967), (0.653400567768, 0.00825140015856, 0.756967378713), (0.604017097249, -0.608442018275, -0.514744263327)-34.5235668261, -53.8270583508, 96.7237421069
6given(-0.656237116185, -0.240466005628, 0.715212519101), (-0.252444863714, -0.823270912647, -0.508425604365), (0.711072737577, -0.514199479314, 0.479556521536)33.2602153224, 91.4498223177, 15.528752865
7given(0.553221465363, 0.676504653937, 0.486094089104), (0.683580509581, -0.0351744354399, -0.729027054376), (-0.476092109977, 0.735597860446, -0.48190464879)-20.1289963489, 46.7017251423, 114.206343844
8given(-0.181258712801, -0.954279949128, 0.2376868901), (-0.956979796906, 0.226836156433, 0.180928235629), (-0.226572168077, -0.194666732716, -0.95434266164)67.8501054748, 55.6526849468, 155.775852958
9given(-0.78865783646, -0.532370590625, -0.307571733466), (0.10735715227, -0.611807303087, 0.783687607243), (-0.605386867091, 0.585041347365, 0.539660414545)48.8244292726, -14.9517642421, 48.1270729973
10given(0.442959961316, 0.793083616654, -0.418096698942), (0.633201211181, 0.0533962903353, 0.772143161814), (0.634698904071, -0.606767841249, -0.478529087932)-33.3861034158, -55.7003935413, 96.3566421481
11given(-0.644324940306, -0.231695364078, 0.728809048767), (-0.247554124555, -0.838498810818, -0.485424247101), (0.723576068368, -0.493190635072, 0.482908553209)32.3850521854, 91.2747294509, 14.2560406844
12given(0.585926771693, 0.630678400587, 0.508856141996), (0.693138965893, -0.0647322152626, -0.717891436269), (-0.419819237499, 0.77333983173, -0.475076112307)-19.9882304537, 46.5915120323, 110.53884384
13given(-0.26146631871, -0.920764797797, 0.289529879838), (-0.941917402301, 0.308910465804, 0.131779859461), (-0.210777065695, -0.238257237572, -0.948054068775)68.6340160241, 53.4691078626, 156.417253234
14given(-0.683847376035, -0.728983844062, -0.030583024487), (-0.72920247768, 0.681424186167, 0.0626484241753), (-0.0248296765082, 0.0651431777158, -0.997566966956)-11.9971844669, -10.6602259186, 146.686390379
15given(-0.645545874881, -0.239126925663, 0.725319816941), (-0.250126840457, -0.831140260321, -0.496631081746), (0.721600365235, -0.502020100291, 0.476727104113)32.7891368238, 91.5516355723, 14.8359784218
16given(0.59059059735, 0.655663905381, 0.470433406023), (0.665305173423, -0.0656939559379, -0.743675554506), (-0.456696586957, 0.752189568748, -0.475014820957)-20.0980166101, 48.8196258482, 112.830824219
17given(-0.219101641668, -0.934206903723, 0.281517196019), (-0.942471843752, 0.277297615939, 0.18668919607), (-0.252470383121, -0.224418121439, -0.941220065881)67.5522752587, 52.883538388, 157.676043107
18given(-0.675996960837, -0.239063324385, 0.697048661051), (-0.254673093006, -0.811838556083, -0.525413907844), (0.691498173994, -0.53269774337, 0.487917400357)32.9312094658, 90.394366417, 16.9870962537
19given(0.521681018618, 0.703601378717, 0.482487320746), (0.702893530922, -0.0339488716728, -0.710484453243), (-0.483517940723, 0.709783469784, -0.512267339404)-21.5351053972, 46.8171195592, 115.085056843
20given(-0.179036255471, -0.962121102241, 0.20559426998), (-0.961850134306, 0.21510697837, 0.1690364073), (-0.206858256696, -0.167487230792, -0.963928259342)67.4970401283, 56.1601929332, 153.659691903
21given(-0.653151905248, -0.757138676232, -0.0115591359794), (-0.756032144303, 0.651188191937, 0.0661009490282), (-0.0425204121861, 0.0519130391573, -0.997745985165)-12.960780665, -11.6455657883, 146.396248404
22given(-0.637332834729, -0.76926940347, -0.0450715282802), (-0.769982642002, 0.633422195452, 0.0768313303523), (-0.0305546852723, 0.0836714239936, -0.996024851103)-11.3595980956, -13.0460095897, 148.126322977

-
Components

#1: Protein
Putative ABC transport system, ATP-binding protein


Mass: 24851.355 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium diphtheriae NCTC 13129 (bacteria)
Strain: ATCC 700971 / NCTC 13129 / Biotype gravis / Gene: DIP2323 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: Q6NEF2
#2: Protein
Putative ABC transport system integral membrane protein


Mass: 35866.180 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium diphtheriae NCTC 13129 (bacteria)
Strain: ATCC 700971 / NCTC 13129 / Biotype gravis / Gene: DIP2324 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: Q6NEF1
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.23 Å3/Da / Density % sol: 70.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 22% PEG 3000, 0.2 M Mg acetate, 0.2 M KCl, 0.1 M HEPES pH 7.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1.74 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.74 Å / Relative weight: 1
ReflectionResolution: 3.27→49.29 Å / Num. obs: 187978 / % possible obs: 97.2 % / Redundancy: 4 % / Biso Wilson estimate: 123.56 Å2 / Rrim(I) all: 0.092 / Net I/σ(I): 10.6
Reflection shellResolution: 3.27→3.47 Å / Num. unique obs: 29851 / CC1/2: 0.526

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LLL

6lll
PDB Unreleased entry


Resolution: 3.4→49.29 Å / SU ML: 0.5473 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 36.9366
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2848 5213 3.11 %
Rwork0.2546 162615 -
obs0.2555 167828 97.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 167.65 Å2
Refinement stepCycle: LAST / Resolution: 3.4→49.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24966 0 86 0 25052
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002625460
X-RAY DIFFRACTIONf_angle_d0.452434709
X-RAY DIFFRACTIONf_chiral_restr0.03744261
X-RAY DIFFRACTIONf_plane_restr0.00294420
X-RAY DIFFRACTIONf_dihedral_angle_d11.55549052
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.627093947047
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.857728133833
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.799591816704
ens_1d_5AX-RAY DIFFRACTIONTorsion NCS0.838894906704
ens_1d_6AX-RAY DIFFRACTIONTorsion NCS0.766987081885
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS0.760029924566
ens_2d_3BX-RAY DIFFRACTIONTorsion NCS0.872151694742
ens_2d_4BX-RAY DIFFRACTIONTorsion NCS0.859338956837
ens_2d_5BX-RAY DIFFRACTIONTorsion NCS1.68525001289
ens_2d_6BX-RAY DIFFRACTIONTorsion NCS1.62024835612
ens_3d_2AX-RAY DIFFRACTIONTorsion NCS0.673294919914
ens_3d_3AX-RAY DIFFRACTIONTorsion NCS1.00613400253
ens_3d_4AX-RAY DIFFRACTIONTorsion NCS1.00946175233
ens_4d_2KX-RAY DIFFRACTIONTorsion NCS0.82796813366
ens_5d_2BX-RAY DIFFRACTIONTorsion NCS0.614772876924
ens_5d_3BX-RAY DIFFRACTIONTorsion NCS0.696726989978
ens_5d_4BX-RAY DIFFRACTIONTorsion NCS0.736657936657
ens_6d_2BX-RAY DIFFRACTIONTorsion NCS0.912249983825
ens_6d_3BX-RAY DIFFRACTIONTorsion NCS0.880334161853
ens_6d_4BX-RAY DIFFRACTIONTorsion NCS0.987926352401
ens_7d_2LX-RAY DIFFRACTIONTorsion NCS0.661224579629
ens_8d_2LX-RAY DIFFRACTIONTorsion NCS0.890954019213
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.440.44061830.47095412X-RAY DIFFRACTION96.04
3.44-3.480.48941420.44825365X-RAY DIFFRACTION96.51
3.48-3.520.41271400.42255307X-RAY DIFFRACTION96.48
3.52-3.570.38571780.39345445X-RAY DIFFRACTION96.45
3.57-3.610.38792080.37655268X-RAY DIFFRACTION96.82
3.61-3.660.40841680.35685373X-RAY DIFFRACTION96.57
3.66-3.710.32151480.34495418X-RAY DIFFRACTION96.77
3.71-3.770.34232020.3315302X-RAY DIFFRACTION97
3.77-3.830.33871780.32875385X-RAY DIFFRACTION97.12
3.83-3.890.41421500.32225460X-RAY DIFFRACTION97.4
3.89-3.960.3511780.31595438X-RAY DIFFRACTION97.33
3.96-4.030.3431740.31835381X-RAY DIFFRACTION97.15
4.03-4.110.29311780.27765435X-RAY DIFFRACTION97.55
4.11-4.190.28721800.26085333X-RAY DIFFRACTION97.54
4.19-4.280.26241700.25015441X-RAY DIFFRACTION97.62
4.28-4.380.28931840.24335496X-RAY DIFFRACTION97.76
4.38-4.490.26141770.23645395X-RAY DIFFRACTION97.72
4.49-4.610.26761660.23485413X-RAY DIFFRACTION98.05
4.61-4.750.28091740.2295413X-RAY DIFFRACTION97.95
4.75-4.90.25191780.23345484X-RAY DIFFRACTION98.3
4.9-5.080.29371860.2425432X-RAY DIFFRACTION98.29
5.08-5.280.29031560.24345465X-RAY DIFFRACTION98.34
5.28-5.520.31151900.26295458X-RAY DIFFRACTION98.4
5.52-5.810.33431700.26065469X-RAY DIFFRACTION98.62
5.81-6.170.30971800.24845465X-RAY DIFFRACTION98.76
6.17-6.650.2411720.25235543X-RAY DIFFRACTION98.77
6.65-7.320.24361840.22795460X-RAY DIFFRACTION98.98
7.32-8.370.26571680.21325504X-RAY DIFFRACTION99.09
8.37-10.530.18271820.16345485X-RAY DIFFRACTION99.11
10.53-49.290.28581690.24865370X-RAY DIFFRACTION96.67
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.70668786608-0.8199618668770.4749580106415.909623574414.024811562579.28537656477-0.6088479429750.3350758128450.7811970967380.8629009491960.845858246883-0.658117094370.3943190599631.22703537866-0.2463205202750.630686525216-0.0473418680445-0.1429414839771.011183134890.07607176165831.2545743517451.74335.3544.32
26.729293832191.13540908028-2.798112333586.077270099262.86663107233.0302970790.1604473087050.3258552714430.903276066441-0.468514535248-0.509747409672-1.143545922340.3431353487111.117689653930.6146189747881.422717772940.5892428063360.1177021220241.614958853630.1596780975811.0669770613828.45540.2228.202
35.321828397981.648185198581.054274295519.46772257922-1.867686344227.19035319655-0.06603939124240.3357077259730.036978306709-0.6768200455570.07887924272650.664215813242-0.62276556255-1.58144166612-0.01502481692481.480232443580.611792424851-0.1242102036541.764794246880.06213559379290.91541641928112.80660.189-28.393
43.77359877514-2.584445628712.550168536774.207644149-1.581660320467.108803357420.2968496702530.8649965790460.530042010169-0.669429633785-0.366827049549-0.0412185850121-0.6660151843690.2686479341970.2375426184390.665449102935-0.09321423939440.2665187253041.029319549110.2493387631271.0797207156628.22450.7658.115
55.68296110758-3.37324205924-0.4562081119668.522311414740.5894780391618.30581362159-0.493306542441-0.0867824305374-0.232563868870.540345038120.4900672773890.441745960160.169611536364-0.3609152993570.02577872956241.147329897930.1772990237750.1979935532320.8165343649250.2373078281641.2810133698723.22227.20855.719
67.21061084741-4.619222051623.533849401358.48218821245-5.651769889794.35825585529-0.2383695166550.9305948040260.07978200117660.799906503837-1.007929458440.664709432161-2.12269077395-3.033580932021.24422626042.473910968081.339399285990.07125825891132.638155976990.3045443599871.3451137889610.71746.86519.03
72.736200360320.312602396688-3.157475247915.22857584136-2.330390405883.745634949150.0747926134156-0.1908095110480.164231645611-1.407120285230.1496686583390.7084542131721.07685929502-1.62963560653-0.3829240594182.18629035580.235114070176-0.3596241912013.0178396080.5595151865241.609796618-9.9653.213-20.06
80.4982290165520.2590575169381.509424305421.78740396486-1.550330303727.720571237160.100098793880.116676415058-0.524581597303-0.6082330036740.5097194568780.8612453392570.269945831683-1.75562179145-0.597943212411.05212759336-0.0131855844298-0.0727763132981.728737518790.2112473694781.472867677828.50638.34913.574
96.98410412658-1.991338100373.732478103721.789197317420.646013095755.220682421070.1086216243970.688250156572-0.27953314045-0.538497657565-0.548919734456-0.7063148023341.857463872981.977662161580.331398421211.983511268040.3988156868360.7869225060291.36188124620.3153818291921.8488272438455.0648.30295.123
104.85831301437-2.04941926826-5.706399666213.568873138641.182362379966.80498277899-1.34650708006-0.1376420801710.3951117913570.565301132850.0219889964073-1.470709469520.572967449871-1.051891610081.215057283832.185486160720.6735654344980.09231146315751.88350973727-0.3709687098711.6766451151626.89359.121126.171
119.72045901164-1.3001008035-4.570337651237.399189530573.086460826818.28120644384-0.523395501218-0.393245779089-0.143121706260.5383761385530.4548360238270.401284624550.655087740509-0.1069060866340.1686004405521.435354469640.4648643878970.1337456176691.49589392934-0.2358657731441.0486185052713.83173.981166.143
120.540197494139-1.730513771161.136726486985.86421816024-0.02180435791838.32360128044-0.656853402169-0.5580735776320.8028652039271.596467959730.687420071669-1.03029287619-0.0388515833921-0.6070189723780.3169379144371.2703327993-0.000568037669743-0.3810976867011.13454598317-0.5516790649321.4313749298633.82858.147134.011
138.39880357225-1.99436400795-1.353561639335.580462456680.6182206528366.80185888108-0.175372273933-2.192719490630.527983940330.55108585570.517753159676-0.3101380342660.5434465452321.95617767156-0.3173166299451.097393525570.275325715087-0.06733888861961.74563442414-0.3776540947621.1438406298335.55721.46494.331
143.21108971421.24883050467-0.8342481398471.606772448882.2183157898.73688325035-0.391039190146-0.2397476023560.4706306717563.462111686641.073655044590.427376532872-0.3988156154110.106357932398-0.7877658652162.778950722670.6121938742590.7184444331021.66332975492-0.1819767013541.316675737425.92338.761133.824
151.54259225323-0.153030117542-0.9695363576791.98171725181-1.032288419970.987031385151-0.235866318410.384323486999-0.4168399501040.08235973623150.2398478672160.1819529862950.743518055951-0.227804509940.07753533073342.623953226490.1011544080630.7916546499692.09760390633-0.2480082032232.01562245311.48151.953168.327
164.4051425233-0.934013469326-6.673637890371.450710026813.309739413637.065493713790.3467191647330.583320607980.2425280554080.767224035859-0.2079894808720.1627398394260.223327336733-1.39236540678-0.3007117008382.074000025320.02888213595660.1760335303832.00678494823-0.2421974204581.3767315415416.21341.668131.71
173.70294589398-2.2288386144-1.720609155474.55366430735-0.5461260942765.026939539030.3403923562610.560738892532-0.318934917029-0.485143989483-0.2525853916910.447861326827-0.120720226204-0.720834017016-0.09677023134211.258635714270.457679405828-0.28311119521.24102382342-0.2504434158181.29397116251-24.2414.66264.245
185.82700597214-2.066703104551.358646658790.788232658289-0.6584927629890.633246488754-0.1554482217491.54432337738-0.433208579602-1.61481983318-0.682971058232-0.6896613564722.57934216210.8850769354270.341077208482.884265474341.063603474160.6785420333511.17594358371-0.07819202070612.024715642421.915-30.11458.237
197.1784683646-0.703911326075-2.088655332546.728708822521.106443307164.498538329630.958328137144-0.218974746381.98597081877-0.21626959713-0.349696236124-1.83503755864-0.542798114206-0.133608135652-0.5161877266842.51405999430.6401895545080.2216219147651.197137945640.03319630739612.6016176636113.296-72.05862.547
203.45412985286-2.5301992951-2.672263463185.52286043576-0.4937203120993.5501593081-0.703271907294-0.816569447932-0.882207200684-0.09001959351250.2732693957620.3167394120012.129729349581.219923953420.4696135813191.936356106520.712302232009-0.1690566457031.15934718684-0.1701070069631.71821410453-4.487-27.43863.413
216.5959511399-0.81258176668-1.928341339167.78681455024-2.651847154239.048376194790.712179980258-0.004280941935570.647409870659-0.642337879538-0.756503641889-0.485183662883-0.7542863098030.102311268710.02648228042210.7427763043370.074852820036-0.02277155371710.697834222029-0.1173189408581.0731411643-0.75114.02283.545
222.70001702491-1.69631638693-2.977904866524.304899719880.3789066655945.239896700921.19048436590.4658183467660.193689786516-0.590487364387-0.788028367764-2.336379037530.4825335448060.460819908553-0.7649136011581.269448581970.3115220616550.1210277079461.038268267630.09498929449781.933185069287.95-28.8386.676
237.71868194779-2.08503663388-0.1402989414016.79848759661-0.9064749290756.947885822970.2995181189910.335277403842-0.819214640287-0.595042404423-0.536141075041.72526781484-0.243317795853-0.525587976610.109585233021.706355924740.4862907762710.03943450874791.06791996158-0.09332350834692.0507139377332.771-64.12279.397
243.465350905-3.15606532510.4892477689079.850466753941.695010172455.09610640163-0.359456764360.0381139426813-0.5004304594240.01686406637040.3056661585960.2948045095970.0189021516464-0.2108433896920.07267731421071.099782446440.300368420852-0.161960492140.901551528326-0.1469843952321.1682937516710.012-21.9581.863
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 3:218 )A3 - 218
2X-RAY DIFFRACTION2( CHAIN B AND RESID 1:42 )B1 - 42
3X-RAY DIFFRACTION3( CHAIN B AND RESID 43:189 )B43 - 189
4X-RAY DIFFRACTION4( CHAIN B AND RESID 190:341 )B190 - 341
5X-RAY DIFFRACTION5( CHAIN C AND RESID 3:219 )C3 - 219
6X-RAY DIFFRACTION6( CHAIN D AND RESID 1:42 )D1 - 42
7X-RAY DIFFRACTION7( CHAIN D AND RESID 43:189 )D43 - 189
8X-RAY DIFFRACTION8( CHAIN D AND RESID 190:342 )D190 - 342
9X-RAY DIFFRACTION9( CHAIN E AND RESID 5:218 )E5 - 218
10X-RAY DIFFRACTION10( CHAIN F AND RESID 1:42 )F1 - 42
11X-RAY DIFFRACTION11( CHAIN F AND RESID 43:189 )F43 - 189
12X-RAY DIFFRACTION12( CHAIN F AND RESID 190:342 )F190 - 342
13X-RAY DIFFRACTION13( CHAIN G AND RESID 3:225 )G3 - 225
14X-RAY DIFFRACTION14( CHAIN H AND RESID 1:42 )H1 - 42
15X-RAY DIFFRACTION15( CHAIN H AND RESID 43:189 )H43 - 189
16X-RAY DIFFRACTION16( CHAIN H AND RESID 190:341 )H190 - 341
17X-RAY DIFFRACTION17( CHAIN I AND RESID 3:223 )I3 - 223
18X-RAY DIFFRACTION18( CHAIN J AND RESID 1:42 )J1 - 42
19X-RAY DIFFRACTION19( CHAIN J AND RESID 43:219 )J43 - 219
20X-RAY DIFFRACTION20( CHAIN J AND RESID 220:343 )J220 - 343
21X-RAY DIFFRACTION21( CHAIN K AND RESID 4:221 )K4 - 221
22X-RAY DIFFRACTION22( CHAIN L AND RESID 1:42 )L1 - 42
23X-RAY DIFFRACTION23( CHAIN L AND RESID 43:219 )L43 - 219
24X-RAY DIFFRACTION24( CHAIN L AND RESID 220:343 )L220 - 343

+
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