PDB-8qja: T6SS-linked Rhs repeat protein - Advenella mimigardefordensis Vgr...

ID or keywords:

Entry

Database: PDB / ID: 8qja

Title

T6SS-linked Rhs repeat protein - Advenella mimigardefordensis VgrG-Rhs core

Components

Putative type VI secretion system YD repeat-containing Rhs element Vgr protein

Keywords

CELL INVASION / Rhs / T6SS / VgrG-Rhs / toxin cannister / Rhs-repeat

Function / homology

Function and homology information

Bacteriophage T4 gp5 C-terminal trimerisation domain / Domain of unknown function DUF6531 / RHS protein / Domain of unknown function (DUF6531) / RHS protein / Type VI secretion system, RhsGE-associated Vgr family subset / Type VI secretion system, RhsGE-associated Vgr protein / RHS repeat / RHS Repeat / Phage tail baseplate hub (GPD) ...
Similarity search - Domain/homology

Biological species

Advenella mimigardefordensis DPN7 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.36 Å

Authors

Kielkopf, C.S. / Shneider, M.M. / Leiman, P.G. / Taylor, N.M.I.

Funding support

Switzerland, 1items

Citation

Journal: Structure / Year: 2024
Title: T6SS-associated Rhs toxin-encapsulating shells: Structural and bioinformatical insights into bacterial weaponry and self-protection.
Authors: Kielkopf, C.S. / Shneider, M.M. / Leiman, P.G. / Taylor, N.M.I.

History

Deposition	Sep 13, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 25, 2024	Provider: repository / Type: Initial release
Revision 1.1	Nov 13, 2024	Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details 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 / _citation_author.identifier_ORCID
Revision 1.2	Dec 18, 2024	Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8qja.cif.gz	2 MB	Display	PDBx/mmCIF format
PDB format	pdb8qja.ent.gz	1.4 MB	Display	PDB format
PDBx/mmJSON format	8qja.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qj/8qja ftp://data.pdbj.org/pub/pdb/validation_reports/qj/8qja	HTTPS FTP

-
Related structure data

Related structure data	8qjbC 8qjcC 8qjdC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Putative type VI secretion system YD repeat-containing Rhs element Vgr protein

B: Putative type VI secretion system YD repeat-containing Rhs element Vgr protein

C: Putative type VI secretion system YD repeat-containing Rhs element Vgr protein

D: Putative type VI secretion system YD repeat-containing Rhs element Vgr protein

851 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Putative type VI secretion system YD repeat-containing Rhs element Vgr protein

defined by author
213 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Putative type VI secretion system YD repeat-containing Rhs element Vgr protein

defined by author
213 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Putative type VI secretion system YD repeat-containing Rhs element Vgr protein

defined by author
213 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Putative type VI secretion system YD repeat-containing Rhs element Vgr protein

defined by author
213 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	66.239, 97.783, 215.006
Angle α, β, γ (deg.)	85.690, 89.990, 76.890
Int Tables number	1
Space group name H-M	P1
Space group name Hall	P1
Symmetry operation	#1: x,y,z

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
d_1	ens_1	(chain "A" and (resid 23 through 110 or resid 112...
d_2	ens_1	(chain "B" and (resid 23 through 110 or resid 112...
d_3	ens_1	(chain "C" and (resid 23 through 110 or resid 112...
d_4	ens_1	(chain "D" and (resid 23 through 110 or resid 112...

NCS domain segments:

Ens-ID: ens_1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
d_1	1	ALA	ALA	ILE	ILE	A	A	23 - 110	826 - 913
d_1	2	LEU	LEU	LEU	LEU	A	A	112	915
d_1	3	PRO	PRO	GLU	GLU	A	A	114 - 117	917 - 920
d_1	4	TYR	TYR	ASP	ASP	A	A	119 - 120	922 - 923
d_1	5	THR	THR	GLU	GLU	A	A	122 - 123	925 - 926
d_1	6	LEU	LEU	TRP	TRP	A	A	125 - 127	928 - 930
d_1	7	ARG	ARG	PHE	PHE	A	A	129 - 147	932 - 950
d_1	8	ARG	ARG	PHE	PHE	A	A	149 - 154	952 - 957
d_1	9	LEU	LEU	GLY	GLY	A	A	156 - 196	959 - 999
d_1	10	ILE	ILE	VAL	VAL	A	A	198 - 205	1001 - 1008
d_1	11	GLY	GLY	GLY	GLY	A	A	210	1013
d_1	12	PRO	PRO	ARG	ARG	A	A	212 - 214	1015 - 1017
d_1	13	THR	THR	TYR	TYR	A	A	216 - 276	1019 - 1079
d_1	14	ASP	ASP	LEU	LEU	A	A	278 - 284	1081 - 1087
d_1	15	PHE	PHE	PHE	PHE	A	A	286	1089
d_1	16	TRP	TRP	ASP	ASP	A	A	288 - 331	1091 - 1134
d_1	17	PHE	PHE	VAL	VAL	A	A	333 - 339	1136 - 1142
d_1	18	TYR	TYR	GLU	GLU	A	A	341 - 347	1144 - 1150
d_1	19	TYR	TYR	ASP	ASP	A	A	349 - 352	1152 - 1155
d_1	20	PHE	PHE	ILE	ILE	A	A	354 - 400	1157 - 1203
d_1	21	GLU	GLU	SER	SER	A	A	402 - 410	1205 - 1213
d_1	22	PHE	PHE	PHE	PHE	A	A	412	1215
d_1	23	TYR	TYR	ASN	ASN	A	A	414 - 478	1217 - 1281
d_1	24	TYR	TYR	LYS	LYS	A	A	480 - 542	1283 - 1345
d_1	25	GLY	GLY	ASP	ASP	A	A	544 - 596	1347 - 1399
d_1	26	GLU	GLU	ASP	ASP	A	A	598 - 704	1401 - 1507
d_1	27	GLN	GLN	VAL	VAL	A	A	706 - 720	1509 - 1523
d_1	28	GLN	GLN	VAL	VAL	A	A	724 - 740	1527 - 1543
d_1	29	GLU	GLU	GLN	GLN	A	A	742 - 743	1545 - 1546
d_1	30	LEU	LEU	GLY	GLY	A	A	745 - 750	1548 - 1553
d_1	31	ARG	ARG	SER	SER	A	A	756 - 757	1559 - 1560
d_1	32	GLN	GLN	SER	SER	A	A	759 - 774	1562 - 1577
d_1	33	HIS	HIS	TYR	TYR	A	A	776 - 781	1579 - 1584
d_1	34	TYR	TYR	THR	THR	A	A	783 - 793	1586 - 1596
d_1	35	ASN	ASN	ASP	ASP	A	A	796 - 813	1599 - 1616
d_1	36	THR	THR	LYS	LYS	A	A	815 - 837	1618 - 1640
d_1	37	CYS	CYS	PHE	PHE	A	A	839 - 844	1642 - 1647
d_1	38	TYR	TYR	LYS	LYS	A	A	846 - 855	1649 - 1658
d_1	39	LYS	LYS	SER	SER	A	A	857 - 882	1660 - 1685
d_1	40	HIS	HIS	GLY	GLY	A	A	884 - 930	1687 - 1733
d_1	41	ALA	ALA	ASP	ASP	A	A	932 - 984	1735 - 1787
d_1	42	ASN	ASN	LEU	LEU	A	A	986 - 1002	1789 - 1805
d_1	43	GLY	GLY	GLY	GLY	A	A	1014	1817
d_1	44	ASN	ASN	ASN	ASN	A	A	1016 - 1034	1819 - 1837
d_1	45	PHE	PHE	PHE	PHE	A	A	1036	1839
d_1	46	TYR	TYR	PRO	PRO	A	A	1038 - 1065	1841 - 1868
d_1	47	THR	THR	ASN	ASN	A	A	1067 - 1069	1870 - 1872
d_1	48	ILE	ILE	ILE	ILE	A	A	1071	1874
d_1	49	PRO	PRO	PRO	PRO	A	A	1073	1876
d_2	1	ALA	ALA	ILE	ILE	B	B	23 - 110	826 - 913
d_2	2	LEU	LEU	LEU	LEU	B	B	112	915
d_2	3	PRO	PRO	GLU	GLU	B	B	114 - 117	917 - 920
d_2	4	TYR	TYR	ASP	ASP	B	B	119 - 120	922 - 923
d_2	5	THR	THR	GLU	GLU	B	B	122 - 123	925 - 926
d_2	6	LEU	LEU	TRP	TRP	B	B	125 - 127	928 - 930
d_2	7	ARG	ARG	PHE	PHE	B	B	129 - 147	932 - 950
d_2	8	ARG	ARG	PHE	PHE	B	B	149 - 154	952 - 957
d_2	9	LEU	LEU	GLY	GLY	B	B	156 - 196	959 - 999
d_2	10	ILE	ILE	VAL	VAL	B	B	198 - 205	1001 - 1008
d_2	11	GLY	GLY	GLY	GLY	B	B	210	1013
d_2	12	PRO	PRO	ARG	ARG	B	B	212 - 214	1015 - 1017
d_2	13	THR	THR	TYR	TYR	B	B	216 - 276	1019 - 1079
d_2	14	ASP	ASP	LEU	LEU	B	B	278 - 284	1081 - 1087
d_2	15	PHE	PHE	PHE	PHE	B	B	286	1089
d_2	16	TRP	TRP	ASP	ASP	B	B	288 - 331	1091 - 1134
d_2	17	PHE	PHE	VAL	VAL	B	B	333 - 339	1136 - 1142
d_2	18	TYR	TYR	GLU	GLU	B	B	341 - 347	1144 - 1150
d_2	19	TYR	TYR	ASP	ASP	B	B	349 - 352	1152 - 1155
d_2	20	PHE	PHE	ILE	ILE	B	B	354 - 400	1157 - 1203
d_2	21	GLU	GLU	SER	SER	B	B	402 - 410	1205 - 1213
d_2	22	PHE	PHE	PHE	PHE	B	B	412	1215
d_2	23	TYR	TYR	ASN	ASN	B	B	414 - 478	1217 - 1281
d_2	24	TYR	TYR	LYS	LYS	B	B	480 - 542	1283 - 1345
d_2	25	GLY	GLY	ASP	ASP	B	B	544 - 596	1347 - 1399
d_2	26	GLU	GLU	ASP	ASP	B	B	598 - 704	1401 - 1507
d_2	27	GLN	GLN	VAL	VAL	B	B	706 - 720	1509 - 1523
d_2	28	GLN	GLN	VAL	VAL	B	B	724 - 740	1527 - 1543
d_2	29	GLU	GLU	GLN	GLN	B	B	742 - 743	1545 - 1546
d_2	30	LEU	LEU	GLY	GLY	B	B	745 - 750	1548 - 1553
d_2	31	ARG	ARG	SER	SER	B	B	756 - 757	1559 - 1560
d_2	32	GLN	GLN	SER	SER	B	B	759 - 774	1562 - 1577
d_2	33	HIS	HIS	TYR	TYR	B	B	776 - 781	1579 - 1584
d_2	34	TYR	TYR	THR	THR	B	B	783 - 793	1586 - 1596
d_2	35	ASN	ASN	ASP	ASP	B	B	796 - 813	1599 - 1616
d_2	36	THR	THR	LYS	LYS	B	B	815 - 837	1618 - 1640
d_2	37	CYS	CYS	PHE	PHE	B	B	839 - 844	1642 - 1647
d_2	38	TYR	TYR	LYS	LYS	B	B	846 - 855	1649 - 1658
d_2	39	LYS	LYS	SER	SER	B	B	857 - 882	1660 - 1685
d_2	40	HIS	HIS	GLY	GLY	B	B	884 - 930	1687 - 1733
d_2	41	ALA	ALA	ASP	ASP	B	B	932 - 984	1735 - 1787
d_2	42	ASN	ASN	LEU	LEU	B	B	986 - 1002	1789 - 1805
d_2	43	GLY	GLY	GLY	GLY	B	B	1014	1817
d_2	44	ASN	ASN	ASN	ASN	B	B	1016 - 1034	1819 - 1837
d_2	45	PHE	PHE	PHE	PHE	B	B	1036	1839
d_2	46	TYR	TYR	PRO	PRO	B	B	1038 - 1065	1841 - 1868
d_2	47	THR	THR	ASN	ASN	B	B	1067 - 1069	1870 - 1872
d_2	48	ILE	ILE	ILE	ILE	B	B	1071	1874
d_2	49	PRO	PRO	PRO	PRO	B	B	1073	1876
d_3	1	ALA	ALA	ILE	ILE	C	C	23 - 110	826 - 913
d_3	2	LEU	LEU	LEU	LEU	C	C	112	915
d_3	3	PRO	PRO	GLU	GLU	C	C	114 - 117	917 - 920
d_3	4	TYR	TYR	ASP	ASP	C	C	119 - 120	922 - 923
d_3	5	THR	THR	GLU	GLU	C	C	122 - 123	925 - 926
d_3	6	LEU	LEU	TRP	TRP	C	C	125 - 127	928 - 930
d_3	7	ARG	ARG	PHE	PHE	C	C	129 - 147	932 - 950
d_3	8	ARG	ARG	PHE	PHE	C	C	149 - 154	952 - 957
d_3	9	LEU	LEU	GLY	GLY	C	C	156 - 196	959 - 999
d_3	10	ILE	ILE	VAL	VAL	C	C	198 - 205	1001 - 1008
d_3	11	GLY	GLY	GLY	GLY	C	C	210	1013
d_3	12	PRO	PRO	ARG	ARG	C	C	212 - 214	1015 - 1017
d_3	13	THR	THR	TYR	TYR	C	C	216 - 276	1019 - 1079
d_3	14	ASP	ASP	LEU	LEU	C	C	278 - 284	1081 - 1087
d_3	15	PHE	PHE	PHE	PHE	C	C	286	1089
d_3	16	TRP	TRP	ASP	ASP	C	C	288 - 331	1091 - 1134
d_3	17	PHE	PHE	VAL	VAL	C	C	333 - 339	1136 - 1142
d_3	18	TYR	TYR	GLU	GLU	C	C	341 - 347	1144 - 1150
d_3	19	TYR	TYR	ASP	ASP	C	C	349 - 352	1152 - 1155
d_3	20	PHE	PHE	ILE	ILE	C	C	354 - 400	1157 - 1203
d_3	21	GLU	GLU	SER	SER	C	C	402 - 410	1205 - 1213
d_3	22	PHE	PHE	PHE	PHE	C	C	412	1215
d_3	23	TYR	TYR	ASN	ASN	C	C	414 - 478	1217 - 1281
d_3	24	TYR	TYR	LYS	LYS	C	C	480 - 542	1283 - 1345
d_3	25	GLY	GLY	ASP	ASP	C	C	544 - 596	1347 - 1399
d_3	26	GLU	GLU	ASP	ASP	C	C	598 - 704	1401 - 1507
d_3	27	GLN	GLN	VAL	VAL	C	C	706 - 720	1509 - 1523
d_3	28	GLN	GLN	VAL	VAL	C	C	724 - 740	1527 - 1543
d_3	29	GLU	GLU	GLN	GLN	C	C	742 - 743	1545 - 1546
d_3	30	LEU	LEU	GLY	GLY	C	C	745 - 750	1548 - 1553
d_3	31	ARG	ARG	SER	SER	C	C	756 - 757	1559 - 1560
d_3	32	GLN	GLN	SER	SER	C	C	759 - 774	1562 - 1577
d_3	33	HIS	HIS	TYR	TYR	C	C	776 - 781	1579 - 1584
d_3	34	TYR	TYR	THR	THR	C	C	783 - 793	1586 - 1596
d_3	35	ASN	ASN	ASP	ASP	C	C	796 - 813	1599 - 1616
d_3	36	THR	THR	LYS	LYS	C	C	815 - 837	1618 - 1640
d_3	37	CYS	CYS	PHE	PHE	C	C	839 - 844	1642 - 1647
d_3	38	TYR	TYR	LYS	LYS	C	C	846 - 855	1649 - 1658
d_3	39	LYS	LYS	SER	SER	C	C	857 - 882	1660 - 1685
d_3	40	HIS	HIS	GLY	GLY	C	C	884 - 930	1687 - 1733
d_3	41	ALA	ALA	ASP	ASP	C	C	932 - 984	1735 - 1787
d_3	42	ASN	ASN	LEU	LEU	C	C	986 - 1002	1789 - 1805
d_3	43	GLY	GLY	GLY	GLY	C	C	1014	1817
d_3	44	ASN	ASN	ASN	ASN	C	C	1016 - 1034	1819 - 1837
d_3	45	PHE	PHE	PHE	PHE	C	C	1036	1839
d_3	46	TYR	TYR	PRO	PRO	C	C	1038 - 1065	1841 - 1868
d_3	47	THR	THR	ASN	ASN	C	C	1067 - 1069	1870 - 1872
d_3	48	ILE	ILE	ILE	ILE	C	C	1071	1874
d_3	49	PRO	PRO	PRO	PRO	C	C	1073	1876
d_4	1	ALA	ALA	ILE	ILE	D	D	23 - 110	826 - 913
d_4	2	LEU	LEU	LEU	LEU	D	D	112	915
d_4	3	PRO	PRO	GLU	GLU	D	D	114 - 117	917 - 920
d_4	4	TYR	TYR	ASP	ASP	D	D	119 - 120	922 - 923
d_4	5	THR	THR	GLU	GLU	D	D	122 - 123	925 - 926
d_4	6	LEU	LEU	TRP	TRP	D	D	125 - 127	928 - 930
d_4	7	ARG	ARG	PHE	PHE	D	D	129 - 147	932 - 950
d_4	8	ARG	ARG	PHE	PHE	D	D	149 - 154	952 - 957
d_4	9	LEU	LEU	GLY	GLY	D	D	156 - 196	959 - 999
d_4	10	ILE	ILE	VAL	VAL	D	D	198 - 205	1001 - 1008
d_4	11	GLY	GLY	GLY	GLY	D	D	210	1013
d_4	12	PRO	PRO	ARG	ARG	D	D	212 - 214	1015 - 1017
d_4	13	THR	THR	TYR	TYR	D	D	216 - 276	1019 - 1079
d_4	14	ASP	ASP	LEU	LEU	D	D	278 - 284	1081 - 1087
d_4	15	PHE	PHE	PHE	PHE	D	D	286	1089
d_4	16	TRP	TRP	ASP	ASP	D	D	288 - 331	1091 - 1134
d_4	17	PHE	PHE	VAL	VAL	D	D	333 - 339	1136 - 1142
d_4	18	TYR	TYR	GLU	GLU	D	D	341 - 347	1144 - 1150
d_4	19	TYR	TYR	ASP	ASP	D	D	349 - 352	1152 - 1155
d_4	20	PHE	PHE	ILE	ILE	D	D	354 - 400	1157 - 1203
d_4	21	GLU	GLU	SER	SER	D	D	402 - 410	1205 - 1213
d_4	22	PHE	PHE	PHE	PHE	D	D	412	1215
d_4	23	TYR	TYR	ASN	ASN	D	D	414 - 478	1217 - 1281
d_4	24	TYR	TYR	LYS	LYS	D	D	480 - 542	1283 - 1345
d_4	25	GLY	GLY	ASP	ASP	D	D	544 - 596	1347 - 1399
d_4	26	GLU	GLU	ASP	ASP	D	D	598 - 704	1401 - 1507
d_4	27	GLN	GLN	VAL	VAL	D	D	706 - 720	1509 - 1523
d_4	28	GLN	GLN	VAL	VAL	D	D	724 - 740	1527 - 1543
d_4	29	GLU	GLU	GLN	GLN	D	D	742 - 743	1545 - 1546
d_4	30	LEU	LEU	GLY	GLY	D	D	745 - 750	1548 - 1553
d_4	31	ARG	ARG	SER	SER	D	D	756 - 757	1559 - 1560
d_4	32	GLN	GLN	SER	SER	D	D	759 - 774	1562 - 1577
d_4	33	HIS	HIS	TYR	TYR	D	D	776 - 781	1579 - 1584
d_4	34	TYR	TYR	THR	THR	D	D	783 - 793	1586 - 1596
d_4	35	ASN	ASN	ASP	ASP	D	D	796 - 813	1599 - 1616
d_4	36	THR	THR	LYS	LYS	D	D	815 - 837	1618 - 1640
d_4	37	CYS	CYS	PHE	PHE	D	D	839 - 844	1642 - 1647
d_4	38	TYR	TYR	LYS	LYS	D	D	846 - 855	1649 - 1658
d_4	39	LYS	LYS	SER	SER	D	D	857 - 882	1660 - 1685
d_4	40	HIS	HIS	GLY	GLY	D	D	884 - 930	1687 - 1733
d_4	41	ALA	ALA	ASP	ASP	D	D	932 - 984	1735 - 1787
d_4	42	ASN	ASN	LEU	LEU	D	D	986 - 1002	1789 - 1805
d_4	43	GLY	GLY	GLY	GLY	D	D	1014	1817
d_4	44	ASN	ASN	ASN	ASN	D	D	1016 - 1034	1819 - 1837
d_4	45	PHE	PHE	PHE	PHE	D	D	1036	1839
d_4	46	TYR	TYR	PRO	PRO	D	D	1038 - 1065	1841 - 1868
d_4	47	THR	THR	ASN	ASN	D	D	1067 - 1069	1870 - 1872
d_4	48	ILE	ILE	ILE	ILE	D	D	1071	1874
d_4	49	PRO	PRO	PRO	PRO	D	D	1073	1876

NCS oper:

ID	Code	Matrix	Vector
1	given	(0.999997613345, -0.00209631413585, 0.000615443316212), (-0.00209525491792, -0.999996331427, -0.00171669440534), (0.000619039789162, 0.00171540079755, -0.999998337094)	33.2055769122, 152.988687443, 28.0592609078
2	given	(-0.999997073632, -0.00115249439275, -0.00212708368882), (0.000822813114978, -0.988844531203, 0.148949038563), (-0.00227501800485, 0.148946852491, 0.988842585767)	-79.1937068705, 157.844790037, 95.8927903885
3	given	(-0.999991924811, 0.00336322108887, -0.00219978571018), (0.00364862968784, 0.98925433596, -0.146159318165), (0.00168458145079, -0.146166164105, -0.989258618692)	-46.4001632512, 10.8741728552, 146.406674132

#1: Protein	Putative type VI secretion system YD repeat-containing Rhs element Vgr protein Mass: 212823.016 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Advenella mimigardefordensis DPN7 (bacteria) Gene: MIM_c35070 / Production host: Escherichia coli B (bacteria) / References: UniProt: W0PIA9
Has protein modification	N

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal grow	Temperature: 292.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: Protein solution (1 ul, 13.8 mg/ml) was mixed with 1 ul of mother liquor (0.1 M TRIS pH 8.5, 45% PEP426, 400 mM KCl)

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
Detector	Type: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 1, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 3.36→48.48 Å / Num. obs: 70262 / % possible obs: 93.88 % / Redundancy: 3.52 % / B_iso Wilson estimate: 53.06 Å² / CC_1/2: 0.986 / CC star: 0.996 / R_merge(I) obs: 0.1586 / R_pim(I) all: 0.09792 / R_rim(I) all: 0.1869 / Net I/σ(I): 7.5
Reflection shell	Resolution: 3.36→3.48 Å / R_merge(I) obs: 0.5538 / Num. unique obs: 7161 / CC_1/2: 0.862 / CC star: 0.962 / R_pim(I) all: 0.3406 / R_rim(I) all: 0.6516 / % possible all: 95.02

-
Processing

Software

Name	Version	Classification
PHENIX	1.18.2_3874	refinement
PHENIX	1.20.1_4487	refinement
Coot	0.9.3	model building
BUSTER		refinement
XDS		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.36→48.48 Å / SU ML: 0.463 / Cross valid method: FREE R-VALUE / σ(F): 1.28 / Phase error: 34.3075
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.3173	6817	4.99 %
R_work	0.2568	129699	-
obs	0.2598	70090	91.2 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 65.79 Å²

Refinement step

Cycle: LAST / Resolution: 3.36→48.48 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	33470	0	0	0	33470

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	34270
X-RAY DIFFRACTION	f_angle_d	0.5682	46441
X-RAY DIFFRACTION	f_chiral_restr	0.0444	4799
X-RAY DIFFRACTION	f_plane_restr	0.004	6188
X-RAY DIFFRACTION	f_dihedral_angle_d	11.7969	12543

Refine LS restraints NCS

Ens-ID	Dom-ID	Asym-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)
ens_1	d_2	A	A	X-RAY DIFFRACTION	Torsion NCS	0.753943377878
ens_1	d_3	A	A	X-RAY DIFFRACTION	Torsion NCS	0.703109459278
ens_1	d_4	A	A	X-RAY DIFFRACTION	Torsion NCS	0.728520696752

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
3.36-3.4	0.41	213	0.4006	4005	X-RAY DIFFRACTION	85.45
3.4-3.44	0.3994	248	0.3465	4455	X-RAY DIFFRACTION	93.98
3.44-3.48	0.3743	241	0.2989	4572	X-RAY DIFFRACTION	93.53
3.48-3.52	0.3583	261	0.2884	4350	X-RAY DIFFRACTION	93.95
3.52-3.57	0.3465	229	0.2857	4358	X-RAY DIFFRACTION	93.46
3.57-3.62	0.3577	223	0.2829	4497	X-RAY DIFFRACTION	92.62
3.62-3.67	0.3751	229	0.2796	4311	X-RAY DIFFRACTION	91.83
3.67-3.72	0.3391	231	0.286	4380	X-RAY DIFFRACTION	92.33
3.72-3.78	0.4293	219	0.2902	4312	X-RAY DIFFRACTION	91.79
3.78-3.84	0.336	254	0.2828	4311	X-RAY DIFFRACTION	91.41
3.84-3.91	0.36	220	0.2568	4404	X-RAY DIFFRACTION	90.21
3.91-3.98	0.3052	228	0.2542	4018	X-RAY DIFFRACTION	88.98
3.98-4.06	0.335	227	0.253	4135	X-RAY DIFFRACTION	85.46
4.06-4.14	0.287	215	0.2419	4443	X-RAY DIFFRACTION	92.71
4.14-4.23	0.3151	230	0.258	4325	X-RAY DIFFRACTION	92.21
4.23-4.33	0.2839	213	0.2429	4404	X-RAY DIFFRACTION	92.71
4.33-4.44	0.2991	243	0.2425	4437	X-RAY DIFFRACTION	92.09
4.44-4.56	0.2646	229	0.2204	4281	X-RAY DIFFRACTION	92.04
4.56-4.69	0.2626	245	0.2137	4354	X-RAY DIFFRACTION	91.14
4.69-4.84	0.2485	204	0.212	4241	X-RAY DIFFRACTION	90.86
4.84-5.01	0.2922	225	0.2163	4337	X-RAY DIFFRACTION	89.52
5.01-5.21	0.3205	205	0.2385	4167	X-RAY DIFFRACTION	88.32
5.21-5.45	0.3257	230	0.2486	4175	X-RAY DIFFRACTION	88.03
5.45-5.74	0.2722	205	0.2603	4449	X-RAY DIFFRACTION	94.25
5.74-6.1	0.3621	225	0.2743	4499	X-RAY DIFFRACTION	93.54
6.1-6.57	0.3466	229	0.2781	4405	X-RAY DIFFRACTION	92.79
6.57-7.22	0.351	232	0.287	4278	X-RAY DIFFRACTION	90.93
7.23-8.27	0.2745	232	0.2585	4119	X-RAY DIFFRACTION	86.99
8.27-10.4	0.286	214	0.2154	4359	X-RAY DIFFRACTION	92.53
10.4-48.48	0.2727	218	0.2342	4318	X-RAY DIFFRACTION	90.39

Refinement TLS params.

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

ID	L11 (°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)
1	1.14242646623	0.385912994009	-0.0163386493178	1.52678758023	0.292783733225	1.62775912889	0.0681886632341	-0.0444748350706	-0.0132430440263	0.255719569115	0.0206332387939	0.0715801826398	-0.0525835838121	-0.107648341822	0.03172668418	0.3911037958	-0.00548224260649	0.00266738689659	0.235433308386	-0.0744638508736	0.336547940011	-8.25050865524	123.335628	48.6004405474
2	0.796396881547	0.367370067515	0.463813769914	0.593875338935	0.329944569298	0.987390756637	-0.0962439428272	-0.097225302449	0.0712956134506	-0.144891196151	0.088100092923	0.090301546396	-0.214597901643	0.00553494983611	0.0189011617423	0.402791258135	-0.0727071601191	0.0462748115489	0.135580914356	-0.0156767596682	0.34368834133	-1.59091627346	116.109180822	26.8758814665
3	0.396833329212	-0.0179124149837	-0.29408832488	0.559343367721	0.314415699145	0.766866247863	-0.0368145270093	-0.182622576628	0.00773018185684	0.0643657673084	-0.00326624564258	-0.00683881408283	0.0368996830064	0.105785256034	0.0356909406792	0.292594019569	-0.0466276311218	0.00574640134647	0.250008668521	-0.0308489587488	0.282262200061	-11.6350235262	95.4633490266	40.4602645022
4	0.731889102756	0.244799027668	0.309659738699	0.201730347165	-0.275721230232	1.18657448415	-0.159852028578	-0.111379022445	-0.157299928993	0.0969111610861	0.0147504362215	0.0865866082316	-0.00465903442276	-0.299212187757	0.165205759068	0.333192886417	0.0516159789707	0.0237884087944	0.26470135092	-0.02970496342	0.391204753029	-26.4128973683	72.9620217774	41.4635387531
5	0.8003208649	0.109736656029	-0.0780947436066	0.148938766056	0.279730282132	0.910570542715	-0.115567841015	-0.00867172011364	-0.296594506398	0.109373671649	0.0274533644737	-0.125833504674	0.193107863943	-0.16479283148	0.0651571487549	0.333134918936	-0.0132951884509	0.0441800640887	0.200872594178	-0.0195536840736	0.432540767846	-7.59177718052	60.5359612296	33.095684185
6	1.43754592525	0.423017918888	-0.503858403102	0.150769469594	-0.325330262997	1.55363541465	0.0536122090565	-0.155196096834	-0.443980959324	-0.0244552156286	-0.193538200083	-0.0328951115703	0.354860984207	0.239211826938	0.109394042104	0.530557449079	-0.0191716169336	0.0355726552508	0.125336728132	0.114893445642	0.430154310578	-14.6901261233	58.1346530646	45.0097681667
7	0.0719271182863	-0.100457448767	0.130275681709	1.60745447029	-0.261689354447	0.240403725406	-0.0610382102082	-0.252451288045	0.152921778868	-0.147699367852	-0.427581448114	0.0433230160862	0.0242852899604	-0.378722791864	0.278290137867	0.310383182674	-0.0653542443618	0.0183088204685	0.388083454375	0.0214383953356	0.546003145541	-6.07904101961	69.7778395477	32.1467805049
8	1.21393486009	-0.0125574890755	-0.0552622099642	0.77251687939	0.12073246665	0.85645796293	-0.139611400215	-0.0137454971264	-0.127423002801	-0.0477022634898	-0.0446118493965	0.193061363866	0.191538546283	-0.0276238297911	0.0632535373987	0.471938438612	-0.0084187042695	0.0811093438421	0.14253795093	-0.0850271246823	0.401973721724	27.6590707839	30.6400172758	-18.4142741307
9	0.88443262122	-0.575119661919	0.151140294077	0.668719357859	0.481006250641	1.12120030357	-0.239025291697	-0.0742292878613	-0.202358924227	0.0970494212886	0.0965731343178	0.107322761747	-0.0302816487638	-0.0367030974948	0.0955311638356	0.366757656583	-0.0370454195904	0.0782332680953	0.124897539568	-0.0419744223229	0.35453672235	11.7003153911	43.2385808822	-2.97084570321
10	0.569950021912	-0.159063037249	-0.129244917251	0.636988285817	0.293885317843	0.505564609749	-0.037422868039	0.0240610081451	0.0554982034231	-0.142266182975	0.06753041569	0.0541923291703	-0.0662572743364	0.0767878407204	-0.0126362929417	0.311081461322	-0.00639113822099	0.0285244256671	0.18347769445	0.0151465429012	0.340425035525	23.1980859838	76.4370093356	-10.8606323244
11	1.04599595077	0.113625753137	-0.502823080357	0.0838458250191	-0.374973228595	1.54598762159	-0.0126025967999	0.322515936912	0.234287196364	-0.109667099639	-0.0629390309226	0.3597093982	-0.321077163762	-0.0185799192203	-0.0502674165852	0.572443433264	0.109745345006	-0.0232283306909	0.378310137699	0.0577156897777	0.473200978888	13.9012526141	94.716327354	-11.3759763353
12	0.197423788967	-0.263916170223	-0.372460353115	2.75487181416	-0.350092648483	0.998694986703	0.075311899836	0.101480437275	-0.366803270904	-0.522200090296	0.0461446762115	0.339459055058	-0.163549587953	-0.0480742565389	0.091808270055	0.301466441	-0.0160136797026	-0.0333452278614	0.106240465215	-0.0987041864584	0.625539217758	26.0272231422	83.9726580047	-4.0658674404
13	0.746945722017	-0.116259966237	-0.466064987522	0.959909509318	0.211750631249	1.57440874323	-0.102009449232	-0.232915233496	-0.0125478026231	0.0757998235802	0.0165678930486	-0.0708926224945	0.351478039632	0.178094270963	0.0153072230893	0.664987193602	-0.00334177818435	0.0362160067138	0.592851428442	0.0333591943167	0.399714961109	-74.7824949814	43.9543908736	157.795507656
14	0.533743650087	0.344869559666	-0.39113896696	0.492401737078	0.0523568445361	1.13135385155	-0.0310021467892	-0.0782528928414	-0.122249388571	0.0115132643259	-0.0880669331659	-0.12472054816	0.154626291829	0.377645935701	0.0410746689616	0.470146373482	0.0426463742101	0.0218053042624	0.586749161916	0.0709629734583	0.35584284314	-55.5393224378	59.9610103914	151.048078517
15	0.621515836694	0.00226341944194	-0.190353493184	0.571063090377	0.21424811158	0.800948810915	0.0709327425253	0.0211931591951	0.0564463396445	0.0921389822589	-0.0462268691661	0.0165175279351	-0.088234057502	0.00120204231237	-0.00132871671656	0.334723213928	0.000623721149173	0.042026111063	0.54416261301	0.0131189713881	0.271322859685	-68.3987927767	86.2527205197	147.26512493
16	2.58608281014	0.0827186109014	-1.03838073223	0.898619716844	-0.728699112728	1.68221583096	-0.00901810743213	0.394337086192	0.0254280712886	-0.0789203145379	0.122441194709	0.352014652807	-0.0483617452126	-0.337742862449	-0.123784702227	0.270627928993	-0.081645583028	0.0286522045925	0.446470484538	0.0714987392402	0.388135306262	-80.4038253096	99.8349066328	130.204557942
17	0.888476858119	-0.0116091513399	-0.0339761113739	0.820390709535	-0.0804854224108	1.26220318185	-0.217418664398	-0.0725541057434	0.405209391393	0.0723788743811	0.246876163104	-0.109768493367	-0.264735949904	-0.0686435499552	0.00973812019881	0.391362538396	-0.102403261663	-0.00490854450005	0.567652203405	-0.046268811508	0.358076741694	-61.2840485411	105.785479592	140.339849517
18	0.850916545301	0.187458456098	0.199431332021	2.4700921414	0.350850012959	0.761280738553	0.120338591249	-0.233973973149	-0.412117632221	0.511506736794	-0.00937126838612	0.245143609878	0.0530186725151	0.165175632096	0.0232137346569	0.353386466298	0.02953436667	0.025851337248	0.352986814302	0.0503651926897	0.502910631687	-73.2684101914	93.3290199394	138.174514378
19	1.08036877107	0.479947103943	0.0657239333232	0.728832745758	-0.133529876222	1.30658018764	-0.0994749306496	-0.161476906193	0.0791541046077	-0.119490489201	-0.119845089605	-0.0559867694618	-0.449700891978	-0.071429520524	0.0714668800521	0.594371382215	0.154516264041	-0.017220370906	0.436771565097	0.067288228621	0.335382719654	-41.2649454236	124.945986295	85.8441621728
20	0.93137024489	0.0805811187455	-0.204489187127	0.411070473156	-0.156029494142	1.33414224492	-0.00449194830141	0.245139281116	0.02635916282	-0.01876804095	-0.109590876248	0.0593269768967	-0.095859217758	0.0194541297243	0.0604837813392	0.319732741373	0.0356471136549	0.0265706640727	0.43464050059	0.022724118873	0.263406870316	-34.1296935863	101.461507527	94.0913531639
21	0.373353986209	-0.185840977764	0.337161068608	0.853366709164	-0.0516335403026	0.941441702572	-0.0687055848572	0.00497717142224	-0.123965516631	-0.0882722353283	-0.0778555091285	-0.108515181611	0.156122262425	0.0310170191861	0.101500347732	0.330091082981	-0.0207905979083	0.0933227191713	0.643720409919	-0.0538688062883	0.36960183086	-22.2320604145	75.384467394	93.2605500633
22	0.0416022177846	-0.0180771996381	-0.333989791631	0.787489106676	0.322849374777	2.94487577331	-0.166613796029	-0.19573569645	-0.261271919947	-0.297304364333	-0.0218222760891	0.275589709369	0.26124413156	-0.195834762804	0.183485369806	0.477239559043	-0.0108801862676	0.100584248018	0.811362156661	-0.0798700924149	0.476205756535	-52.8391256219	67.3595358964	99.6470281306
23	1.63416569174	-0.164225777831	-0.476238691042	0.838073989966	-0.289575485665	1.36370498077	-0.152748202789	0.336766530291	-0.412189436841	0.00688725145354	0.112215761131	0.0444670591471	0.298827833195	0.260417352686	0.158133397153	0.366294236066	0.0178496840045	0.0174173298324	0.443444147418	0.00710141988599	0.510131804814	-29.4825365863	65.4609196864	107.48946799
24	1.28968083581	-0.0488345547697	-0.925825042737	0.502353761159	0.839449012669	1.95550718579	0.0141648087978	0.349743154073	-0.111107172682	-0.102095354573	-0.298671487065	0.26315168616	0.243560039253	-0.227031901976	0.146254033751	0.37396208574	-0.0721316432138	-0.0294131492765	0.572753812768	-0.0173953573009	0.461196958452	-37.7390749496	68.8732642912	101.065026633

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 23 through 222 )	A	A	23 - 222	1 - 200
2	2	chain 'A' and (resid 223 through 330 )	A	A	223 - 330	201 - 308
3	3	chain 'A' and (resid 331 through 599 )	A	A	331 - 599	309 - 577
4	4	chain 'A' and (resid 600 through 747 )	A	A	600 - 747	578 - 725
5	5	chain 'A' and (resid 748 through 940 )	A	A	748 - 940	726 - 905
6	6	chain 'A' and (resid 941 through 1026 )	A	A	941 - 1026	906 - 971
7	7	chain 'A' and (resid 1027 through 1076 )	A	A	1027 - 1076	972 - 1021
8	8	chain 'B' and (resid 23 through 263 )	B	B	23 - 263	1 - 241
9	9	chain 'B' and (resid 264 through 414 )	B	B	264 - 414	242 - 392
10	10	chain 'B' and (resid 415 through 892 )	B	B	415 - 892	393 - 857
11	11	chain 'B' and (resid 893 through 1020 )	B	B	893 - 1020	858 - 970
12	12	chain 'B' and (resid 1021 through 1076 )	B	B	1021 - 1076	971 - 1026
13	13	chain 'C' and (resid 23 through 289 )	C	C	23 - 289	1 - 267
14	14	chain 'C' and (resid 290 through 456 )	C	C	290 - 456	268 - 434
15	15	chain 'C' and (resid 457 through 793 )	C	C	457 - 793	435 - 771
16	16	chain 'C' and (resid 794 through 871 )	C	C	794 - 871	772 - 836
17	17	chain 'C' and (resid 872 through 1026 )	C	C	872 - 1026	837 - 970
18	18	chain 'C' and (resid 1027 through 1076 )	C	C	1027 - 1076	971 - 1020
19	19	chain 'D' and (resid 23 through 299 )	D	D	23 - 299	1 - 277
20	20	chain 'D' and (resid 300 through 597 )	D	D	300 - 597	278 - 575
21	21	chain 'D' and (resid 598 through 767 )	D	D	598 - 767	576 - 745
22	22	chain 'D' and (resid 768 through 842 )	D	D	768 - 842	746 - 807
23	23	chain 'D' and (resid 843 through 983 )	D	D	843 - 983	808 - 936
24	24	chain 'D' and (resid 984 through 1076 )	D	D	984 - 1076	937 - 1021

-
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

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

+
Jul 12, 2017. Major update of PDB

-
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

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

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

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

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

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi