PDB-1s4d: Crystal Structure Analysis of the S-adenosyl-L-methionine depende...

ID or keywords:

Entry

Database: PDB / ID: 1s4d

Title

Crystal Structure Analysis of the S-adenosyl-L-methionine dependent uroporphyrinogen-III C-methyltransferase SUMT

Components

Uroporphyrin-III C-methyltransferase

Keywords

TRANSFERASE / tetrapyrrole biosynthesis / cobalamin / SAM / SAH / uroporphyrinogen-III methyltransferase

Function / homology

Function and homology information

uroporphyrinogen-III C-methyltransferase / uroporphyrin-III C-methyltransferase activity / siroheme biosynthetic process / cobalamin biosynthetic process / methylation
Similarity search - Function

Biological species

Pseudomonas denitrificans (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.7 Å

Authors

Vevodova, J. / Graham, R.M. / Raux, E. / Schubert, H.L. / Roper, D.I. / Brindley, A.A. / Scott, A.I. / Roessner, C.A. / Stamford, N.P.J. / Stroupe, M.E. ...

Citation

Journal: J.Mol.Biol. / Year: 2004
Title: Structure/Function Studies on a S-Adenosyl-l-methionine-dependent Uroporphyrinogen III C Methyltransferase (SUMT), a Key Regulatory Enzyme of Tetrapyrrole Biosynthesis
Authors: Vevodova, J. / Graham, R.M. / Raux, E. / Schubert, H.L. / Roper, D.I. / Brindley, A.A. / Scott, A.I. / Roessner, C.A. / Stamford, N.P.J. / Stroupe, M.E. / Getzoff, E.D. / Warren, M.J. / Wilson, K.S.

History

Deposition	Jan 16, 2004	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Nov 30, 2004	Provider: repository / Type: Initial release
Revision 1.1	Apr 29, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Oct 25, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	1s4d.cif.gz	580.6 KB	Display	PDBx/mmCIF format
PDB format	pdb1s4d.ent.gz	474.6 KB	Display	PDB format
PDBx/mmJSON format	1s4d.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/s4/1s4d ftp://data.pdbj.org/pub/pdb/validation_reports/s4/1s4d	HTTPS FTP

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Related structure data

Related structure data	1pjqS S: Starting model for refinement
Similar structure data	3wnz-d 2e0n-d 1ere-2 3vmm-d 1ve2-d 3vot-2 3keo-d 2ybo-1 1v9a-d 1ere-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

1pjqS

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Uroporphyrin-III C-methyltransferase

B: Uroporphyrin-III C-methyltransferase

D: Uroporphyrin-III C-methyltransferase

E: Uroporphyrin-III C-methyltransferase

F: Uroporphyrin-III C-methyltransferase

G: Uroporphyrin-III C-methyltransferase

H: Uroporphyrin-III C-methyltransferase

I: Uroporphyrin-III C-methyltransferase

J: Uroporphyrin-III C-methyltransferase

K: Uroporphyrin-III C-methyltransferase

L: Uroporphyrin-III C-methyltransferase

M: Uroporphyrin-III C-methyltransferase

hetero molecules

358 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Uroporphyrin-III C-methyltransferase

B: Uroporphyrin-III C-methyltransferase

hetero molecules

defined by author&software
59.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: Uroporphyrin-III C-methyltransferase

E: Uroporphyrin-III C-methyltransferase

hetero molecules

defined by author&software
59.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

F: Uroporphyrin-III C-methyltransferase

G: Uroporphyrin-III C-methyltransferase

hetero molecules

defined by author&software
59.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

H: Uroporphyrin-III C-methyltransferase

I: Uroporphyrin-III C-methyltransferase

hetero molecules

defined by author&software
59.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

J: Uroporphyrin-III C-methyltransferase

K: Uroporphyrin-III C-methyltransferase

hetero molecules

defined by author&software
59.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

6

L: Uroporphyrin-III C-methyltransferase

M: Uroporphyrin-III C-methyltransferase

hetero molecules

defined by author&software
59.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	218.097, 218.097, 190.341
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	79
Space group name H-M	I4

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Refine code: 4

Dom-ID	Component-ID	Ens-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
1	1	1	VAL	VAL	GLY	GLY	A	A	17 - 21	17 - 21
2	1	1	VAL	VAL	GLY	GLY	D	C	17 - 21	17 - 21
3	1	1	VAL	VAL	GLY	GLY	F	E	17 - 21	17 - 21
4	1	1	VAL	VAL	GLY	GLY	H	G	17 - 21	17 - 21
5	1	1	VAL	VAL	GLY	GLY	J	I	17 - 21	17 - 21
6	1	1	VAL	VAL	GLY	GLY	L	K	17 - 21	17 - 21
7	2	1	GLY	GLY	PRO	PRO	A	A	23 - 27	23 - 27
8	2	1	GLY	GLY	PRO	PRO	D	C	23 - 27	23 - 27
9	2	1	GLY	GLY	PRO	PRO	F	E	23 - 27	23 - 27
10	2	1	GLY	GLY	PRO	PRO	H	G	23 - 27	23 - 27
11	2	1	GLY	GLY	PRO	PRO	J	I	23 - 27	23 - 27
12	2	1	GLY	GLY	PRO	PRO	L	K	23 - 27	23 - 27
13	3	1	LEU	LEU	HIS	HIS	A	A	29 - 33	29 - 33
14	3	1	LEU	LEU	HIS	HIS	D	C	29 - 33	29 - 33
15	3	1	LEU	LEU	HIS	HIS	F	E	29 - 33	29 - 33
16	3	1	LEU	LEU	HIS	HIS	H	G	29 - 33	29 - 33
17	3	1	LEU	LEU	HIS	HIS	J	I	29 - 33	29 - 33
18	3	1	LEU	LEU	HIS	HIS	L	K	29 - 33	29 - 33
19	4	1	ASP	ASP	VAL	VAL	A	A	80 - 86	80 - 86
20	4	1	ASP	ASP	VAL	VAL	D	C	80 - 86	80 - 86
21	4	1	ASP	ASP	VAL	VAL	F	E	80 - 86	80 - 86
22	4	1	ASP	ASP	VAL	VAL	H	G	80 - 86	80 - 86
23	4	1	ASP	ASP	VAL	VAL	J	I	80 - 86	80 - 86
24	4	1	ASP	ASP	VAL	VAL	L	K	80 - 86	80 - 86
25	5	1	GLU	GLU	ARG	ARG	A	A	87 - 90	87 - 90
26	5	1	GLU	GLU	ARG	ARG	D	C	87 - 90	87 - 90
27	5	1	GLU	GLU	ARG	ARG	F	E	87 - 90	87 - 90
28	5	1	GLU	GLU	ARG	ARG	H	G	87 - 90	87 - 90
29	5	1	GLU	GLU	ARG	ARG	J	I	87 - 90	87 - 90
30	5	1	GLU	GLU	ARG	ARG	L	K	87 - 90	87 - 90
31	6	1	GLY	GLY	GLY	GLY	A	A	92 - 109	92 - 109
32	6	1	GLY	GLY	GLY	GLY	D	C	92 - 109	92 - 109
33	6	1	GLY	GLY	GLY	GLY	F	E	92 - 109	92 - 109
34	6	1	GLY	GLY	GLY	GLY	H	G	92 - 109	92 - 109
35	6	1	GLY	GLY	GLY	GLY	J	I	92 - 109	92 - 109
36	6	1	GLY	GLY	GLY	GLY	L	K	92 - 109	92 - 109
37	7	1	PRO	PRO	VAL	VAL	A	A	122 - 143	122 - 143
38	7	1	PRO	PRO	VAL	VAL	D	C	122 - 143	122 - 143
39	7	1	PRO	PRO	VAL	VAL	F	E	122 - 143	122 - 143
40	7	1	PRO	PRO	VAL	VAL	H	G	122 - 143	122 - 143
41	7	1	PRO	PRO	VAL	VAL	J	I	122 - 143	122 - 143
42	7	1	PRO	PRO	VAL	VAL	L	K	122 - 143	122 - 143
43	8	1	SER	SER	TYR	TYR	A	A	177 - 183	177 - 183
44	8	1	SER	SER	TYR	TYR	D	C	177 - 183	177 - 183
45	8	1	SER	SER	TYR	TYR	F	E	177 - 183	177 - 183
46	8	1	SER	SER	TYR	TYR	H	G	177 - 183	177 - 183
47	8	1	SER	SER	TYR	TYR	J	I	177 - 183	177 - 183
48	8	1	SER	SER	TYR	TYR	L	K	177 - 183	177 - 183
49	9	1	ILE	ILE	ALA	ALA	A	A	189 - 194	189 - 194
50	9	1	ILE	ILE	ALA	ALA	D	C	189 - 194	189 - 194
51	9	1	ILE	ILE	ALA	ALA	F	E	189 - 194	189 - 194
52	9	1	ILE	ILE	ALA	ALA	H	G	189 - 194	189 - 194
53	9	1	ILE	ILE	ALA	ALA	J	I	189 - 194	189 - 194
54	9	1	ILE	ILE	ALA	ALA	L	K	189 - 194	189 - 194
55	10	1	ARG	ARG	PRO	PRO	A	A	201 - 216	201 - 216
56	10	1	ARG	ARG	PRO	PRO	D	C	201 - 216	201 - 216
57	10	1	ARG	ARG	PRO	PRO	F	E	201 - 216	201 - 216
58	10	1	ARG	ARG	PRO	PRO	H	G	201 - 216	201 - 216
59	10	1	ARG	ARG	PRO	PRO	J	I	201 - 216	201 - 216
60	10	1	ARG	ARG	PRO	PRO	L	K	201 - 216	201 - 216
61	11	1	GLN	GLN	GLU	GLU	A	A	218 - 222	218 - 222
62	11	1	GLN	GLN	GLU	GLU	D	C	218 - 222	218 - 222
63	11	1	GLN	GLN	GLU	GLU	F	E	218 - 222	218 - 222
64	11	1	GLN	GLN	GLU	GLU	H	G	218 - 222	218 - 222
65	11	1	GLN	GLN	GLU	GLU	J	I	218 - 222	218 - 222
66	11	1	GLN	GLN	GLU	GLU	L	K	218 - 222	218 - 222
67	12	1	ALA	ALA	TRP	TRP	A	A	241 - 257	241 - 257
68	12	1	ALA	ALA	TRP	TRP	D	C	241 - 257	241 - 257
69	12	1	ALA	ALA	TRP	TRP	F	E	241 - 257	241 - 257
70	12	1	ALA	ALA	TRP	TRP	H	G	241 - 257	241 - 257
71	12	1	ALA	ALA	TRP	TRP	J	I	241 - 257	241 - 257
72	12	1	ALA	ALA	TRP	TRP	L	K	241 - 257	241 - 257
1	1	2	LEU	LEU	PRO	PRO	B	B	19 - 27	19 - 27
2	1	2	LEU	LEU	PRO	PRO	E	D	19 - 27	19 - 27
3	1	2	LEU	LEU	PRO	PRO	G	F	19 - 27	19 - 27
4	1	2	LEU	LEU	PRO	PRO	I	H	19 - 27	19 - 27
5	1	2	LEU	LEU	PRO	PRO	K	J	19 - 27	19 - 27
6	1	2	LEU	LEU	PRO	PRO	M	L	19 - 27	19 - 27
7	2	2	LEU	LEU	ALA	ALA	B	B	29 - 35	29 - 35
8	2	2	LEU	LEU	ALA	ALA	E	D	29 - 35	29 - 35
9	2	2	LEU	LEU	ALA	ALA	G	F	29 - 35	29 - 35
10	2	2	LEU	LEU	ALA	ALA	I	H	29 - 35	29 - 35
11	2	2	LEU	LEU	ALA	ALA	K	J	29 - 35	29 - 35
12	2	2	LEU	LEU	ALA	ALA	M	L	29 - 35	29 - 35
13	3	2	ALA	ALA	VAL	VAL	B	B	41 - 43	41 - 43
14	3	2	ALA	ALA	VAL	VAL	E	D	41 - 43	41 - 43
15	3	2	ALA	ALA	VAL	VAL	G	F	41 - 43	41 - 43
16	3	2	ALA	ALA	VAL	VAL	I	H	41 - 43	41 - 43
17	3	2	ALA	ALA	VAL	VAL	K	J	41 - 43	41 - 43
18	3	2	ALA	ALA	VAL	VAL	M	L	41 - 43	41 - 43
19	4	2	ASP	ASP	GLY	GLY	B	B	80 - 92	80 - 92
20	4	2	ASP	ASP	GLY	GLY	E	D	80 - 92	80 - 92
21	4	2	ASP	ASP	GLY	GLY	G	F	80 - 92	80 - 92
22	4	2	ASP	ASP	GLY	GLY	I	H	80 - 92	80 - 92
23	4	2	ASP	ASP	GLY	GLY	K	J	80 - 92	80 - 92
24	4	2	ASP	ASP	GLY	GLY	M	L	80 - 92	80 - 92
25	5	2	GLY	GLY	GLY	GLY	B	B	100 - 109	100 - 109
26	5	2	GLY	GLY	GLY	GLY	E	D	100 - 109	100 - 109
27	5	2	GLY	GLY	GLY	GLY	G	F	100 - 109	100 - 109
28	5	2	GLY	GLY	GLY	GLY	I	H	100 - 109	100 - 109
29	5	2	GLY	GLY	GLY	GLY	K	J	100 - 109	100 - 109
30	5	2	GLY	GLY	GLY	GLY	M	L	100 - 109	100 - 109
31	6	2	PHE	PHE	GLY	GLY	B	B	123 - 132	123 - 132
32	6	2	PHE	PHE	GLY	GLY	E	D	123 - 132	123 - 132
33	6	2	PHE	PHE	GLY	GLY	G	F	123 - 132	123 - 132
34	6	2	PHE	PHE	GLY	GLY	I	H	123 - 132	123 - 132
35	6	2	PHE	PHE	GLY	GLY	K	J	123 - 132	123 - 132
36	6	2	PHE	PHE	GLY	GLY	M	L	123 - 132	123 - 132
37	7	2	GLY	GLY	ARG	ARG	B	B	134 - 146	134 - 146
38	7	2	GLY	GLY	ARG	ARG	E	D	134 - 146	134 - 146
39	7	2	GLY	GLY	ARG	ARG	G	F	134 - 146	134 - 146
40	7	2	GLY	GLY	ARG	ARG	I	H	134 - 146	134 - 146
41	7	2	GLY	GLY	ARG	ARG	K	J	134 - 146	134 - 146
42	7	2	GLY	GLY	ARG	ARG	M	L	134 - 146	134 - 146
43	8	2	VAL	VAL	ASN	ASN	B	B	148 - 149	148 - 149
44	8	2	VAL	VAL	ASN	ASN	E	D	148 - 149	148 - 149
45	8	2	VAL	VAL	ASN	ASN	G	F	148 - 149	148 - 149
46	8	2	VAL	VAL	ASN	ASN	I	H	148 - 149	148 - 149
47	8	2	VAL	VAL	ASN	ASN	K	J	148 - 149	148 - 149
48	8	2	VAL	VAL	ASN	ASN	M	L	148 - 149	148 - 149
49	9	2	ALA	ALA	THR	THR	B	B	151 - 156	151 - 156
50	9	2	ALA	ALA	THR	THR	E	D	151 - 156	151 - 156
51	9	2	ALA	ALA	THR	THR	G	F	151 - 156	151 - 156
52	9	2	ALA	ALA	THR	THR	I	H	151 - 156	151 - 156
53	9	2	ALA	ALA	THR	THR	K	J	151 - 156	151 - 156
54	9	2	ALA	ALA	THR	THR	M	L	151 - 156	151 - 156
55	10	2	VAL	VAL	TYR	TYR	B	B	179 - 183	179 - 183
56	10	2	VAL	VAL	TYR	TYR	E	D	179 - 183	179 - 183
57	10	2	VAL	VAL	TYR	TYR	G	F	179 - 183	179 - 183
58	10	2	VAL	VAL	TYR	TYR	I	H	179 - 183	179 - 183
59	10	2	VAL	VAL	TYR	TYR	K	J	179 - 183	179 - 183
60	10	2	VAL	VAL	TYR	TYR	M	L	179 - 183	179 - 183
61	11	2	GLU	GLU	GLU	GLU	B	B	205 - 222	205 - 222
62	11	2	GLU	GLU	GLU	GLU	E	D	205 - 222	205 - 222
63	11	2	GLU	GLU	GLU	GLU	G	F	205 - 222	205 - 222
64	11	2	GLU	GLU	GLU	GLU	I	H	205 - 222	205 - 222
65	11	2	GLU	GLU	GLU	GLU	K	J	205 - 222	205 - 222
66	11	2	GLU	GLU	GLU	GLU	M	L	205 - 222	205 - 222
67	12	2	ILE	ILE	ALA	ALA	B	B	242 - 254	242 - 254
68	12	2	ILE	ILE	ALA	ALA	E	D	242 - 254	242 - 254
69	12	2	ILE	ILE	ALA	ALA	G	F	242 - 254	242 - 254
70	12	2	ILE	ILE	ALA	ALA	I	H	242 - 254	242 - 254
71	12	2	ILE	ILE	ALA	ALA	K	J	242 - 254	242 - 254
72	12	2	ILE	ILE	ALA	ALA	M	L	242 - 254	242 - 254
73	13	2	ASP	ASP	TRP	TRP	B	B	256 - 257	256 - 257
74	13	2	ASP	ASP	TRP	TRP	E	D	256 - 257	256 - 257
75	13	2	ASP	ASP	TRP	TRP	G	F	256 - 257	256 - 257
76	13	2	ASP	ASP	TRP	TRP	I	H	256 - 257	256 - 257
77	13	2	ASP	ASP	TRP	TRP	K	J	256 - 257	256 - 257
78	13	2	ASP	ASP	TRP	TRP	M	L	256 - 257	256 - 257

NCS ensembles :

ID
1
2

Details

The biological unit is a homodimer. There are six independent dimers in the asymmetric unit.

#1: Protein	Uroporphyrin-III C-methyltransferase / S-adenosyl-L-methionine uroporphyrinogen-III C-methyltransferase / Urogen III methylase / SUMT / ...S-adenosyl-L-methionine uroporphyrinogen-III C-methyltransferase / Urogen III methylase / SUMT / Uroporphyrinogen III methylase / UROM Mass: 29286.779 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas denitrificans (bacteria) / Gene: COBA / Plasmid: pET14b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P21631, uroporphyrinogen-III C-methyltransferase
#2: Chemical	ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₁₄H₂₀N₆O₅S
#3: Chemical	... ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 523 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.45 Å³/Da / Density % sol: 64.07 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: PEG 20000, sodium citrate, lithium sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.978 Å
Detector	Type: MARRESEARCH / Detector: IMAGE PLATE / Details: mirrors
Radiation	Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.978 Å / Relative weight: 1
Reflection	Resolution: 2.7→19.84 Å / Num. all: 937874 / Num. obs: 121731 / % possible obs: 100 % / Redundancy: 7.7 % / B_iso Wilson estimate: 58.9 Å² / R_merge(I) obs: 0.057 / R_sym value: 0.077 / Net I/σ(I): 19.52
Reflection shell	Resolution: 2.7→2.8 Å / Redundancy: 7.2 % / R_merge(I) obs: 0.416 / Mean I/σ(I) obs: 3.27 / Num. unique all: 12142 / R_sym value: 0.486 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.1.24	refinement
DENZO		data reduction
SCALEPACK		data scaling
AMoRE		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PJQ

1pjq

Resolution: 2.7→19.84 Å / Cor.coef. F_o:F_c: 0.927 / Cor.coef. F_o:F_c free: 0.899 / SU B: 11.376 / SU ML: 0.238 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.613 / ESU R Free: 0.323 / Stereochemistry target values: Engh & Huber
Details: TLS & restrained refinement with maximum likelihood procedure has been used.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26032	6099	5 %	RANDOM
R_work	0.21286	-	-	-
obs	0.21526	115288	99.72 %	-
all	-	115288	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 30.959 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.03 Å²	0 Å²	0 Å²
2-	-	0.03 Å²	0 Å²
3-	-	-	-0.06 Å²

Refinement step

Cycle: LAST / Resolution: 2.7→19.84 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	22413	0	468	523	23404

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.021	23368
X-RAY DIFFRACTION	r_angle_refined_deg	1.744	1.984	31780
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.704	5	3046
X-RAY DIFFRACTION	r_chiral_restr	0.113	0.2	3710
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	17527
X-RAY DIFFRACTION	r_nbd_refined	0.247	0.2	11855
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.191	0.2	880
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.281	0.2	109
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.34	0.2	18
X-RAY DIFFRACTION	r_mcbond_it	0.762	1.5	15269
X-RAY DIFFRACTION	r_mcangle_it	1.393	2	24232
X-RAY DIFFRACTION	r_scbond_it	1.673	3	8099
X-RAY DIFFRACTION	r_scangle_it	2.885	4.5	7548

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	865	medium positional	0.27	0.5
1	2	D	865	medium positional	0.24	0.5
1	3	F	865	medium positional	0.2	0.5
1	4	H	865	medium positional	0.23	0.5
1	5	J	865	medium positional	0.33	0.5
1	6	L	865	medium positional	0.29	0.5
2	1	B	802	medium positional	0.24	0.5
2	2	E	802	medium positional	0.23	0.5
2	3	G	802	medium positional	0.29	0.5
2	4	I	802	medium positional	0.23	0.5
2	5	K	802	medium positional	0.23	0.5
2	6	M	802	medium positional	0.31	0.5
1	1	A	865	medium thermal	0.6	2
1	2	D	865	medium thermal	0.66	2
1	3	F	865	medium thermal	0.53	2
1	4	H	865	medium thermal	0.78	2
1	5	J	865	medium thermal	0.54	2
1	6	L	865	medium thermal	0.65	2
2	1	B	802	medium thermal	0.77	2
2	2	E	802	medium thermal	0.64	2
2	3	G	802	medium thermal	0.65	2
2	4	I	802	medium thermal	0.95	2
2	5	K	802	medium thermal	0.55	2
2	6	M	802	medium thermal	0.63	2

LS refinement shell

Resolution: 2.7→2.77 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.34	457
R_work	0.278	8517

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	1.2591	-0.18	0.4227	1.9446	-0.0683	0.8094	-0.1406	-0.1681	-0.0555	0.2305	0.0862	-0.0855	0.0133	-0.0709	0.0544	0.1082	0.0099	0.011	0.069	-0.0035	0.0827	78.2945	88.9299	0.2587
2	1.2223	0.4089	-0.137	0.8007	0.3449	1.7308	-0.0675	-0.0803	-0.1194	0.1171	0.0969	-0.1561	0.2509	0.1437	-0.0294	0.2069	-0.0007	0.0365	0.0633	-0.0072	0.0867	111.0786	39.1186	-43.3979
3	1.81	-0.1872	-0.0423	0.8326	0.1925	1.9723	-0.1646	-0.0704	-0.1652	0.1437	0.0779	-0.1673	0.2197	0.1756	0.0867	0.1528	0.0983	-0.0294	0.1185	-0.0852	0.2773	79.7478	79.1887	-80.6571
4	1.1117	0.3171	-0.5427	0.9718	-0.1324	0.5926	-0.0518	0.1081	0.0324	-0.1885	0.1318	0.1109	-0.0015	-0.1201	-0.08	0.1264	-0.0265	0.0107	0.0925	0.0757	0.0708	64.5786	33.6802	-22.2321
5	1.5584	-0.0156	-0.5063	1.8138	-0.4493	1.9487	-0.138	0.1888	-0.2628	-0.164	0.1029	-0.0966	0.4551	0.0875	0.0351	0.2615	0.081	0.0414	0.1861	-0.0117	0.1242	83.7598	-18.1221	6.2747
6	1.9451	0.1314	-0.5165	3.8607	1.0635	3.3376	0.1041	0.3113	0.2486	-0.4649	-0.1283	-0.3888	-0.6389	0.0869	0.0242	0.3939	0.0532	0.0525	0.2731	0.1443	0.4621	35.6034	-7.9967	-44.3286

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	6 - 158
2	X-RAY DIFFRACTION	1	A	166 - 270
3	X-RAY DIFFRACTION	1	B	4 - 267
4	X-RAY DIFFRACTION	2	D	7 - 263
5	X-RAY DIFFRACTION	2	E	4 - 270
6	X-RAY DIFFRACTION	3	F	7 - 158
7	X-RAY DIFFRACTION	3	F	164 - 269
8	X-RAY DIFFRACTION	3	G	8 - 162
9	X-RAY DIFFRACTION	3	G	165 - 267
10	X-RAY DIFFRACTION	4	H	6 - 159
11	X-RAY DIFFRACTION	4	H	167 - 271
12	X-RAY DIFFRACTION	4	I	4 - 269
13	X-RAY DIFFRACTION	5	J	6 - 159
14	X-RAY DIFFRACTION	5	J	167 - 268
15	X-RAY DIFFRACTION	5	K	5 - 263
16	X-RAY DIFFRACTION	6	L	7 - 158
17	X-RAY DIFFRACTION	6	L	164 - 260
18	X-RAY DIFFRACTION	6	M	10 - 159
19	X-RAY DIFFRACTION	6	M	167 - 269

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