PDB-3cky: Structural and Kinetic Properties of a beta-hydroxyacid dehydroge...

ID or keywords:

Entry

Database: PDB / ID: 3cky

Title

Structural and Kinetic Properties of a beta-hydroxyacid dehydrogenase involved in nicotinate fermentation

Components

2-hydroxymethyl glutarate dehydrogenase

Keywords

OXIDOREDUCTASE / rossmann fold / two domain enzyme

Function / homology

Function and homology information

2-hydroxymethylglutarate dehydrogenase / 2-hydroxymethylglutarate dehydrogenase activity / nicotinate catabolic process / NAD binding / NADP binding
Similarity search - Function

Biological species

Eubacterium barkeri (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.3 Å

Authors

Reitz, S. / Alhapel, A. / Pierik, A.J. / Essen, L.-O.

Citation

Journal: J.Mol.Biol. / Year: 2008
Title: Structural and Kinetic Properties of a beta-Hydroxyacid Dehydrogenase Involved in Nicotinate Fermentation.
Authors: Reitz, S. / Alhapel, A. / Essen, L.O. / Pierik, A.J.

History

Deposition	Mar 18, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 26, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Feb 21, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3cky.cif.gz	215.9 KB	Display	PDBx/mmCIF format
PDB format	pdb3cky.ent.gz	173.7 KB	Display	PDB format
PDBx/mmJSON format	3cky.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ck/3cky ftp://data.pdbj.org/pub/pdb/validation_reports/ck/3cky	HTTPS FTP

-
Related structure data

Similar structure data	6sm7-d 6smy-d 5o4j-d 3jv2-1 5o4n-d 5y28-d 6bdx-1 3l4j-d 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

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#127 - Jul 2010 Crystallins similarity (2) #111 - Mar 2009 Hydrogenase similarity (1) #228 - Dec 2018 Directed Evolution of Enzymes similarity (1)

Deposited unit

A: 2-hydroxymethyl glutarate dehydrogenase

B: 2-hydroxymethyl glutarate dehydrogenase

C: 2-hydroxymethyl glutarate dehydrogenase

D: 2-hydroxymethyl glutarate dehydrogenase

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

1

Idetical with deposited unit
defined by author&software

2

A: 2-hydroxymethyl glutarate dehydrogenase

D: 2-hydroxymethyl glutarate dehydrogenase

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

3

B: 2-hydroxymethyl glutarate dehydrogenase

C: 2-hydroxymethyl glutarate dehydrogenase

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

Unit cell

Length a, b, c (Å)	82.978, 175.779, 83.709
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	ILE	ILE	PHE	PHE	1	A	A	7 - 9	7 - 9
2	1	1	ILE	ILE	PHE	PHE	1	B	B	7 - 9	7 - 9
3	1	1	ILE	ILE	PHE	PHE	1	C	C	7 - 9	7 - 9
4	2	1	GLY	GLY	GLY	GLY	1	A	A	11	11
5	2	1	GLY	GLY	GLY	GLY	1	B	B	11	11
6	2	1	GLY	GLY	GLY	GLY	1	C	C	11	11
7	3	1	GLY	GLY	GLY	GLY	1	A	A	13 - 16	13 - 16
8	3	1	GLY	GLY	GLY	GLY	1	B	B	13 - 16	13 - 16
9	3	1	GLY	GLY	GLY	GLY	1	C	C	13 - 16	13 - 16
10	4	1	PRO	PRO	LEU	LEU	1	A	A	18 - 24	18 - 24
11	4	1	PRO	PRO	LEU	LEU	1	B	B	18 - 24	18 - 24
12	4	1	PRO	PRO	LEU	LEU	1	C	C	18 - 24	18 - 24
13	5	1	GLU	GLU	GLY	GLY	1	A	A	26 - 27	26 - 27
14	5	1	GLU	GLU	GLY	GLY	1	B	B	26 - 27	26 - 27
15	5	1	GLU	GLU	GLY	GLY	1	C	C	26 - 27	26 - 27
16	6	1	THR	THR	PHE	PHE	1	A	A	29 - 33	29 - 33
17	6	1	THR	THR	PHE	PHE	1	B	B	29 - 33	29 - 33
18	6	1	THR	THR	PHE	PHE	1	C	C	29 - 33	29 - 33
19	7	1	ALA	ALA	VAL	VAL	1	A	A	38 - 43	38 - 43
20	7	1	ALA	ALA	VAL	VAL	1	B	B	38 - 43	38 - 43
21	7	1	ALA	ALA	VAL	VAL	1	C	C	38 - 43	38 - 43
22	8	1	ALA	ALA	ALA	ALA	1	A	A	45	45
23	8	1	ALA	ALA	ALA	ALA	1	B	B	45	45
24	8	1	ALA	ALA	ALA	ALA	1	C	C	45	45
25	9	1	GLY	GLY	CYS	CYS	1	A	A	47 - 51	47 - 51
26	9	1	GLY	GLY	CYS	CYS	1	B	B	47 - 51	47 - 51
27	9	1	GLY	GLY	CYS	CYS	1	C	C	47 - 51	47 - 51
28	10	1	ASN	ASN	ASN	ASN	1	A	A	53 - 54	53 - 54
29	10	1	ASN	ASN	ASN	ASN	1	B	B	53 - 54	53 - 54
30	10	1	ASN	ASN	ASN	ASN	1	C	C	53 - 54	53 - 54
31	11	1	VAL	VAL	VAL	VAL	1	A	A	57 - 74	57 - 74
32	11	1	VAL	VAL	VAL	VAL	1	B	B	57 - 74	57 - 74
33	11	1	VAL	VAL	VAL	VAL	1	C	C	57 - 74	57 - 74
34	12	1	THR	THR	VAL	VAL	1	A	A	76 - 77	76 - 77
35	12	1	THR	THR	VAL	VAL	1	B	B	76 - 77	76 - 77
36	12	1	THR	THR	VAL	VAL	1	C	C	76 - 77	76 - 77
37	13	1	ASN	ASN	CYS	CYS	1	A	A	79 - 88	79 - 88
38	13	1	ASN	ASN	CYS	CYS	1	B	B	79 - 88	79 - 88
39	13	1	ASN	ASN	CYS	CYS	1	C	C	79 - 88	79 - 88
40	14	1	ALA	ALA	VAL	VAL	1	A	A	90 - 93	90 - 93
41	14	1	ALA	ALA	VAL	VAL	1	B	B	90 - 93	90 - 93
42	14	1	ALA	ALA	VAL	VAL	1	C	C	90 - 93	90 - 93
43	15	1	VAL	VAL	SER	SER	1	A	A	95 - 98	95 - 98
44	15	1	VAL	VAL	SER	SER	1	B	B	95 - 98	95 - 98
45	15	1	VAL	VAL	SER	SER	1	C	C	95 - 98	95 - 98
46	16	1	VAL	VAL	THR	THR	1	A	A	100 - 105	100 - 105
47	16	1	VAL	VAL	THR	THR	1	B	B	100 - 105	100 - 105
48	16	1	VAL	VAL	THR	THR	1	C	C	100 - 105	100 - 105
49	17	1	ALA	ALA	ALA	ALA	1	A	A	109	109
50	17	1	ALA	ALA	ALA	ALA	1	B	B	109	109
51	17	1	ALA	ALA	ALA	ALA	1	C	C	109	109
52	18	1	VAL	VAL	ALA	ALA	1	A	A	111 - 113	111 - 113
53	18	1	VAL	VAL	ALA	ALA	1	B	B	111 - 113	111 - 113
54	18	1	VAL	VAL	ALA	ALA	1	C	C	111 - 113	111 - 113
55	19	1	GLY	GLY	TYR	TYR	1	A	A	116 - 119	116 - 119
56	19	1	GLY	GLY	TYR	TYR	1	B	B	116 - 119	116 - 119
57	19	1	GLY	GLY	TYR	TYR	1	C	C	116 - 119	116 - 119
58	20	1	ASP	ASP	PHE	PHE	1	A	A	121 - 147	121 - 147
59	20	1	ASP	ASP	PHE	PHE	1	B	B	121 - 147	121 - 147
60	20	1	ASP	ASP	PHE	PHE	1	C	C	121 - 147	121 - 147
61	21	1	ILE	ILE	GLY	GLY	1	A	A	150 - 158	150 - 158
62	21	1	ILE	ILE	GLY	GLY	1	B	B	150 - 158	150 - 158
63	21	1	ILE	ILE	GLY	GLY	1	C	C	150 - 158	150 - 158
64	22	1	ASP	ASP	GLY	GLY	1	A	A	160 - 168	160 - 168
65	22	1	ASP	ASP	GLY	GLY	1	B	B	160 - 168	160 - 168
66	22	1	ASP	ASP	GLY	GLY	1	C	C	160 - 168	160 - 168
1	1	2	ALA	ALA	VAL	VAL	1	A	A	169 - 173	169 - 173
2	1	2	ALA	ALA	VAL	VAL	1	B	B	169 - 173	169 - 173
3	1	2	ALA	ALA	VAL	VAL	1	C	C	169 - 173	169 - 173
4	1	2	ALA	ALA	VAL	VAL	1	D	D	169 - 173	169 - 173
5	2	2	ILE	ILE	LEU	LEU	1	A	A	175 - 200	175 - 200
6	2	2	ILE	ILE	LEU	LEU	1	B	B	175 - 200	175 - 200
7	2	2	ILE	ILE	LEU	LEU	1	C	C	175 - 200	175 - 200
8	2	2	ILE	ILE	LEU	LEU	1	D	D	175 - 200	175 - 200
9	3	2	PRO	PRO	PRO	PRO	1	A	A	202	202
10	3	2	PRO	PRO	PRO	PRO	1	B	B	202	202
11	3	2	PRO	PRO	PRO	PRO	1	C	C	202	202
12	3	2	PRO	PRO	PRO	PRO	1	D	D	202	202
13	4	2	MET	MET	GLN	GLN	1	A	A	205 - 206	205 - 206
14	4	2	MET	MET	GLN	GLN	1	B	B	205 - 206	205 - 206
15	4	2	MET	MET	GLN	GLN	1	C	C	205 - 206	205 - 206
16	4	2	MET	MET	GLN	GLN	1	D	D	205 - 206	205 - 206
17	5	2	ILE	ILE	GLY	GLY	1	A	A	209 - 210	209 - 210
18	5	2	ILE	ILE	GLY	GLY	1	B	B	209 - 210	209 - 210
19	5	2	ILE	ILE	GLY	GLY	1	C	C	209 - 210	209 - 210
20	5	2	ILE	ILE	GLY	GLY	1	D	D	209 - 210	209 - 210
21	6	2	SER	SER	GLY	GLY	1	A	A	213 - 214	213 - 214
22	6	2	SER	SER	GLY	GLY	1	B	B	213 - 214	213 - 214
23	6	2	SER	SER	GLY	GLY	1	C	C	213 - 214	213 - 214
24	6	2	SER	SER	GLY	GLY	1	D	D	213 - 214	213 - 214
25	7	2	SER	SER	MET	MET	1	A	A	216 - 219	216 - 219
26	7	2	SER	SER	MET	MET	1	B	B	216 - 219	216 - 219
27	7	2	SER	SER	MET	MET	1	C	C	216 - 219	216 - 219
28	7	2	SER	SER	MET	MET	1	D	D	216 - 219	216 - 219
29	8	2	ALA	ALA	LYS	LYS	1	A	A	221 - 222	221 - 222
30	8	2	ALA	ALA	LYS	LYS	1	B	B	221 - 222	221 - 222
31	8	2	ALA	ALA	LYS	LYS	1	C	C	221 - 222	221 - 222
32	8	2	ALA	ALA	LYS	LYS	1	D	D	221 - 222	221 - 222
33	9	2	GLU	GLU	ILE	ILE	1	A	A	224 - 227	224 - 227
34	9	2	GLU	GLU	ILE	ILE	1	B	B	224 - 227	224 - 227
35	9	2	GLU	GLU	ILE	ILE	1	C	C	224 - 227	224 - 227
36	9	2	GLU	GLU	ILE	ILE	1	D	D	224 - 227	224 - 227
37	10	2	SER	SER	ASP	ASP	1	A	A	229 - 239	229 - 239
38	10	2	SER	SER	ASP	ASP	1	B	B	229 - 239	229 - 239
39	10	2	SER	SER	ASP	ASP	1	C	C	229 - 239	229 - 239
40	10	2	SER	SER	ASP	ASP	1	D	D	229 - 239	229 - 239
41	11	2	GLN	GLN	HIS	HIS	1	A	A	241 - 242	241 - 242
42	11	2	GLN	GLN	HIS	HIS	1	B	B	241 - 242	241 - 242
43	11	2	GLN	GLN	HIS	HIS	1	C	C	241 - 242	241 - 242
44	11	2	GLN	GLN	HIS	HIS	1	D	D	241 - 242	241 - 242
45	12	2	ASP	ASP	ALA	ALA	1	A	A	244 - 263	244 - 263
46	12	2	ASP	ASP	ALA	ALA	1	B	B	244 - 263	244 - 263
47	12	2	ASP	ASP	ALA	ALA	1	C	C	244 - 263	244 - 263
48	12	2	ASP	ASP	ALA	ALA	1	D	D	244 - 263	244 - 263
49	13	2	ALA	ALA	GLY	GLY	1	A	A	265 - 278	265 - 278
50	13	2	ALA	ALA	GLY	GLY	1	B	B	265 - 278	265 - 278
51	13	2	ALA	ALA	GLY	GLY	1	C	C	265 - 278	265 - 278
52	13	2	ALA	ALA	GLY	GLY	1	D	D	265 - 278	265 - 278
53	14	2	GLU	GLU	ASP	ASP	1	A	A	280 - 281	280 - 281
54	14	2	GLU	GLU	ASP	ASP	1	B	B	280 - 281	280 - 281
55	14	2	GLU	GLU	ASP	ASP	1	C	C	280 - 281	280 - 281
56	14	2	GLU	GLU	ASP	ASP	1	D	D	280 - 281	280 - 281
57	15	2	SER	SER	GLU	GLU	4	A	A	283 - 290	283 - 290
58	15	2	SER	SER	GLU	GLU	4	B	B	283 - 290	283 - 290
59	15	2	SER	SER	GLU	GLU	4	C	C	283 - 290	283 - 290
60	15	2	SER	SER	GLU	GLU	4	D	D	283 - 290	283 - 290
61	16	2	MET	MET	GLY	GLY	4	A	A	292 - 299	292 - 299
62	16	2	MET	MET	GLY	GLY	4	B	B	292 - 299	292 - 299
63	16	2	MET	MET	GLY	GLY	4	C	C	292 - 299	292 - 299
64	16	2	MET	MET	GLY	GLY	4	D	D	292 - 299	292 - 299
1	1	3	PHE	PHE	PHE	PHE	1	A	A	9	9
2	1	3	PHE	PHE	PHE	PHE	1	D	D	9	9
3	2	3	GLY	GLY	GLY	GLY	1	A	A	11	11
4	2	3	GLY	GLY	GLY	GLY	1	D	D	11	11
5	3	3	GLY	GLY	ALA	ALA	1	A	A	13 - 14	13 - 14
6	3	3	GLY	GLY	ALA	ALA	1	D	D	13 - 14	13 - 14
7	4	3	VAL	VAL	VAL	VAL	1	A	A	57 - 74	57 - 74
8	4	3	VAL	VAL	VAL	VAL	1	D	D	57 - 74	57 - 74
9	5	3	THR	THR	VAL	VAL	1	A	A	76 - 77	76 - 77
10	5	3	THR	THR	VAL	VAL	1	D	D	76 - 77	76 - 77
11	6	3	ASN	ASN	ASN	ASN	1	A	A	79	79
12	6	3	ASN	ASN	ASN	ASN	1	D	D	79	79
13	7	3	THR	THR	VAL	VAL	1	A	A	92 - 93	92 - 93
14	7	3	THR	THR	VAL	VAL	1	D	D	92 - 93	92 - 93
15	8	3	VAL	VAL	SER	SER	1	A	A	95 - 98	95 - 98
16	8	3	VAL	VAL	SER	SER	1	D	D	95 - 98	95 - 98
17	9	3	VAL	VAL	THR	THR	1	A	A	100 - 105	100 - 105
18	9	3	VAL	VAL	THR	THR	1	D	D	100 - 105	100 - 105
19	10	3	ALA	ALA	ALA	ALA	1	A	A	109	109
20	10	3	ALA	ALA	ALA	ALA	1	D	D	109	109
21	11	3	VAL	VAL	ALA	ALA	1	A	A	111 - 113	111 - 113
22	11	3	VAL	VAL	ALA	ALA	1	D	D	111 - 113	111 - 113
23	12	3	GLY	GLY	TYR	TYR	1	A	A	116 - 119	116 - 119
24	12	3	GLY	GLY	TYR	TYR	1	D	D	116 - 119	116 - 119
25	13	3	ASP	ASP	PHE	PHE	1	A	A	121 - 147	121 - 147
26	13	3	ASP	ASP	PHE	PHE	1	D	D	121 - 147	121 - 147
27	14	3	ILE	ILE	GLY	GLY	1	A	A	150 - 158	150 - 158
28	14	3	ILE	ILE	GLY	GLY	1	D	D	150 - 158	150 - 158
29	15	3	ASP	ASP	GLY	GLY	1	A	A	160 - 168	160 - 168
30	15	3	ASP	ASP	GLY	GLY	1	D	D	160 - 168	160 - 168

NCS ensembles :

ID
1
2
3

Details

The biological unit is a tetramer. There is 1 biological unit in the asymmetric unit.

#1: Protein	2-hydroxymethyl glutarate dehydrogenase Mass: 30898.869 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Eubacterium barkeri (bacteria) / Gene: Hgd / Plasmid: pPR-IBA2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q0QLF5, 2-hydroxymethylglutarate dehydrogenase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 447 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

2-hydroxymethyl glutarate dehydrogenase

Mass: 30898.869 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Eubacterium barkeri (bacteria) / Gene: Hgd / Plasmid: pPR-IBA2 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q0QLF5, 2-hydroxymethylglutarate dehydrogenase

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 447 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.47 Å³/Da / Density % sol: 50.2 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion / pH: 5.5 Details: 19% PEG 8000, 0.1 M Sodium cacodylate, 0.1 M Ammonium sulfate, pH 5.5, VAPOR DIFFUSION, temperature 291K

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

EMBL/DESY, HAMBURG

/ Beamline: BW7A / Wavelength: 0.9795 Å

Detector

Type: MARRESEARCH / Detector: CCD / Date: Sep 27, 2005

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9795 Å / Relative weight: 1

Reflection

Resolution: 2.3→41.849 Å / Num. obs: 55151 / % possible obs: 94.1 % / Redundancy: 4.6 % / R_merge(I) obs: 0.109 / R_sym value: 0.109 / Net I/σ(I): 5.2

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	R_sym value	% possible all
2.3-2.42	3.7	0.384	2	22272	6091	0.384	77.2
2.42-2.57	4.6	0.305	2.5	30485	6678	0.305	89.1
2.57-2.75	4.5	0.24	3	29574	6629	0.24	93.7
2.75-2.97	4.5	0.176	4.1	29520	6538	0.176	99
2.97-3.25	4.8	0.137	4.9	29294	6100	0.137	99.9
3.25-3.64	4.9	0.106	5.9	26923	5548	0.106	99.9
3.64-4.2	4.8	0.085	7	23861	4936	0.085	99.9
4.2-5.14	4.8	0.074	7.6	20195	4175	0.074	99.6
5.14-7.27	4.8	0.071	7.9	15665	3275	0.071	99.6
7.27-41.85	4.5	0.057	8.8	8408	1865	0.057	97

-
Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	3.5 Å	24.56 Å
Translation	3.5 Å	24.56 Å

-
Processing

Software

Name	Version	Classification
SCALA		data scaling
PHASER		phasing
REFMAC		refinement
PDB_EXTRACT	3.004	data extraction
MOSFLM		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.3→24.47 Å / Cor.coef. F_o:F_c: 0.941 / Cor.coef. F_o:F_c free: 0.929 / SU B: 12.031 / SU ML: 0.153 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.338 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.222	2674	5.1 %	RANDOM
R_work	0.194	-	-	-
obs	0.195	52485	95.06 %	-
all	-	55151	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 43.011 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-3.08 Å²	0 Å²	0 Å²
2-	-	1.55 Å²	0 Å²
3-	-	-	1.52 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→24.47 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8045	0	0	447	8492

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.022	8140
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	5325
X-RAY DIFFRACTION	r_angle_refined_deg	1.063	1.981	10977
X-RAY DIFFRACTION	r_angle_other_deg	0.871	3	13227
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.376	5	1133
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.361	26.746	252
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.286	15	1442
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.398	15	12
X-RAY DIFFRACTION	r_chiral_restr	0.057	0.2	1305
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	9143
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	1393
X-RAY DIFFRACTION	r_nbd_refined	0.203	0.2	2051
X-RAY DIFFRACTION	r_nbd_other	0.175	0.2	5429
X-RAY DIFFRACTION	r_nbtor_refined	0.165	0.2	4223
X-RAY DIFFRACTION	r_nbtor_other	0.086	0.2	4104
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.159	0.2	471
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.045	0.2	1
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.179	0.2	18
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.227	0.2	35
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.197	0.2	9
X-RAY DIFFRACTION	r_mcbond_it	0.548	1.5	7182
X-RAY DIFFRACTION	r_mcbond_other	0.085	1.5	2372
X-RAY DIFFRACTION	r_mcangle_it	0.548	2	8794
X-RAY DIFFRACTION	r_scbond_it	1.279	3	2919
X-RAY DIFFRACTION	r_scangle_it	1.878	4.5	2178

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	1416	TIGHT POSITIONAL	0.02	0.05
1	2	B	1416	TIGHT POSITIONAL	0.02	0.05
1	3	C	1416	TIGHT POSITIONAL	0.02	0.05
1	1	A	1416	TIGHT THERMAL	0.04	0.5
1	2	B	1416	TIGHT THERMAL	0.06	0.5
1	3	C	1416	TIGHT THERMAL	0.04	0.5
2	1	A	1133	TIGHT POSITIONAL	0.03	0.05
2	2	B	1133	TIGHT POSITIONAL	0.04	0.05
2	3	C	1133	TIGHT POSITIONAL	0.03	0.05
2	4	D	1133	TIGHT POSITIONAL	0.03	0.05
2	1	A	186	MEDIUM POSITIONAL	0.45	0.5
2	2	B	186	MEDIUM POSITIONAL	0.26	0.5
2	3	C	186	MEDIUM POSITIONAL	0.33	0.5
2	4	D	186	MEDIUM POSITIONAL	0.31	0.5
2	1	A	1133	TIGHT THERMAL	0.09	0.5
2	2	B	1133	TIGHT THERMAL	0.08	0.5
2	3	C	1133	TIGHT THERMAL	0.08	0.5
2	4	D	1133	TIGHT THERMAL	0.07	0.5
2	1	A	186	MEDIUM THERMAL	0.39	2
2	2	B	186	MEDIUM THERMAL	0.34	2
2	3	C	186	MEDIUM THERMAL	0.39	2
2	4	D	186	MEDIUM THERMAL	0.31	2
3	1	A	977	TIGHT POSITIONAL	0.02	0.05
3	1	A	977	TIGHT THERMAL	0.05	0.5

LS refinement shell

Resolution: 2.3→2.36 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.306	128	-
R_work	0.235	2605	-
all	-	2733	-
obs	-	-	67.95 %

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	6.5249	0.2693	-0.1086	5.661	1.4718	4.2684	-0.0579	0.2939	-1.0603	-0.1907	0.3142	-0.5021	0.3962	0.6322	-0.2562	-0.1953	0.11	-0.0507	-0.1595	-0.0878	0.0583	9.8123	13.5541	-28.5477
2	1.3348	-0.16	-0.0214	1.0516	-0.4701	1.1682	0.0267	0.0606	-0.0174	-0.0679	0.001	-0.0702	0.0326	0.1202	-0.0277	-0.0536	-0.0088	0.0165	-0.0695	0.0096	-0.0707	-11.2854	36.3318	-32.1894
3	3.1993	-0.3068	0.5316	2.4753	-0.8599	2.2206	-0.0961	0.0543	-0.0367	0.0324	0.0894	0.0229	-0.1193	-0.1976	0.0067	-0.2909	0.0221	0.028	-0.2333	-0.0035	-0.403	-58.6026	47.2556	-18.587
4	1.483	-0.5437	-0.3355	1.2428	0.1931	1.1147	0.0167	0.1664	-0.1932	-0.1238	-0.0754	0.222	0.0158	-0.0938	0.0587	-0.0578	0.0002	-0.0215	-0.0807	-0.0043	-0.0302	-37.1717	29.9292	-33.8134
5	6.9299	-3.5792	0.7314	10.4922	0.0627	4.0966	0.2476	0.3075	-1.9265	0.5529	-0.2338	1.7262	0.7695	-0.0963	-0.0138	0.1375	-0.0032	-0.0754	-0.2572	-0.2347	0.6919	-26.7724	-5.6767	-35.0164
6	1.6406	-0.7525	-0.29	0.8939	0.4462	1.6546	-0.107	-0.2206	-0.5066	0.1307	0.022	0.2243	0.2348	0.0072	0.085	0.0061	-0.0132	0.0307	-0.101	0.0703	0.0578	-33.6113	19.7214	-20.1724
7	57.0234	-16.3695	5.7511	27.1366	38.9657	167.0058	1.8798	-4.5596	2.4032	-1.1713	0.7519	-2.577	-0.1851	-1.154	-2.6318	0.0268	-0.0755	0.0474	0.027	-0.0268	0.0196	-21.4767	66.1591	-7.381
8	9.8687	0.1124	1.838	26.6187	5.7493	18.8673	-0.8233	0.0108	0.984	2.7253	0.6133	0.6192	-2.207	-1.2253	0.21	0.544	0.4428	0.2829	0.2075	-0.0134	0.145	-28.1074	67.5579	-13.8511
9	12.6773	-2.0698	-5.1292	14.1377	-1.2954	12.9585	0.694	-0.1239	2.419	1.0516	0.2772	-1.0104	-2.2833	0.1138	-0.9712	0.4364	0.025	0.1608	-0.2505	-0.0948	0.3985	-18.0801	64.8372	-21.5213
10	1.894	-0.2894	-0.0775	1.1343	-0.2453	1.4141	-0.0082	-0.3994	0.1359	0.2067	0.0309	-0.0887	-0.0776	0.1046	-0.0227	-0.0146	-0.0086	-0.0195	-0.0047	-0.0189	-0.0828	-14.7649	38.0442	-15.1648

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	4 - 168	4 - 168
2	X-RAY DIFFRACTION	2	A	A	169 - 300	169 - 300
3	X-RAY DIFFRACTION	3	B	B	5 - 168	5 - 168
4	X-RAY DIFFRACTION	4	B	B	169 - 299	169 - 299
5	X-RAY DIFFRACTION	5	C	C	5 - 168	5 - 168
6	X-RAY DIFFRACTION	6	C	C	169 - 299	169 - 299
7	X-RAY DIFFRACTION	7	D	D	9 - 14	9 - 14
8	X-RAY DIFFRACTION	8	D	D	55 - 79	55 - 79
9	X-RAY DIFFRACTION	9	D	D	92 - 168	92 - 168
10	X-RAY DIFFRACTION	10	D	D	169 - 300	169 - 300

-
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

-
Phasing

-
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

-Phasing

-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

-
Phasing

-
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