PDB-3q08: Crystal Structure of Chlorite Dismutase from D. Aromatica at pH 6.5

ID or keywords:

Entry

Database: PDB / ID: 3q08

Title

Crystal Structure of Chlorite Dismutase from D. Aromatica at pH 6.5

Components

Chlorite dismutase

Keywords

OXIDOREDUCTASE / Ferrodoxin Fold / Chlorite Decomposition / O2 generation / Periplasim

Function / homology

Function and homology information

chlorite O2-lyase /

chlorite O2-lyase activity /

periplasmic space /

heme binding /

metal ion binding
Similarity search - Function

Biological species

Dechloromonas aromatica (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Phaser / Resolution: 3.05 Å

Authors

Goblirsch, B.R. / Wilmot, C.M.

Citation

Journal: J.Biol.Inorg.Chem. / Year: 2010
Title: Structural features promoting dioxygen production by Dechloromonas aromatica chlorite dismutase.
Authors: Goblirsch, B.R. / Streit, B.R. / DuBois, J.L. / Wilmot, C.M.

History

Deposition	Dec 15, 2010	Deposition site: RCSB / Processing site: RCSB
Supersession	Jan 5, 2011	ID: 3M2Q
Revision 1.0	Jan 5, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Nov 8, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.3	Feb 21, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3q08.cif.gz	1.9 MB	Display	PDBx/mmCIF format
PDB format	pdb3q08.ent.gz	1.6 MB	Display	PDB format
PDBx/mmJSON format	3q08.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/q0/3q08 ftp://data.pdbj.org/pub/pdb/validation_reports/q0/3q08	HTTPS FTP

-
Related structure data

Related structure data	3q09C C: citing same article (ref.)
Similar structure data	3q09-3 3q09-4 3q09-1 3q09-2 4m06-d 3nn1-d 5a13-2 5a12-d 4m07-d 4m09-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) 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

3q09C

C: citing same article (ref.)

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Chlorite dismutase

B: Chlorite dismutase

C: Chlorite dismutase

D: Chlorite dismutase

E: Chlorite dismutase

F: Chlorite dismutase

G: Chlorite dismutase

H: Chlorite dismutase

I: Chlorite dismutase

J: Chlorite dismutase

K: Chlorite dismutase

L: Chlorite dismutase

M: Chlorite dismutase

N: Chlorite dismutase

O: Chlorite dismutase

P: Chlorite dismutase

Q: Chlorite dismutase

R: Chlorite dismutase

S: Chlorite dismutase

T: Chlorite dismutase

hetero molecules

582 kDa, 20 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Chlorite dismutase

B: Chlorite dismutase

C: Chlorite dismutase

D: Chlorite dismutase

E: Chlorite dismutase

hetero molecules

defined by author
145 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

F: Chlorite dismutase

G: Chlorite dismutase

H: Chlorite dismutase

I: Chlorite dismutase

J: Chlorite dismutase

hetero molecules

defined by author
145 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

K: Chlorite dismutase

L: Chlorite dismutase

M: Chlorite dismutase

N: Chlorite dismutase

O: Chlorite dismutase

hetero molecules

defined by author
145 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

P: Chlorite dismutase

Q: Chlorite dismutase

R: Chlorite dismutase

S: Chlorite dismutase

T: Chlorite dismutase

hetero molecules

defined by author
145 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	122.704, 202.850, 247.103
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	5	A	8 - 3001
2	1	1	5	B	8 - 3001
3	1	1	5	C	8 - 3001
4	1	1	5	D	8 - 3001
5	1	1	5	E	8 - 3001
6	1	1	5	F	8 - 3001
7	1	1	5	G	8 - 3001
8	1	1	5	H	8 - 3001
9	1	1	5	I	8 - 3001
10	1	1	5	J	8 - 3001
11	1	1	5	K	8 - 3001
12	1	1	5	L	8 - 3001
13	1	1	5	M	8 - 3001
14	1	1	5	N	8 - 3001
15	1	1	5	O	8 - 3001
16	1	1	5	P	8 - 3001
17	1	1	5	Q	8 - 3001
18	1	1	5	R	8 - 3001
19	1	1	5	S	8 - 3001
20	1	1	5	T	8 - 3001

-
Protein , 1 types, 20 molecules ABCDEFGHIJKLMNOPQRST

#1: Protein	Chlorite dismutase / Mass: 28179.314 Da / Num. of mol.: 20 / Fragment: UNP residues 32-282 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dechloromonas aromatica (bacteria) / Strain: RCB / Gene: Daro_2580 / Plasmid: pBSCld / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner(de3) / References: UniProt: Q47CX0, chlorite O2-lyase

#1: Protein

Chlorite dismutase /

Mass: 28179.314 Da / Num. of mol.: 20 / Fragment: UNP residues 32-282
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Dechloromonas aromatica (bacteria) / Strain: RCB / Gene: Daro_2580 / Plasmid: pBSCld / Production host:

Escherichia coli (E. coli) / Strain (production host): Tuner(de3) / References: UniProt: Q47CX0,

chlorite O2-lyase

-
Non-polymers , 5 types, 100 molecules

#2: Chemical	ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B Mass: 616.487 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C₃₄H₃₂FeN₄O₄
#3: Chemical	ChemComp-NO2 / NITRITE ION / Nitrite Mass: 46.005 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: NO₂
#4: Chemical	ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer) Mass: 195.237 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C₆H₁₃NO₄S / Comment: pH buffer*YM
#5: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Ca
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.73 Å³/Da / Density % sol: 54.92 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 16% PEG 8000, 200mM CaAc2, 25mM NaNO2, 100mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298 K, temperature 298.0K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 20, 2007
Radiation	Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 3.05→50 Å / Num. all: 117022 / Num. obs: 117263 / % possible obs: 99.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 3 / Redundancy: 7.6 % / R_merge(I) obs: 0.105
Reflection shell	Resolution: 3.05→3.1 Å / Redundancy: 6.7 % / R_merge(I) obs: 0.348 / Mean I/σ(I) obs: 4.682 / % possible all: 97.2

-
Processing

Software

Name	Version	Classification
SBC-Collect		data collection
PHASER		phasing
REFMAC	5.5.0109	refinement
HKL-2000		data reduction
SCALEPACK		data scaling

Refinement

Method to determine structure: Phaser / Resolution: 3.05→46.91 Å / Cor.coef. F_o:F_c: 0.925 / Cor.coef. F_o:F_c free: 0.873 / SU B: 36.628 / SU ML: 0.293 / Cross valid method: THROUGHOUT / ESU R Free: 0.411 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22079	5833	5 %	RANDOM
R_work	0.17822	-	-	-
obs	0.18037	110579	99.34 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 33.44 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0 Å²	-0 Å²	-0 Å²
2-	-	0.01 Å²	-0 Å²
3-	-	-	-0.01 Å²

Refinement step

Cycle: LAST / Resolution: 3.05→46.91 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	38560	0	1180	20	39760

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.022	40740
X-RAY DIFFRACTION	r_angle_refined_deg	1.723	2.032	55500
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.114	5	4800
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.473	24.023	1740
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.475	15	6940
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.015	15	220
X-RAY DIFFRACTION	r_chiral_restr	0.107	0.2	6080
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	30400
X-RAY DIFFRACTION	r_mcbond_it	0.544	1.5	24100
X-RAY DIFFRACTION	r_mcangle_it	1.064	2	39160
X-RAY DIFFRACTION	r_scbond_it	1.521	3	16640
X-RAY DIFFRACTION	r_scangle_it	2.584	4.5	16340

Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
A	967	medium positional	0.17	0.5
B	967	medium positional	0.25	0.5
C	967	medium positional	0.15	0.5
D	967	medium positional	0.25	0.5
E	967	medium positional	0.16	0.5
F	967	medium positional	0.17	0.5
G	967	medium positional	0.15	0.5
H	967	medium positional	0.16	0.5
I	967	medium positional	0.25	0.5
J	967	medium positional	0.2	0.5
K	967	medium positional	0.2	0.5
L	967	medium positional	0.15	0.5
M	967	medium positional	0.24	0.5
N	967	medium positional	0.16	0.5
O	967	medium positional	0.16	0.5
P	967	medium positional	0.23	0.5
Q	967	medium positional	0.26	0.5
R	967	medium positional	0.21	0.5
S	967	medium positional	0.21	0.5
T	967	medium positional	0.23	0.5
A	1021	loose positional	0.24	5
B	1021	loose positional	0.33	5
C	1021	loose positional	0.22	5
D	1021	loose positional	0.3	5
E	1021	loose positional	0.33	5
F	1021	loose positional	0.27	5
G	1021	loose positional	0.24	5
H	1021	loose positional	0.24	5
I	1021	loose positional	0.29	5
J	1021	loose positional	0.25	5
K	1021	loose positional	0.28	5
L	1021	loose positional	0.23	5
M	1021	loose positional	0.3	5
N	1021	loose positional	0.25	5
O	1021	loose positional	0.25	5
P	1021	loose positional	0.33	5
Q	1021	loose positional	0.35	5
R	1021	loose positional	0.33	5
S	1021	loose positional	0.3	5
T	1021	loose positional	0.33	5
A	967	medium thermal	0.55	2
B	967	medium thermal	0.56	2
C	967	medium thermal	0.52	2
D	967	medium thermal	0.5	2
E	967	medium thermal	0.53	2
F	967	medium thermal	0.44	2
G	967	medium thermal	0.5	2
H	967	medium thermal	0.51	2
I	967	medium thermal	0.49	2
J	967	medium thermal	0.51	2
K	967	medium thermal	0.48	2
L	967	medium thermal	0.49	2
M	967	medium thermal	0.49	2
N	967	medium thermal	0.44	2
O	967	medium thermal	0.5	2
P	967	medium thermal	0.43	2
Q	967	medium thermal	0.46	2
R	967	medium thermal	0.43	2
S	967	medium thermal	0.44	2
T	967	medium thermal	0.42	2
A	1021	loose thermal	0.79	10
B	1021	loose thermal	0.94	10
C	1021	loose thermal	0.77	10
D	1021	loose thermal	0.75	10
E	1021	loose thermal	0.82	10
F	1021	loose thermal	0.69	10
G	1021	loose thermal	0.68	10
H	1021	loose thermal	0.78	10
I	1021	loose thermal	0.75	10
J	1021	loose thermal	0.71	10
K	1021	loose thermal	0.7	10
L	1021	loose thermal	0.69	10
M	1021	loose thermal	0.8	10
N	1021	loose thermal	0.7	10
O	1021	loose thermal	0.64	10
P	1021	loose thermal	0.67	10
Q	1021	loose thermal	0.72	10
R	1021	loose thermal	0.63	10
S	1021	loose thermal	0.66	10
T	1021	loose thermal	0.68	10

LS refinement shell

Resolution: 3.05→3.121 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.301	327	-
R_work	0.242	6283	-
obs	-	-	92.9 %

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	1.1376	-0.3278	0.0789	0.6919	0.1703	1.3727	-0.0834	-0.0863	-0.1246	0.0812	-0.0078	0.1232	0.4377	-0.14	0.0912	0.1711	-0.0355	0.0266	0.0204	-0.0023	0.0424	-32.9579	-44.3135	18.0502
2	1.1968	-0.3863	0.4399	1.5127	-0.2836	0.6905	-0.015	0.1839	-0.0173	-0.2691	0.0127	-0.0463	0.1188	0.1518	0.0023	0.1398	0.0412	0.0476	0.092	0.0198	0.0223	-11.0543	-26.9486	-18.4694
3	1.5309	-0.7265	-0.1671	1.003	0.0324	1.4379	0.1849	0.0189	0.2263	0.0185	-0.0409	-0.1426	-0.2051	0.2862	-0.144	0.0645	-0.0383	0.0497	0.0596	-0.0181	0.1024	-9.8889	-7.5619	2.3596
4	1.5364	-0.159	0.2828	0.5787	-0.1979	1.5978	-0.0387	0.1315	-0.1517	-0.1866	0.0313	0.0264	0.5097	-0.0324	0.0074	0.2883	-0.0029	0.0122	0.0301	-0.0214	0.0339	-25.2473	-49.8033	-8.7308
5	1.5717	-0.0622	0.0202	0.9379	-0.3645	1.112	0.0299	-0.1901	0.1447	0.1292	-0.0115	0.0222	-0.1106	0.1262	-0.0184	0.047	-0.0041	0.0172	0.0474	-0.0198	0.0223	-23.3993	-18.252	24.9135
6	2.1631	0.5005	-0.0854	1.3708	0.1127	1.4223	0.1548	-0.6635	-0.3733	0.4419	-0.257	-0.2944	0.0457	0.3213	0.1022	0.1747	-0.1372	-0.1462	0.3932	0.2392	0.2089	7.924	5.4581	-36.2566
7	0.8434	0.2317	0.086	1.9833	0.4838	1.1832	0.1255	-0.0736	-0.1879	0.0596	-0.1789	-0.4474	-0.0425	0.4074	0.0534	0.0468	-0.0686	-0.0462	0.2492	0.1159	0.2171	17.8824	14.7378	-61.199
8	1.6505	0.3137	0.1901	1.2388	0.4917	1.413	-0.0091	0.3065	0.2208	-0.0916	0.0278	-0.0587	-0.2564	0.1044	-0.0187	0.0839	-0.0544	-0.0361	0.1077	0.0932	0.0988	-3.2976	28.2819	-74.5151
9	1.2368	0.7237	0.0942	1.6141	-0.1103	1.7797	0.0276	-0.1024	0.3148	0.0837	0.0308	0.2907	-0.2592	-0.2235	-0.0583	0.0793	0.0242	0.0418	0.0641	0.0275	0.1749	-26.3498	27.5388	-57.8857
10	1.5519	0.4929	0.1035	1.841	-0.4081	1.3951	0.1039	-0.4512	0.0949	0.4173	-0.1721	0.1571	-0.247	0.0379	0.0683	0.2252	-0.0821	0.0335	0.23	0.0376	0.0763	-19.497	13.2357	-34.1943
11	1.6055	-0.3836	0.4307	0.8686	-0.0553	1.8352	0.1366	-0.0706	-0.2555	0.1077	-0.0102	0.0776	0.4355	-0.1809	-0.1264	0.2265	-0.109	-0.0724	0.1177	0.0831	0.1254	-59.9089	-44.3087	-45.9391
12	1.1208	0.1649	0.5153	1.583	-0.0395	1.4384	0.088	-0.1228	-0.0118	0.1935	0.0063	0.2165	-0.003	-0.3593	-0.0943	0.0434	-0.0289	0.0502	0.2605	0.0427	0.1145	-70.0168	-17.8077	-42.9235
13	2.0044	0.6359	0.2826	0.9644	-0.2512	1.6711	0.0542	-0.024	0.2541	-0.1112	-0.0069	0.1499	-0.2359	-0.2621	-0.0472	0.087	0.0689	0.0187	0.1387	0.0813	0.1573	-64.2532	-3.433	-66.7347
14	1.9699	0.0224	0.7039	1.5054	0.0399	1.058	0.1038	0.4323	0.0122	-0.4703	-0.0766	-0.0991	0.2305	0.1721	-0.0272	0.2433	0.1325	0.0482	0.2709	0.0469	0.0761	-50.7151	-21.0236	-84.5073
15	1.6449	-0.1431	0.279	1.0523	-0.2946	1.2616	0.1834	0.2333	-0.3363	-0.3075	-0.1216	-0.043	0.4843	0.0709	-0.0618	0.368	0.1382	-0.0717	0.1446	-0.0499	0.1927	-47.9404	-46.3574	-71.625
16	1.6178	-0.246	-0.1253	1.7273	-0.1877	1.6324	0.2532	-0.0691	0.1872	0.0717	0.006	0.2588	-0.5347	-0.6682	-0.2591	0.4328	0.4009	0.2404	0.586	0.1268	0.3998	-80.3876	21.2801	26.2768
17	0.94	-0.5443	-0.0871	1.7057	-0.276	1.5647	0.2234	0.1225	0.4911	0.215	0.0537	-0.1357	-0.8684	-0.0649	-0.2771	0.6601	0.0855	0.2561	0.0999	0.0575	0.394	-41.9643	30.3382	2.5186
18	1.9319	-0.7518	0.1837	2.6739	-0.6469	1.2655	0.1804	0.5258	0.1807	-0.216	0.0068	0.1518	-0.5073	-0.5341	-0.1873	0.423	0.2585	0.0792	0.4457	0.1336	0.2303	-60.6669	18.2969	-15.1099
19	1.9793	-0.785	-0.3586	1.6236	-0.4627	1.8727	0.2036	0.4192	-0.0176	-0.126	0.0116	0.3665	-0.2158	-0.9784	-0.2152	0.2721	0.3031	0.0487	0.8994	0.1623	0.4301	-84.4027	12.545	-0.4177
20	1.8827	-0.4675	-0.5355	1.9151	-0.2898	1.8168	0.1763	-0.4063	0.511	0.2277	0.1047	-0.0618	-0.8681	-0.0443	-0.281	0.7837	0.1778	0.278	0.2231	-0.0924	0.436	-54.0834	32.2825	28.1491

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	-10 - 9999
2	X-RAY DIFFRACTION	2	B	-10 - 9999
3	X-RAY DIFFRACTION	3	C	-10 - 9999
4	X-RAY DIFFRACTION	4	D	-10 - 9999
5	X-RAY DIFFRACTION	5	E	-10 - 9999
6	X-RAY DIFFRACTION	6	F	-10 - 9999
7	X-RAY DIFFRACTION	7	G	-10 - 9999
8	X-RAY DIFFRACTION	8	H	-10 - 9999
9	X-RAY DIFFRACTION	9	I	-10 - 9999
10	X-RAY DIFFRACTION	10	J	-10 - 9999
11	X-RAY DIFFRACTION	11	K	-10 - 9999
12	X-RAY DIFFRACTION	12	L	-10 - 9999
13	X-RAY DIFFRACTION	13	M	-10 - 9999
14	X-RAY DIFFRACTION	14	N	-10 - 9999
15	X-RAY DIFFRACTION	15	O	-10 - 9999
16	X-RAY DIFFRACTION	16	P	-10 - 9999
17	X-RAY DIFFRACTION	17	Q	-10 - 9999
18	X-RAY DIFFRACTION	18	R	-10 - 9999
19	X-RAY DIFFRACTION	19	S	-10 - 9999
20	X-RAY DIFFRACTION	20	T	-10 - 9999

-
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

-
Protein , 1 types, 20 molecules ABCDEFGHIJKLMNOPQRST

-
Non-polymers , 5 types, 100 molecules

-
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

-Protein , 1 types, 20 molecules ABCDEFGHIJKLMNOPQRST

-Non-polymers , 5 types, 100 molecules

-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

-
Protein , 1 types, 20 molecules ABCDEFGHIJKLMNOPQRST

-
Non-polymers , 5 types, 100 molecules

-
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