PDB-4i5f: Crystal structure of Ralstonia sp. alcohol dehydrogenase mutant N...

ID or keywords:

Entry

Database: PDB / ID: 4i5f

Title

Crystal structure of Ralstonia sp. alcohol dehydrogenase mutant N15G, G37D, R38V, R39S

Components

Alclohol dehydrogenase/short-chain dehydrogenase

Keywords

OXIDOREDUCTASE / short-chain-dehydrogenases/reductases / Rossmann fold / Ralstonia sp. / alcohol dehydrogenase / RasADH / cosubstrate specificity / NADH / S-phenylethanol

Function / homology

Function and homology information

oxidoreductase activity, acting on NAD(P)H, oxygen as acceptor / nucleotide binding
Similarity search - Function

Biological species

Ralstonia sp. (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Jarasch, A. / Lerchner, A. / Meining, W. / Schiefner, A. / Skerra, A.

Citation

Journal: Biotechnol.Bioeng. / Year: 2013
Title: Crystallographic analysis and structure-guided engineering of NADPH-dependent Ralstonia sp. Alcohol dehydrogenase toward NADH cosubstrate specificity.
Authors: Lerchner, A. / Jarasch, A. / Meining, W. / Schiefner, A. / Skerra, A.

History

Deposition	Nov 28, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 12, 2013	Provider: repository / Type: Initial release
Revision 1.1	Oct 9, 2013	Group: Database references
Revision 1.2	Nov 15, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.3	Sep 20, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4i5f.cif.gz	701.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4i5f.ent.gz	586 KB	Display	PDB format
PDBx/mmJSON format	4i5f.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/i5/4i5f ftp://data.pdbj.org/pub/pdb/validation_reports/i5/4i5f	HTTPS FTP

-
Related structure data

Related structure data	4i5dC 4i5eSC 4i5gC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4i5d-1 4i5g-2 4i5g-1 4bmn-d 4i5d-2 3gr6-d 2yw9-1 3edm-d 2yw9-2 5thz-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	#13 - Jan 2001 Alcohol Dehydrogenase similarity (1) #90 - Jun 2007 Fatty Acid Synthase similarity (1) #77 - May 2006 Glucose Oxidase similarity (1)

Deposited unit

A: Alclohol dehydrogenase/short-chain dehydrogenase

B: Alclohol dehydrogenase/short-chain dehydrogenase

C: Alclohol dehydrogenase/short-chain dehydrogenase

D: Alclohol dehydrogenase/short-chain dehydrogenase

E: Alclohol dehydrogenase/short-chain dehydrogenase

F: Alclohol dehydrogenase/short-chain dehydrogenase

G: Alclohol dehydrogenase/short-chain dehydrogenase

H: Alclohol dehydrogenase/short-chain dehydrogenase

224 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Alclohol dehydrogenase/short-chain dehydrogenase

B: Alclohol dehydrogenase/short-chain dehydrogenase

C: Alclohol dehydrogenase/short-chain dehydrogenase

D: Alclohol dehydrogenase/short-chain dehydrogenase

defined by author&software
112 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

E: Alclohol dehydrogenase/short-chain dehydrogenase

F: Alclohol dehydrogenase/short-chain dehydrogenase

G: Alclohol dehydrogenase/short-chain dehydrogenase

H: Alclohol dehydrogenase/short-chain dehydrogenase

defined by author&software
112 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	72.796, 72.974, 132.893
Angle α, β, γ (deg.)	80.740, 86.530, 64.180
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS ensembles :

ID
1
2
3
4
5
6
7

#1: Protein	Alclohol dehydrogenase/short-chain dehydrogenase Mass: 28050.668 Da / Num. of mol.: 8 / Mutation: N15G, G37D, R38V, R39S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ralstonia sp. (bacteria) / Strain: DSMZ 6428 / Gene: RasADH / Plasmid: pASK-IBA35plus / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: C0IR58
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 636 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Alclohol dehydrogenase/short-chain dehydrogenase

Mass: 28050.668 Da / Num. of mol.: 8 / Mutation: N15G, G37D, R38V, R39S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Ralstonia sp. (bacteria) / Strain: DSMZ 6428 / Gene: RasADH / Plasmid: pASK-IBA35plus / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: C0IR58

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 636 / 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: 2.79 Å³/Da / Density % sol: 55.99 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: 7% PEG2000, 50mM Hepes/NaOH, 100 mM LiCl, 5mM NAD+ , pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

BESSY

/ Beamline: 14.2 / Wavelength: 0.91841 Å

Detector

Type: RAYONIX MX-225 / Detector: CCD / Date: Dec 7, 2011

Radiation

Monochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.91841 Å / Relative weight: 1

Reflection

Resolution: 2.1→30 Å / Num. all: 136876 / Num. obs: 136876 / % possible obs: 96.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.236 % / B_iso Wilson estimate: 34.752 Å² / R_merge(I) obs: 0.084 / Net I/σ(I): 11.56

Reflection shell

Resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Diffraction-ID	% possible all
2.1-2.2	0.507	2.61	1	95
2.3-2.4	0.411	3.3	1	95.9
2.4-2.5	0.326	4.16	1	96.6
2.5-3	0.162	7.72	1	97.1
3-4	0.059	18.27	1	97.1
4-5	0.035	29.66	1	96.7

-
Processing

Software

Name	Version	Classification
REFMAC	5.6.0117	refinement
PDB_EXTRACT	3.11	data extraction
MAR345dtb		data collection
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4I5E

4i5e

Resolution: 2.1→29.58 Å / Cor.coef. F_o:F_c: 0.948 / Cor.coef. F_o:F_c free: 0.927 / Occupancy max: 1 / Occupancy min: 1 / SU B: 10.582 / SU ML: 0.141 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.2 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2441	6862	5 %	RANDOM
R_work	0.2047	-	-	-
obs	0.2066	136875	96.53 %	-
all	-	136875	-	-

Solvent computation

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

Displacement parameters

B_iso max: 184.38 Å² / B_iso mean: 34.5608 Å² / B_iso min: 12.04 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.25 Å²	-1.1 Å²	2.01 Å²
2-	-	2.35 Å²	-2.23 Å²
3-	-	-	-2.17 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→29.58 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13944	0	0	636	14580

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.019	0.019	14120
X-RAY DIFFRACTION	r_angle_refined_deg	1.98	1.972	19152
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.69	5	1848
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.893	23.099	568
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.548	15	2336
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.05	15	128
X-RAY DIFFRACTION	r_chiral_restr	0.13	0.2	2320
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.021	10480

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	795	MEDIUM POSITIONAL	0.44	0.5
1	2	B	795	MEDIUM POSITIONAL	0.31	0.5
1	3	C	795	MEDIUM POSITIONAL	0.45	0.5
1	4	D	795	MEDIUM POSITIONAL	0.45	0.5
1	5	E	795	MEDIUM POSITIONAL	0.33	0.5
1	6	F	795	MEDIUM POSITIONAL	0.37	0.5
1	7	G	795	MEDIUM POSITIONAL	0.25	0.5
1	8	H	795	MEDIUM POSITIONAL	0.27	0.5
1	1	A	912	TIGHT THERMAL	1.06	0.5
1	2	B	912	TIGHT THERMAL	1.16	0.5
1	3	C	912	TIGHT THERMAL	1.15	0.5
1	4	D	912	TIGHT THERMAL	0.96	0.5
1	5	E	912	TIGHT THERMAL	1.64	0.5
1	6	F	912	TIGHT THERMAL	0.97	0.5
1	7	G	912	TIGHT THERMAL	2.1	0.5
1	8	H	912	TIGHT THERMAL	1.08	0.5
1	1	A	795	MEDIUM THERMAL	1.71	2
1	2	B	795	MEDIUM THERMAL	1.91	2
1	3	C	795	MEDIUM THERMAL	2.1	2
1	4	D	795	MEDIUM THERMAL	1.75	2
1	5	E	795	MEDIUM THERMAL	2.53	2
1	6	F	795	MEDIUM THERMAL	1.44	2
1	7	G	795	MEDIUM THERMAL	2.49	2
1	8	H	795	MEDIUM THERMAL	1.61	2
2	1	B	795	MEDIUM POSITIONAL	0.32	0.5
2	2	C	795	MEDIUM POSITIONAL	0.44	0.5
2	3	D	795	MEDIUM POSITIONAL	0.43	0.5
2	4	E	795	MEDIUM POSITIONAL	0.35	0.5
2	5	F	795	MEDIUM POSITIONAL	0.35	0.5
2	6	G	795	MEDIUM POSITIONAL	0.25	0.5
2	7	H	795	MEDIUM POSITIONAL	0.26	0.5
2	1	B	912	TIGHT THERMAL	1.18	0.5
2	2	C	912	TIGHT THERMAL	1.17	0.5
2	3	D	912	TIGHT THERMAL	0.95	0.5
2	4	E	912	TIGHT THERMAL	1.71	0.5
2	5	F	912	TIGHT THERMAL	0.92	0.5
2	6	G	912	TIGHT THERMAL	2.01	0.5
2	7	H	912	TIGHT THERMAL	1.08	0.5
2	1	B	795	MEDIUM THERMAL	1.96	2
2	2	C	795	MEDIUM THERMAL	2.08	2
2	3	D	795	MEDIUM THERMAL	1.72	2
2	4	E	795	MEDIUM THERMAL	2.63	2
2	5	F	795	MEDIUM THERMAL	1.38	2
2	6	G	795	MEDIUM THERMAL	2.38	2
2	7	H	795	MEDIUM THERMAL	1.54	2
3	1	C	795	MEDIUM POSITIONAL	0.42	0.5
3	2	D	795	MEDIUM POSITIONAL	0.43	0.5
3	3	E	795	MEDIUM POSITIONAL	0.35	0.5
3	4	F	795	MEDIUM POSITIONAL	0.34	0.5
3	5	G	795	MEDIUM POSITIONAL	0.27	0.5
3	6	H	795	MEDIUM POSITIONAL	0.25	0.5
3	1	C	912	TIGHT THERMAL	1.19	0.5
3	2	D	912	TIGHT THERMAL	0.9	0.5
3	3	E	912	TIGHT THERMAL	1.74	0.5
3	4	F	912	TIGHT THERMAL	0.92	0.5
3	5	G	912	TIGHT THERMAL	1.97	0.5
3	6	H	912	TIGHT THERMAL	1.01	0.5
3	1	C	795	MEDIUM THERMAL	2.11	2
3	2	D	795	MEDIUM THERMAL	1.65	2
3	3	E	795	MEDIUM THERMAL	2.61	2
3	4	F	795	MEDIUM THERMAL	1.27	2
3	5	G	795	MEDIUM THERMAL	2.37	2
3	6	H	795	MEDIUM THERMAL	1.5	2
4	1	D	795	MEDIUM POSITIONAL	0.4	0.5
4	2	E	795	MEDIUM POSITIONAL	0.31	0.5
4	3	F	795	MEDIUM POSITIONAL	0.38	0.5
4	4	G	795	MEDIUM POSITIONAL	0.24	0.5
4	5	H	795	MEDIUM POSITIONAL	0.24	0.5
4	1	D	912	TIGHT THERMAL	0.91	0.5
4	2	E	912	TIGHT THERMAL	1.75	0.5
4	3	F	912	TIGHT THERMAL	0.95	0.5
4	4	G	912	TIGHT THERMAL	1.85	0.5
4	5	H	912	TIGHT THERMAL	1.03	0.5
4	1	D	795	MEDIUM THERMAL	1.63	2
4	2	E	795	MEDIUM THERMAL	2.52	2
4	3	F	795	MEDIUM THERMAL	1.36	2
4	4	G	795	MEDIUM THERMAL	2.23	2
4	5	H	795	MEDIUM THERMAL	1.52	2
5	1	E	795	MEDIUM POSITIONAL	0.31	0.5
5	2	F	795	MEDIUM POSITIONAL	0.35	0.5
5	3	G	795	MEDIUM POSITIONAL	0.23	0.5
5	4	H	795	MEDIUM POSITIONAL	0.22	0.5
5	1	E	912	TIGHT THERMAL	1.71	0.5
5	2	F	912	TIGHT THERMAL	0.9	0.5
5	3	G	912	TIGHT THERMAL	1.79	0.5
5	4	H	912	TIGHT THERMAL	1.14	0.5
5	1	E	795	MEDIUM THERMAL	2.42	2
5	2	F	795	MEDIUM THERMAL	1.31	2
5	3	G	795	MEDIUM THERMAL	2.13	2
5	4	H	795	MEDIUM THERMAL	1.66	2
6	1	F	795	MEDIUM POSITIONAL	0.29	0.5
6	2	G	795	MEDIUM POSITIONAL	0.26	0.5
6	3	H	795	MEDIUM POSITIONAL	0.21	0.5
6	1	F	912	TIGHT THERMAL	0.97	0.5
6	2	G	912	TIGHT THERMAL	1.42	0.5
6	3	H	912	TIGHT THERMAL	1.18	0.5
6	1	F	795	MEDIUM THERMAL	1.36	2
6	2	G	795	MEDIUM THERMAL	1.75	2
6	3	H	795	MEDIUM THERMAL	1.46	2
7	1	G	795	MEDIUM POSITIONAL	0.18	0.5
7	1	G	912	TIGHT THERMAL	1.21	0.5
7	1	G	795	MEDIUM THERMAL	1.46	2

LS refinement shell

Resolution: 2.1→2.154 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.321	481	-
R_work	0.288	9421	-
all	-	9902	-
obs	-	-	94.66 %

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	3.5806	0.3235	-2.1504	4.373	-1.0566	2.7376	-0.1191	0.1386	-0.315	-0.1473	-0.0786	0.1404	0.2891	-0.2049	0.1977	0.1512	0.0155	0.0159	0.1273	-0.0812	0.1655	12.8205	-19.0504	7.0886
2	3.764	1.2024	0.7933	5.2026	0.021	2.8297	0.0009	-0.0332	-0.507	-0.0235	0.0474	-0.3066	0.5081	0.3101	-0.0483	0.2023	0.0637	0.0641	0.2507	-0.0495	0.212	25.066	-19.0523	5.791
3	0.6943	0.0779	-0.0079	1.4624	0.277	2.7056	-0.0008	0.0446	-0.1402	-0.0072	0.0426	0.0197	0.1776	0.3232	-0.0418	0.0256	0.0365	-0.0086	0.1767	-0.0073	0.1401	20.5989	-8.1438	21.0024
4	8.2086	-0.1145	10.1859	0.0112	0.0019	15.4262	-0.6646	0.353	-0.2029	0.1012	0.2265	-0.007	0.6631	2.6492	0.4381	1.4228	0.9869	0.1666	2.0073	0.3829	0.8781	12.0986	-23.3916	32.958
5	1.1878	-0.0571	-0.3279	2.4794	0.2161	3.2682	-0.0672	0.0788	-0.2993	0.0943	-0.0529	0.049	0.2578	0.0239	0.1201	0.0565	0.0053	0.0022	0.1608	-0.0306	0.1898	5.4245	-13.7645	21.2576
6	2.6772	-0.697	-1.0302	2.6933	0.408	4.2746	0.0324	0.3387	-0.0366	-0.2425	-0.0677	0.3866	0.1107	-0.5916	0.0353	0.0406	-0.0589	-0.073	0.4762	-0.1015	0.3873	-18.5744	-10.2121	13.321
7	4.0663	-0.8443	-2.2163	1.2322	0.4452	6.4313	0.1387	0.0141	-0.1133	0.2247	-0.1269	0.3093	0.1004	-0.8559	-0.0118	0.0773	-0.0729	0.0216	0.4701	-0.075	0.4578	-22.2769	-13.8312	24.1002
8	1.1255	-0.0029	-0.1769	3.6248	0.6047	2.0526	-0.0393	-0.0144	-0.0576	-0.1013	-0.0961	0.4138	0.0076	-0.3867	0.1354	0.0045	0.0029	-0.0124	0.293	-0.0536	0.2259	-10.6312	-1.6557	29.4065
9	2.5911	-6.2652	3.4605	15.1921	-8.4226	4.7472	-0.0571	0.4909	0.2741	0.8352	-0.7178	-0.5828	-0.3704	0.2601	0.7749	0.8232	-0.0833	0.4609	1.3913	-0.21	1.3036	-3.2845	10.9378	14.2216
10	2.3162	0.2886	0.2809	2.7524	-0.4433	3.2805	-0.0112	0.2275	-0.0055	-0.0482	-0.077	0.3872	-0.0505	-0.3068	0.0882	0.003	0.0189	-0.0104	0.2108	-0.0795	0.1543	-0.062	-5.0326	17.0397
11	2.9091	-0.6154	-0.0436	3.5052	0.6727	1.9103	0.073	0.01	0.2329	-0.0572	-0.0171	-0.3013	-0.3082	0.3897	-0.0559	0.1072	-0.0605	-0.0458	0.3715	-0.0003	0.1854	34.6471	12.2653	45.0526
12	2.1156	-0.8572	1.1757	4.6464	0.1528	1.7595	0.0502	0.3202	-0.1045	0.2238	0.0885	-0.5043	0.0622	0.7485	-0.1387	0.2029	0.0046	-0.029	0.4419	-0.0078	0.1584	33.3157	5.2311	48.2026
13	0.65	0.0167	0.166	1.4963	0.3828	3.5402	-0.023	-0.0454	0.0377	0.0294	0.0787	-0.1441	-0.1701	0.4581	-0.0557	0.0175	0.0105	-0.0149	0.2194	-0.0002	0.1626	25.3215	1.6206	32.7536
14	1.1475	1.3931	-4.398	1.6989	-5.3534	17.0116	-0.472	0.0984	-0.2498	-0.3136	-0.0766	-0.3411	1.0172	0.0187	0.5486	0.9388	0.0692	0.1138	1.2566	-0.6201	1.0419	16.3808	19.7281	26.021
15	1.2199	-0.2487	0.1082	1.7705	0.4694	1.9887	-0.0335	-0.1129	0.2201	0.0139	-0.0387	-0.0588	-0.2064	0.24	0.0721	0.0737	0.0133	-0.0202	0.1967	-0.0118	0.1369	14.6998	11.8174	40.3122
16	2.1466	-1.1262	1.5399	1.9786	-0.2188	3.7956	-0.0293	-0.3799	-0.0777	0.3355	-0.0336	0.2584	0.0715	-0.2302	0.0629	0.2142	0.063	0.0553	0.2521	-0.0725	0.2142	-3.9134	15.3746	57.9026
17	5.6167	-1.8915	1.0013	2.4444	0.5788	5.2759	-0.0655	0.0419	0.0534	0.0273	-0.0621	0.4079	-0.5312	-0.2903	0.1276	0.2437	0.0748	-0.0008	0.2425	-0.1065	0.2011	-7.7052	24.2943	52.3989
18	0.9191	0.1698	0.0489	2.2516	0.5769	1.7875	-0.003	-0.1873	0.0303	0.2373	-0.1344	0.2911	-0.055	-0.2658	0.1374	0.0468	0.0376	0.0133	0.2675	-0.0507	0.2003	-6.0811	6.0513	42.0275
19	0.1465	1.0952	-0.7366	9.651	-6.8874	5.0138	0.0879	-0.1832	0.132	-0.0506	-0.1661	0.3479	0.1079	-0.1139	0.0782	0.4435	-0.1551	0.0897	1.2918	-0.2876	1.1693	4.1576	-9.08	52.0178
20	1.3182	-0.3502	0.1948	3.6556	-0.3966	3.4471	-0.0575	-0.1973	-0.0193	0.3033	0.0042	0.1932	-0.0042	0.0158	0.0533	0.0384	0.0275	-0.0003	0.187	-0.0236	0.1315	9.4172	5.38	47.0862
21	4.3025	-0.1269	0.754	4.3884	0.7719	3.7742	-0.0244	-0.249	0.099	0.3782	0.006	0.3925	-0.2378	-0.2978	0.0184	0.2196	-0.0081	0.0493	0.0807	-0.0248	0.1484	15.1334	4.819	116.0723
22	6.3381	-0.1838	-0.6122	2.3045	-0.5867	4.0625	0.0408	-0.0966	0.6742	-0.0093	0.0255	0.333	-0.4726	-0.3021	-0.0663	0.3873	-0.0314	0.0061	0.0619	-0.0392	0.2531	20.621	15.8808	114.5679
23	1.2063	-0.0146	0.1752	0.9696	0.0848	3.2066	0.0041	0.0043	0.1069	0.0448	0.0248	0.0949	-0.384	0.0321	-0.0289	0.247	-0.0303	0.0234	0.0334	0.0273	0.1265	25.1573	4.7074	99.6589
24	6.7519	-0.0968	7.968	15.2532	1.3625	33.1172	-0.1977	0.0456	0.231	-0.6842	-0.5355	1.0616	-1.7901	0.3549	0.7333	0.811	0.0572	0.158	0.5231	0.2329	0.6883	5.9035	4.0549	92.6304
25	3.1776	-0.3388	-0.272	2.1708	0.956	2.2495	-0.0601	0.1416	0.0524	0.1153	-0.1158	0.3015	-0.1559	-0.2269	0.1759	0.1974	-0.029	0.0456	0.0614	0.0244	0.1561	13.2859	-5.96	102.7843
26	2.2333	-0.4008	-0.3658	3.6558	0.483	2.8536	-0.0939	0.0278	0.153	-0.057	0.1727	-0.4633	-0.1545	0.734	-0.0788	0.3244	-0.1243	0.0314	0.3791	0.0437	0.1719	43.8762	4.2936	70.4214
27	3.3149	0.5408	0.753	3.4137	-1.7114	3.9877	-0.0674	0.0361	0.4853	-0.1822	0.0455	-0.1832	-0.5626	0.0568	0.0219	0.3164	-0.0624	0.0389	0.2973	-0.0028	0.1962	36.4489	5.9338	68.6263
28	0.7811	-0.1471	-0.0112	0.9891	0.4065	3.06	-0.0323	0.0371	0.0872	-0.1215	0.0826	-0.1376	-0.2943	0.4225	-0.0503	0.2553	-0.0735	0.0193	0.1291	0.0416	0.1336	33.183	2.7245	85.8298
29	23.2906	6.8135	6.92	2.0443	2.7238	13.2144	1.4412	-1.1101	-0.5988	0.2435	-0.382	-0.3068	-2.6933	-0.9633	-1.0592	0.9858	0.0706	0.1281	0.7613	-0.2244	0.9424	47.2004	-11.7798	91.9753
30	1.5418	-0.189	-0.9998	1.9437	0.4172	1.7718	-0.0651	0.0102	-0.0052	-0.1085	0.0327	-0.2281	-0.0258	0.5441	0.0324	0.2425	-0.0021	-0.0009	0.2804	0.021	0.0746	36.0442	-12.4443	79.7544
31	39.4423	-21.514	1.9806	20.2435	-4.7434	1.6926	-0.1951	-0.3255	-0.2919	2.5801	0.1637	-0.6478	-1.1287	-0.2644	0.0314	0.9674	0.0436	-0.0272	1.2995	0.2277	0.4463	3.4209	-13.5229	118.5676
32	3.9885	-0.4919	0.2728	3.5212	2.5118	3.5917	0.0143	-0.206	-0.4635	0.5867	-0.1219	0.2273	0.5287	-0.1417	0.1076	0.4837	-0.1324	0.1057	0.1398	0.0786	0.2653	8.7038	-26.4104	114.6177
33	1.2826	-0.1473	-0.6017	0.9736	0.3108	1.9273	-0.0572	-0.1366	-0.3323	0.192	-0.0348	0.2649	0.5563	-0.1687	0.092	0.3914	-0.0784	0.0425	0.1136	0.0374	0.2833	11.6127	-28.5946	101.9764
34	8.6789	-5.3505	3.0604	3.3286	-1.9514	1.3279	-0.0807	0.6368	-0.1519	0.0172	-0.3284	-0.1033	0.5135	0.1689	0.4092	1.7178	-0.1933	0.379	0.2618	-0.0555	1.3018	32.5318	-21.1716	109.7076
35	2.6816	-0.224	0.07	1.3746	0.5211	2.1223	-0.0714	-0.157	-0.1542	0.3552	-0.0289	0.1728	0.4015	-0.0726	0.1003	0.2814	-0.0417	0.0611	0.027	0.0317	0.1225	18.4781	-14.318	107.2453
36	1.1218	-0.4198	-0.0108	2.5033	-1.0989	4.2695	-0.0669	0.1895	-0.158	-0.2231	0.0603	0.2319	0.2163	-0.2015	0.0067	0.2943	0.0648	0.004	0.228	-0.0926	0.2181	27.3413	-32.642	66.0256
37	1.0461	-1.664	0.32	7.6478	1.0362	3.4226	0.0471	0.0902	-0.3521	0.0279	-0.1071	0.1154	0.3096	0.2772	0.06	0.3758	0.0909	0.0601	0.2272	-0.0748	0.2317	34.7689	-39.3103	71.0303
38	2.0607	-0.4811	-0.3175	1.1752	0.4375	2.0092	-0.0577	0.2717	-0.3144	-0.0537	-0.0411	0.1437	0.3864	-0.0776	0.0989	0.3208	-0.0107	0.0191	0.1135	-0.0254	0.1843	21.5423	-28.1216	83.1917
39	32.9277	-9.8744	10.67	2.9866	-3.2178	3.4803	-0.5616	-0.8677	0.083	0.0059	0.4054	0.032	-0.0365	-0.3404	0.1562	1.5634	-0.4618	-0.0698	0.4033	0.1129	0.9159	11.8698	-11.828	73.3314
40	2.1993	-1.0802	0.1507	2.089	-0.2591	2.3622	0.0657	0.2788	-0.2171	-0.1955	-0.04	0.1463	0.0639	0.1579	-0.0257	0.26	0.0106	0.0098	0.1159	0.002	0.0994	27.0396	-15.3978	75.0448

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 37
2	X-RAY DIFFRACTION	2	A	38 - 80
3	X-RAY DIFFRACTION	3	A	81 - 184
4	X-RAY DIFFRACTION	4	A	185 - 208
5	X-RAY DIFFRACTION	5	A	209 - 249
6	X-RAY DIFFRACTION	6	B	1 - 62
7	X-RAY DIFFRACTION	7	B	63 - 88
8	X-RAY DIFFRACTION	8	B	89 - 184
9	X-RAY DIFFRACTION	9	B	185 - 208
10	X-RAY DIFFRACTION	10	B	209 - 249
11	X-RAY DIFFRACTION	11	C	1 - 74
12	X-RAY DIFFRACTION	12	C	75 - 89
13	X-RAY DIFFRACTION	13	C	90 - 184
14	X-RAY DIFFRACTION	14	C	185 - 209
15	X-RAY DIFFRACTION	15	C	210 - 249
16	X-RAY DIFFRACTION	16	D	1 - 68
17	X-RAY DIFFRACTION	17	D	69 - 84
18	X-RAY DIFFRACTION	18	D	85 - 184
19	X-RAY DIFFRACTION	19	D	185 - 209
20	X-RAY DIFFRACTION	20	D	210 - 249
21	X-RAY DIFFRACTION	21	E	1 - 37
22	X-RAY DIFFRACTION	22	E	38 - 79
23	X-RAY DIFFRACTION	23	E	80 - 184
24	X-RAY DIFFRACTION	24	E	185 - 206
25	X-RAY DIFFRACTION	25	E	207 - 249
26	X-RAY DIFFRACTION	26	F	1 - 74
27	X-RAY DIFFRACTION	27	F	75 - 89
28	X-RAY DIFFRACTION	28	F	90 - 184
29	X-RAY DIFFRACTION	29	F	185 - 208
30	X-RAY DIFFRACTION	30	F	209 - 249
31	X-RAY DIFFRACTION	31	G	1 - 6
32	X-RAY DIFFRACTION	32	G	7 - 40
33	X-RAY DIFFRACTION	33	G	41 - 183
34	X-RAY DIFFRACTION	34	G	184 - 212
35	X-RAY DIFFRACTION	35	G	213 - 249
36	X-RAY DIFFRACTION	36	H	1 - 68
37	X-RAY DIFFRACTION	37	H	69 - 84
38	X-RAY DIFFRACTION	38	H	85 - 184
39	X-RAY DIFFRACTION	39	H	185 - 211
40	X-RAY DIFFRACTION	40	H	212 - 249

-
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