PDB-4o5h: X-ray crystal structure of a putative phenylacetaldehyde dehydrog...

ID or keywords:

Entry

Database: PDB / ID: 4o5h

Title

X-ray crystal structure of a putative phenylacetaldehyde dehydrogenase from Burkholderia cenocepacia

Components

Phenylacetaldehyde dehydrogenase

Keywords

OXIDOREDUCTASE /

Structural Genomics / NIAID /

National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID /

phenylacetaldehyde dehydrogenase

Function / homology

Function and homology information

phenylacetaldehyde dehydrogenase /

phenylacetaldehyde dehydrogenase activity
Similarity search - Function

Biological species

Burkholderia cenocepacia (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: TO BE PUBLISHED
Title: X-ray crystal structure of a putative phenylacetaldehyde dehydrogenase from Burkholderia cenocepacia
Authors: Fairman, J.W. / Abendroth, J. / Edwards, T.E. / Lorimer, D.

History

Deposition	Dec 19, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 19, 2014	Provider: repository / Type: Initial release
Revision 1.1	Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / 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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _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	4o5h.cif.gz	775.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4o5h.ent.gz	643.4 KB	Display	PDB format
PDBx/mmJSON format	4o5h.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/o5/4o5h ftp://data.pdbj.org/pub/pdb/validation_reports/o5/4o5h	HTTPS FTP

-
Related structure data

Related structure data	1cw3S S: Starting model for refinement
Similar structure data	1jju-d 6pc1-2 1pby-d 5jqp-d 4mpb-2 1jmx-d 5mz6-d 7cy7-d 1jmz-d 6lkz-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
Other databases	TargetTrack: SSGCID-BuceA.00020.o

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#127 - Jul 2010 Crystallins similarity (7) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (7)

Deposited unit

A: Phenylacetaldehyde dehydrogenase

B: Phenylacetaldehyde dehydrogenase

C: Phenylacetaldehyde dehydrogenase

D: Phenylacetaldehyde dehydrogenase

hetero molecules

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

1

A: Phenylacetaldehyde dehydrogenase

D: Phenylacetaldehyde dehydrogenase

hetero molecules

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

2

B: Phenylacetaldehyde dehydrogenase

C: Phenylacetaldehyde dehydrogenase

hetero molecules

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

3

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	112.620, 150.070, 345.910
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	C-1128- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	C
1	3	A
2	3	D
1	4	B
2	4	C
1	5	B
2	5	D
1	6	C
2	6	D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-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	ALA	ALA	ALA	ALA	A	A	-7 - 503	1 - 511
2	1	ALA	ALA	ALA	ALA	B	B	-7 - 503	1 - 511
1	2	THR	THR	TYR	TYR	A	A	8 - 502	16 - 510
2	2	THR	THR	TYR	TYR	C	C	8 - 502	16 - 510
1	3	THR	THR	TYR	TYR	A	A	8 - 502	16 - 510
2	3	THR	THR	TYR	TYR	D	D	8 - 502	16 - 510
1	4	THR	THR	TYR	TYR	B	B	8 - 502	16 - 510
2	4	THR	THR	TYR	TYR	C	C	8 - 502	16 - 510
1	5	THR	THR	TYR	TYR	B	B	8 - 502	16 - 510
2	5	THR	THR	TYR	TYR	D	D	8 - 502	16 - 510
1	6	THR	THR	ALA	ALA	C	C	8 - 503	16 - 511
2	6	THR	THR	ALA	ALA	D	D	8 - 503	16 - 511

NCS ensembles :

ID
1
2
3
4
5
6

#1: Protein	Phenylacetaldehyde dehydrogenase / Mass: 54485.082 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia cenocepacia (bacteria) Strain: ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610 Gene: BCAM2298 / Production host: Escherichia coli (E. coli) References: UniProt: B4EH14, phenylacetaldehyde dehydrogenase
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 2003 / 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: 3.35 Å³/Da / Density % sol: 63.32 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.4 uL protein @ 18 mg/mL + 0.4 uL Morpheus H3 - 10% PEG 4000, 20% glycerol, 0.1 M MES/imidazole pH 6.50, 0.02 M sodium L-glutamate, 0.02 M DL-alanine, 0.02 M glycine, 0.02 M DL-lysine, 0.02 ...Details: 0.4 uL protein @ 18 mg/mL + 0.4 uL Morpheus H3 - 10% PEG 4000, 20% glycerol, 0.1 M MES/imidazole pH 6.50, 0.02 M sodium L-glutamate, 0.02 M DL-alanine, 0.02 M glycine, 0.02 M DL-lysine, 0.02 M DL-serine, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal

Density Matthews: 3.35 Å³/Da / Density % sol: 63.32 %

Crystal grow

Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.4 uL protein @ 18 mg/mL + 0.4 uL Morpheus H3 - 10% PEG 4000, 20% glycerol, 0.1 M MES/imidazole pH 6.50, 0.02 M sodium L-glutamate, 0.02 M DL-alanine, 0.02 M glycine, 0.02 M DL-lysine, 0.02 ...

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 5.0.1 / Wavelength: 0.9765 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 4, 2013

Radiation

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

Radiation wavelength

Wavelength: 0.9765 Å / Relative weight: 1

Reflection

Resolution: 2→50 Å / Num. all: 196538 / Num. obs: 195248 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / B_iso Wilson estimate: 22.643 Å² / R_merge(I) obs: 0.102 / Net I/σ(I): 14.62

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Highest resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. unique obs	% possible all
2-2.05		0.482	3.13	65335	14362	99.6
2.05-2.11		0.407	3.73	63561	13971	99.6
2.11-2.17		0.343	4.46	61886	13655	99.7
2.17-2.24		0.287	5.29	60090	13272	99.5
2.24-2.31		0.242	6.28	57612	12810	99.6
2.31-2.39		0.209	7.3	55670	12429	99.6
2.39-2.48		0.185	8.13	53630	12009	99.6
2.48-2.58		0.155	9.57	51589	11543	99.5
2.58-2.7		0.138	10.91	49181	11085	99.4
2.7-2.83		0.12	12.4	47100	10619	99.6
2.83-2.98		0.098	15.09	44270	10050	99.3
2.98-3.16		0.08	17.86	41759	9532	99
3.16-3.38		0.062	22.38	38934	8966	99
3.38-3.65		0.047	28.63	35551	8309	98.5
3.65-4		0.04	32.2	32545	7681	98.6
4-4.47		0.033	37.73	29516	6992	98.8
4.47-5.16		0.031	39.3	26227	6194	99
5.16-6.32		0.04	32.42	23348	5284	99.4
6.32-8.94		0.029	41.82	18378	4133	99.3
	8.94	0.02	57.18	9998	2352	97.8

-
Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	2 Å	47.19 Å
Translation	2 Å	47.19 Å

-
Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHASER	2.5.2	phasing
REFMAC	5.8.0049	refinement
PDB_EXTRACT	3.14	data extraction
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CW3

1cw3

Resolution: 2→50 Å / Cor.coef. F_o:F_c: 0.949 / Cor.coef. F_o:F_c free: 0.934 / Occupancy max: 1 / Occupancy min: 0.29 / SU B: 6.482 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.133 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1929	9833	5 %	RANDOM
R_work	0.1693	-	-	-
obs	0.1705	195247	99.34 %	-
all	-	196538	-	-

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: 57.76 Å² / B_iso mean: 18.596 Å² / B_iso min: 2.84 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.2 Å²	0 Å²	-0 Å²
2-	-	0.64 Å²	0 Å²
3-	-	-	-0.83 Å²

Refinement step

Cycle: LAST / Resolution: 2→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14931	0	48	2003	16982

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.019	15618
X-RAY DIFFRACTION	r_bond_other_d	0.007	0.02	15096
X-RAY DIFFRACTION	r_angle_refined_deg	1.456	1.96	21326
X-RAY DIFFRACTION	r_angle_other_deg	1.149	3	34673
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.079	5	2124
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.314	23.644	634
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.682	15	2465
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.582	15	117
X-RAY DIFFRACTION	r_chiral_restr	0.087	0.2	2453
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	18088
X-RAY DIFFRACTION	r_gen_planes_other	0.005	0.02	3479
X-RAY DIFFRACTION	r_mcbond_it	0.639	0.884	8166
X-RAY DIFFRACTION	r_mcbond_other	0.639	0.884	8165
X-RAY DIFFRACTION	r_mcangle_it	1.064	1.323	10229

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	30264	0.07
1	2	B	30264	0.07
2	1	A	29744	0.07
2	2	C	29744	0.07
3	1	A	29649	0.08
3	2	D	29649	0.08
4	1	B	30146	0.06
4	2	C	30146	0.06
5	1	B	30000	0.07
5	2	D	30000	0.07
6	1	C	30026	0.07
6	2	D	30026	0.07

LS refinement shell

Resolution: 2→2.052 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.279	681	-
R_work	0.256	13653	-
all	-	14334	-
obs	-	-	99.56 %

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	5.5987	3.2968	3.6392	7.0732	5.6935	12.6336	-0.3856	0.2725	0.1233	-0.367	0.0943	0.2729	-0.3397	0.1817	0.2913	0.0521	-0.0334	0.0159	0.0518	0.0119	0.0899	78.8597	112.9024	166.2076
2	1.9509	0.7449	-0.5108	1.3154	-0.2297	1.5601	0.0551	-0.0227	0.3012	-0.0986	-0.0484	0.137	-0.2555	-0.1178	-0.0067	0.1091	0.0503	0.0062	0.0248	-0.0033	0.1084	52.9286	96.3774	145.536
3	1.8945	1.705	-0.0051	2.6968	0.2431	1.0818	0.0938	-0.195	0.1221	0.1826	-0.145	0.1801	-0.1333	-0.1352	0.0512	0.0617	0.039	-0.0114	0.0685	-0.0228	0.0513	49.328	86.6004	154.2316
4	0.2844	0.2047	0.0472	0.7198	0.2419	0.2056	0.0121	0.0023	0.0062	-0.0168	-0.0371	-0.0229	-0.0499	-0.0261	0.025	0.0473	-0.0013	-0.0082	0.0564	-0.0039	0.0466	56.9144	70.2321	137.1799
5	0.5053	-0.0466	-0.0143	0.2805	0.0032	0.294	-0.0274	-0.0139	0.0245	0.021	0.0296	-0.022	-0.0293	0.0032	-0.0021	0.0429	0.0058	-0.0124	0.0416	-0.0174	0.0637	62.4057	76.9324	150.8198
6	0.1452	-0.3016	-0.1313	0.9404	0.119	0.4083	-0.0369	-0.0411	0.0782	0.091	0.081	-0.2144	-0.0465	0.1434	-0.044	0.0364	-0.0194	-0.0338	0.087	-0.0324	0.1144	83.2802	80.9764	154.1079
7	0.9631	1.0083	0.2904	1.4014	0.5489	0.3767	-0.0225	-0.0469	-0.0049	0.02	0.0069	0.0293	0.0582	-0.0367	0.0156	0.0297	0.0049	0.0018	0.0633	0.0018	0.0359	59.5645	59.647	146.4646
8	8.2572	-0.0658	-3.4421	5.8473	2.2521	12.8357	-0.0082	-0.0036	0.2943	0.2383	0.0283	0.3021	0.4578	-0.4378	-0.0201	0.0784	0.0075	-0.0567	0.0604	0.0051	0.1369	98.4409	14.6462	138.7466
9	1.708	-0.8308	0.6194	0.519	-0.6117	1.4782	0.0098	0.0367	-0.336	-0.0685	-0.0275	0.0879	-0.0213	0.0292	0.0177	0.2027	0.0698	-0.0034	0.0924	-0.0601	0.1929	86.46	15.7415	125.0069
10	5.1197	-0.718	0.0286	1.1619	0.3587	1.5021	0.0363	0.3403	-0.4054	-0.107	-0.0742	0.1078	0.2252	-0.0347	0.0379	0.1531	0.0386	-0.0115	0.0399	-0.031	0.0459	74.5365	22.5307	119.1847
11	0.2065	-0.0731	0.0299	0.3111	0.0186	0.2616	0.037	0.0517	-0.0248	-0.0619	-0.0118	-0.0592	0.0808	0.0853	-0.0252	0.0447	0.0451	0.0065	0.0876	-0.0229	0.0583	82.2212	38.2589	125.0238
12	0.3651	0.5267	-0.4006	1.8152	-0.3529	1.4424	0.0044	0.0835	-0.0677	-0.2768	-0.0171	-0.4006	0.0966	0.311	0.0127	0.1159	0.0893	0.088	0.2904	-0.0315	0.1829	103.7824	42.6066	114.4926
13	0.6762	-0.0333	-0.1467	0.2575	0.0597	0.4436	0.0208	0.0827	0.026	-0.106	-0.009	-0.1154	0.044	0.086	-0.0118	0.0608	0.0261	0.0373	0.1242	-0.0066	0.0899	89.1469	54.7797	123.3058
14	5.5048	-1.6103	0.2077	1.3254	0.4707	0.828	-0.0124	0.298	0.0955	-0.0074	0.0041	-0.0519	-0.0034	0.0063	0.0083	0.0351	-0.0044	-0.0051	0.0397	0.013	0.0305	57.0065	46.7651	127.525
15	1.8128	-0.2597	-0.6603	0.9224	-0.0577	1.4271	0.045	0.1237	0.1185	-0.1404	0.0209	0.0569	-0.1826	-0.0281	-0.0659	0.0949	0.023	-0.016	0.0746	0.0171	0.0196	55.859	74.8401	97.6503
16	3.3851	-0.109	1.6168	0.396	-0.034	1.7341	-0.0487	0.243	0.0871	-0.0841	0.0174	-0.0101	-0.0383	0.1712	0.0313	0.0766	0.0038	0.0065	0.0658	0.0088	0.0032	63.4115	66.6599	98.4156
17	0.355	0.0087	0.2378	0.0403	-0.0368	0.5571	-0.0004	0.043	-0.012	-0.0369	0.0057	-0.0064	-0.0217	0.0001	-0.0053	0.0496	0.0046	-0.0091	0.0791	-0.0078	0.0478	62.3013	65.7732	122.2295
18	0.3116	0.0984	-0.1063	0.1917	-0.0694	0.5401	0	0.0554	-0.0083	-0.0559	0.0064	0.0074	0.0362	-0.0189	-0.0064	0.0552	0.0061	-0.0218	0.082	-0.0091	0.0288	57.4507	56.868	109.6043
19	0.5332	0.3196	-0.0484	1.8947	-0.5944	0.9074	0.0143	0.1237	0.0003	-0.2966	0.0551	0.229	0.221	-0.2412	-0.0694	0.1003	-0.0472	-0.0604	0.1734	-0.0139	0.0551	35.4951	47.6203	102.4382
20	0.6741	0.0334	-0.0012	0.3369	-0.1622	0.6192	-0.0301	0.0567	-0.0642	-0.093	0.0307	0.0361	0.1114	-0.0643	-0.0006	0.0614	-0.0168	-0.0158	0.0703	-0.0216	0.0379	46.4732	43.1388	118.5574
21	5.0454	-1.1464	2.6498	0.4937	-0.7412	2.4432	0.0289	0.15	-0.2357	-0.0455	0.0382	0.0232	0.0635	0.0777	-0.067	0.0396	0.0044	0.0195	0.0491	-0.0142	0.0445	75.7469	55.9811	128.1382
22	1.4202	1.2313	0.6251	1.7198	0.621	1.2392	0.0124	-0.1013	-0.1252	0.1238	0.0492	-0.005	0.2584	0.1238	-0.0616	0.1076	0.055	-0.026	0.0613	0.0357	0.0799	68.7013	31.3978	173.3904
23	1.1123	0.7095	-0.1572	1.0522	-0.0242	1.6839	0.1241	-0.1381	-0.0273	0.1782	-0.0555	-0.0791	-0.0404	0.1055	-0.0686	0.0797	0.0317	-0.0125	0.0645	0.006	0.045	69.8898	43.1101	171.3784
24	0.2327	0.0026	-0.0275	0.1027	-0.0035	0.2555	-0.0115	-0.0024	-0.0319	0.0205	0.0171	0.0155	0.0708	-0.009	-0.0056	0.0367	0.0007	-0.0027	0.0533	0.0046	0.0619	58.7934	43.546	157.1661
25	1.9397	-0.6512	-0.0159	1.5233	-0.0701	0.1385	-0.0373	-0.1055	-0.0278	0.0984	0.0132	0.0356	0.0463	-0.0678	0.024	0.0437	-0.0386	0.0276	0.1031	0.009	0.0393	34.6476	41.7373	169.6297
26	0.4338	0.2345	-0.218	0.4594	-0.1937	1.3936	-0.0042	0.0175	-0.0181	-0.0093	0.0224	0.0499	0.031	-0.0734	-0.0182	0.0156	-0.0052	0.0047	0.0738	0.0026	0.0621	38.5562	48.6523	149.8599
27	2.0686	-1.4421	-0.9427	1.2954	0.9336	2.1839	0.0394	-0.0104	0.0861	-0.0644	-0.0162	-0.0382	-0.0512	0.0709	-0.0231	0.0221	-0.0028	-0.0123	0.0452	0.0029	0.0411	56.712	50.7047	150.649
28	2.2696	2.3383	-1.9344	4.322	-2.9308	3.7432	0.1524	-0.0754	0.0468	0.2178	-0.1409	0.0587	-0.259	0.1077	-0.0115	0.0344	0.0104	-0.0152	0.0294	-0.0309	0.0448	75.9865	63.5321	144.0685

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	-7 - 3
2	X-RAY DIFFRACTION	2	A	4 - 37
3	X-RAY DIFFRACTION	3	A	38 - 75
4	X-RAY DIFFRACTION	4	A	76 - 162
5	X-RAY DIFFRACTION	5	A	163 - 316
6	X-RAY DIFFRACTION	6	A	317 - 471
7	X-RAY DIFFRACTION	7	A	472 - 503
8	X-RAY DIFFRACTION	8	B	-7 - 3
9	X-RAY DIFFRACTION	9	B	4 - 42
10	X-RAY DIFFRACTION	10	B	43 - 79
11	X-RAY DIFFRACTION	11	B	80 - 377
12	X-RAY DIFFRACTION	12	B	378 - 404
13	X-RAY DIFFRACTION	13	B	405 - 485
14	X-RAY DIFFRACTION	14	B	486 - 503
15	X-RAY DIFFRACTION	15	C	8 - 40
16	X-RAY DIFFRACTION	16	C	41 - 75
17	X-RAY DIFFRACTION	17	C	76 - 162
18	X-RAY DIFFRACTION	18	C	163 - 316
19	X-RAY DIFFRACTION	19	C	317 - 404
20	X-RAY DIFFRACTION	20	C	405 - 485
21	X-RAY DIFFRACTION	21	C	486 - 503
22	X-RAY DIFFRACTION	22	D	8 - 39
23	X-RAY DIFFRACTION	23	D	40 - 79
24	X-RAY DIFFRACTION	24	D	80 - 355
25	X-RAY DIFFRACTION	25	D	356 - 404
26	X-RAY DIFFRACTION	26	D	405 - 466
27	X-RAY DIFFRACTION	27	D	467 - 490
28	X-RAY DIFFRACTION	28	D	491 - 503

-
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