PDB-3noj: The structure of HMG/CHA aldolase from the protocatechuate degrad...

ID or keywords:

Entry

Database: PDB / ID: 3noj

Title

The structure of HMG/CHA aldolase from the protocatechuate degradation pathway of Pseudomonas putida

Components

4-carboxy-4-hydroxy-2-oxoadipate aldolase/oxaloacetate decarboxylase

Keywords

LYASE / class II aldolase / a-b-b-a sandwich / metalloprotein

Function / homology

Function and homology information

4-hydroxy-4-methyl-2-oxoglutarate aldolase / 4-hydroxy-4-methyl-2-oxoglutarate aldolase activity / oxaloacetate decarboxylase / oxaloacetate decarboxylase activity / metal ion binding
Similarity search - Function

Biological species

Pseudomonas putida (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.82 Å

Authors

Kimber, M.S. / Wang, W. / Mazurkewich, S. / Seah, S.Y.K.

Citation

Journal: J.Biol.Chem. / Year: 2010
Title: Structural and Kinetic Characterization of 4-Hydroxy-4-methyl-2-oxoglutarate/4-Carboxy-4-hydroxy-2-oxoadipate Aldolase, a Protocatechuate Degradation Enzyme Evolutionarily Convergent with the ...
Authors: Wang, W. / Mazurkewich, S. / Kimber, M.S. / Seah, S.Y.

History

Deposition	Jun 25, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 15, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Source and taxonomy / Version format compliance
Revision 1.2	Sep 6, 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_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_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.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_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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0	Nov 15, 2023	Group: Atomic model / Data collection / Derived calculations Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_struct_conn_angle / struct_conn Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _struct_conn.ptnr2_label_atom_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3noj.cif.gz	112.5 KB	Display	PDBx/mmCIF format
PDB format	pdb3noj.ent.gz	89 KB	Display	PDB format
PDBx/mmJSON format	3noj.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3noj_validation.pdf.gz	448.9 KB	Display	wwPDB validaton report
Full document	3noj_full_validation.pdf.gz	449.6 KB	Display
Data in XML	3noj_validation.xml.gz	12.3 KB	Display
Data in CIF	3noj_validation.cif.gz	16.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/no/3noj ftp://data.pdbj.org/pub/pdb/validation_reports/no/3noj	HTTPS FTP

-
Related structure data

Related structure data	1nxjS S: Starting model for refinement
Similar structure data	1n38-d 2r7v-d 1n1h-d 1je6-2 3s13-1 1mwh-d 2vre-1 6rgt-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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	#102 - Jun 2008 Lactate Dehydrogenase similarity (1) #263 - Nov 2021 Acetohydroxyacid Synthase similarity (1)

Deposited unit

A: 4-carboxy-4-hydroxy-2-oxoadipate aldolase/oxaloacetate decarboxylase

hetero molecules

26 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: 4-carboxy-4-hydroxy-2-oxoadipate aldolase/oxaloacetate decarboxylase

hetero molecules

x 6

defined by author
156 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_555	-y,x-y,z	1
crystal symmetry operation	3_555	-x+y,-x,z	1
crystal symmetry operation	4_556	y,x,-z+1	1
crystal symmetry operation	5_556	x-y,-y,-z+1	1
crystal symmetry operation	6_556	-x,-x+y,-z+1	1

2

A: 4-carboxy-4-hydroxy-2-oxoadipate aldolase/oxaloacetate decarboxylase

hetero molecules

A: 4-carboxy-4-hydroxy-2-oxoadipate aldolase/oxaloacetate decarboxylase

hetero molecules

A: 4-carboxy-4-hydroxy-2-oxoadipate aldolase/oxaloacetate decarboxylase

hetero molecules

defined by software
77.9 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	111.180, 111.180, 139.273
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	155
Space group name H-M	H32

#1: Protein	4-carboxy-4-hydroxy-2-oxoadipate aldolase/oxaloacetate decarboxylase Mass: 25476.066 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: F1 / Gene: pput1361, Pput_1361 / Plasmid: PT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(lambda-DE3) References: UniProt: A5W059, 4-hydroxy-4-methyl-2-oxoglutarate aldolase
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-PYR / PYRUVIC ACID Mass: 88.062 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₄O₃
#4: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 128 / 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: 3.25 Å³/Da / Density % sol: 62.17 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 10% PEG 4000, 0.1 M Na acetate, 10 mM MgCl2, 5 mM pyruvate, 21 mg/ml protein, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
Detector	Type: RAYONIX MX-225 / Detector: CCD / Date: Aug 19, 2009 Details: DCM WITH CRYO-COOLED 1ST CRYSTAL SAGITTALLY BENT 2ND CRYSTAL FOLLOWED BY VERTICALLY FOCUSING MIRROR
Radiation	Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.82→40 Å / Num. all: 27093 / Num. obs: 27093 / % possible obs: 90.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.7 % / R_sym value: 0.099 / Net I/σ(I): 12
Reflection shell	Resolution: 1.82→1.85 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 4.4 / R_sym value: 0.273 / % possible all: 89.4

-
Processing

Software

Name	Version	Classification
PHASER		phasing
REFMAC	5.2.0019	refinement
MxDC		data collection
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NXJ

1nxj

Resolution: 1.82→28.22 Å / Cor.coef. F_o:F_c: 0.967 / Cor.coef. F_o:F_c free: 0.963 / SU B: 3.101 / SU ML: 0.051 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.17079	1421	5.2 %	RANDOM
R_work	0.15879	-	-	-
obs	0.15942	25671	90.84 %	-
all	-	27093	-	-

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 mean: 40.182 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.84 Å²	-0.42 Å²	0 Å²
2-	-	-0.84 Å²	0 Å²
3-	-	-	1.26 Å²

Refinement step

Cycle: LAST / Resolution: 1.82→28.22 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1760	0	33	128	1921

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.022	1827
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1244
X-RAY DIFFRACTION	r_angle_refined_deg	1.046	1.99	2469
X-RAY DIFFRACTION	r_angle_other_deg	0.821	3	3033
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.257	5	240
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.591	23.766	77
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.302	15	313
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.391	15	19
X-RAY DIFFRACTION	r_chiral_restr	0.059	0.2	291
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	2053
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	348
X-RAY DIFFRACTION	r_nbd_refined	0.201	0.2	347
X-RAY DIFFRACTION	r_nbd_other	0.186	0.2	1342
X-RAY DIFFRACTION	r_nbtor_refined	0.159	0.2	903
X-RAY DIFFRACTION	r_nbtor_other	0.08	0.2	1024
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.09	0.2	98
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined	0.014	0.2	1
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.159	0.2	17
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.218	0.2	66
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.127	0.2	13
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.412	1.5	1520
X-RAY DIFFRACTION	r_mcbond_other	0.078	1.5	491
X-RAY DIFFRACTION	r_mcangle_it	0.486	2	1882
X-RAY DIFFRACTION	r_scbond_it	0.894	3	717
X-RAY DIFFRACTION	r_scangle_it	1.354	4.5	586
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.82→1.867 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.181	105	-
R_work	0.151	1827	-
obs	-	-	90.53 %

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	7.4091	6.2916	-7.7403	22.3744	-22.6811	23.3212	0.091	-0.7033	0.3382	1.1385	-0.7911	-0.8741	-0.8293	0.5442	0.7001	0.1683	-0.1685	-0.1195	-0.0254	0.0086	-0.0039	27.5843	12.2808	70.228
2	16.9024	-2.8265	-5.7225	23.0589	9.9091	27.8048	-0.4479	0.8042	0.5502	-0.8825	0.1733	-1.7962	-0.2374	1.1041	0.2745	-0.0778	-0.1348	-0.034	0.0871	0.1082	0.2289	33.9947	14.6437	59.7067
3	3.5821	-8.9326	-4.4881	25.9572	18.3453	19.5211	-0.3703	0.7382	-1.0122	0.9382	0.4693	0.6561	1.544	0.3341	-0.099	0.0729	-0.0553	0.0781	0.3503	0.0344	0.4503	33.7628	2.6542	52.3451
4	48.1037	16.0077	3.1968	37.0844	16.0362	20.1765	0.8729	0.7774	1.0636	-1.0139	0.1399	-1.4317	-1.2478	1.3382	-1.0128	0.1648	0.0063	0.2561	0.1107	-0.0071	0.1748	28.5009	-3.4061	45.2249
5	22.238	8.0603	-2.2547	15.3046	1.4241	6.558	-0.1265	1.2685	0.3974	-1.1811	0.3641	-0.3147	-0.4592	-0.2382	-0.2376	0.0606	0.0575	0.1439	-0.0128	-0.0099	-0.0974	22.0496	-8.0419	45.2871
6	2.3081	-1.2007	-0.7536	7.4109	0.4167	5.8201	-0.075	0.2831	-0.2807	-0.1091	-0.0407	-0.0636	-0.0207	0.0804	0.1157	-0.1504	0.036	0.0747	-0.1398	-0.0312	-0.0965	18.1644	-10.9903	52.5125
7	10.0423	1.5225	2.4083	11.1715	-2.4189	11.4911	-0.0309	-0.0874	-0.3877	0.3322	0.1274	-0.0789	0.1109	0.2568	-0.0965	-0.0999	0.0593	0.0591	-0.1072	-0.0049	-0.0805	21.401	-14.1663	58.3947
8	12.0856	-10.1327	-1.3777	26.3961	-4.5419	12.2602	-0.5726	-0.4741	-0.5503	0.4508	0.1957	-0.1412	1.0973	0.4087	0.3769	0.0125	0.066	0.0827	-0.1089	0.0284	-0.1175	19.6075	-10.3393	61.9496
9	9.2844	-7.2911	16.879	12.1957	-13.1467	32.7979	0.1514	-1.1329	-0.3656	0.3018	0.5662	0.7594	0.4875	-1.3511	-0.7176	-0.0396	0.006	0.0551	-0.0519	0.0058	-0.12	9.1403	-1.4993	60.5402
10	8.566	1.5799	0.381	12.0793	8.0645	17.3105	-0.041	0.4638	-0.0777	-0.6036	-0.213	0.7095	0.1627	-0.1991	0.254	-0.0987	0.0053	-0.0018	-0.1099	-0.0001	-0.1564	7.7453	0.7722	48.7362
11	28.8565	4.6754	11.2244	2.0706	-0.3598	7.9802	-0.5888	0.5932	-0.3248	-0.3784	0.3786	-0.2055	-0.366	0.1002	0.2102	-0.0905	0.0223	0.072	-0.0665	-0.0279	-0.1216	17.8098	-1.4823	47.4693
12	0.8205	-0.5351	-1.013	13.022	5.7911	12.4301	-0.0581	0.0347	0.0201	-0.3197	-0.0796	-0.4031	-0.2719	0.2501	0.1377	-0.1747	-0.0468	0.0225	-0.0654	0.0394	-0.0472	25.4533	6.8729	56.8055
13	41.6321	-19.071	4.4502	12.8229	3.4621	7.8794	-0.5813	-2.1746	0.9945	1.0572	0.151	0.2304	-0.2922	-0.8241	0.4303	0.0628	-0.0367	0.0452	0.1034	-0.1386	0.1218	17.5049	14.6155	66.6892
14	3.9044	1.9703	-0.002	1.001	0.1429	3.1207	-0.0462	-0.7457	1.2836	0.3786	-0.3149	0.4059	-0.6875	0.0226	0.361	0.0967	-0.0449	-0.0573	0.073	-0.0665	0.2576	19.0433	18.8177	60.8337
15	16.5998	3.6378	-0.8989	5.3624	4.7487	11.5248	-0.3237	0.2822	1.0196	-0.3825	-0.2309	-0.1678	-0.7669	0.2559	0.5546	-0.0185	-0.0625	-0.0442	-0.0639	0.1127	0.089	24.6461	18.1854	54.0577
16	2.3574	-2.5486	1.283	27.067	23.5873	26.3533	-0.2866	0.4968	0.198	-0.6125	0.8717	-1.6337	-0.4653	1.6554	-0.5852	-0.0408	-0.0618	0.1444	0.1318	0.0789	0.1164	29.4068	10.2905	49.006
17	11.5089	-4.0417	-9.1856	6.037	4.7622	12.0572	0.0548	0.2393	0.3868	-0.1978	-0.1589	-0.3837	-0.1983	0.0535	0.104	-0.1525	-0.0197	0.035	-0.095	0.0459	-0.1052	22.0135	7.1625	54.6895
18	52.4084	-7.3802	-43.3247	3.7745	3.4557	61.0567	-0.1141	-2.7788	0.2024	0.7726	0.3877	-0.0187	-0.2579	1.0689	-0.2736	0.0006	-0.0193	-0.0182	0.0994	0.0076	-0.0529	15.5293	9.7701	68.4626
19	2.4608	1.4686	-5.6336	8.0149	-5.9088	44.1417	-0.2	-0.9307	0.6442	1.3485	0.4189	-0.1322	-0.2591	0.3856	-0.2189	0.0693	0.0386	-0.0329	-0.0634	0.0001	-0.0115	10.0033	13.3272	62.8647
20	5.4343	2.8397	-4.0995	7.4698	-6.0794	11.1212	-0.0043	0.0122	0.5404	-0.0859	-0.0883	-0.179	-0.2647	-0.0252	0.0926	-0.0934	-0.0173	0.0258	-0.127	0.0613	-0.0769	13.2061	16.2059	51.1507
21	5.5349	-2.1826	-2.0014	9.7833	-0.6754	5.4046	0.1505	0.4775	-0.0088	-0.2397	-0.1115	-0.1291	0.0391	0.354	-0.039	-0.0737	-0.0067	0.0812	-0.0367	0.1199	-0.0499	18.2434	14.3685	46.4938
22	8.9404	-1.4979	-4.5492	3.0742	-4.1936	11.0138	0.0203	0.4482	0.0675	0.2239	-0.25	-0.7819	-0.1373	0.3862	0.2297	-0.0225	-0.0145	0.1193	0.1107	0.0873	-0.0104	23.7502	9.6882	45.8199
23	6.7215	-3.4604	-6.7009	6.8337	4.1156	31.4676	-0.284	-0.0876	-0.1027	0.0301	0.1105	-0.2046	0.3342	0.098	0.1735	-0.1789	-0.0165	0.0148	-0.1692	0.0094	-0.1487	15.984	6.1762	56.6637
24	0.5499	-1.3072	1.2272	5.2762	-4.1256	4.3113	0.0281	0.1442	0.238	0.2045	0.1533	0.0666	-0.1997	0.2342	-0.1814	-0.123	-0.0069	0.0311	-0.1493	0.037	-0.1298	7.9869	13.8275	55.7048
25	10.9083	0.3348	-3.4441	2.971	-1.5351	6.0008	-0.1317	0.4683	-0.0727	-0.3497	-0.002	0.1992	-0.0962	-0.0808	0.1337	-0.0793	-0.0035	0.025	-0.1028	0.0438	-0.1395	5.7848	10.0748	46.8724
26	7.9004	-3.6845	6.3811	11.1301	-6.7136	14.684	0.1478	0.4856	0.329	-0.4609	-0.2448	-0.212	-0.1594	0.1509	0.097	-0.0641	0.0052	0.0713	-0.0275	0.0331	-0.1577	11.9583	9.5152	44.6043
27	16.4211	-7.0928	-8.4247	12.3253	4.7764	10.5091	-0.2842	-0.77	-0.2986	0.5968	0.3301	-0.3533	0.2672	0.5093	-0.0459	-0.135	0.0053	-0.0024	-0.1519	0.0304	-0.1615	10.8965	3.8147	57.3288
28	7.9737	-6.0934	-2.1784	45.4757	2.6113	8.9791	-0.2726	-0.4676	0.2617	1.2708	0.1967	-0.1532	-0.3243	0.342	0.0759	-0.1037	0.0047	0.0095	-0.1148	0.0617	-0.1512	4.4682	14.51	59.509
29	32.378	0.3208	8.4562	7.4444	-3.5837	4.0161	-0.4136	-0.0069	2.0343	0.136	0.243	-0.246	-1.0976	0.3546	0.1706	0.2345	-0.0649	-0.0765	0.0905	-0.126	0.2441	15.8299	22.9868	63.9156
30	11.9137	-11.0163	-7.2884	22.1655	9.4914	8.5571	-0.0395	-0.5769	0.3368	0.6454	-0.057	-0.3384	-0.179	0.3178	0.0966	-0.0911	-0.0822	-0.0358	-0.0376	0.0065	0.0238	26.3698	14.9325	63.4975
31	16.9062	11.6345	-3.7436	12.3615	-0.6954	1.6413	0.2567	-0.5818	-0.1518	0.4754	-0.4726	-0.7171	-0.3087	0.275	0.2159	-0.0675	-0.0216	-0.0376	-0.0821	0.0304	-0.0581	24.6176	5.3175	65.5571
32	14.1378	9.9143	-3.0644	8.6003	-2.3495	5.9558	0.0925	-0.0105	-0.1003	0.3505	-0.1008	-0.4456	0.0641	0.0124	0.0083	-0.0848	0.004	0.0026	-0.1356	0.0125	-0.1064	21.1422	-0.6294	64.7054
33	12.4331	6.1166	5.5629	15.9062	5.9704	12.9559	-0.0322	0.1159	0.4095	0.3211	0.0158	-0.7813	0.1685	0.4792	0.0164	-0.1638	0.0033	0.0167	-0.0643	0.0463	0.0165	28.6076	1.1724	58.266
34	38.027	6.0248	8.8569	6.4751	0.3722	4.4836	-0.4026	0.3038	0.0759	-0.3913	0.0669	0.0338	-0.2207	0.1954	0.3357	-0.145	0.0253	0.0673	-0.143	-0.0111	-0.1884	16.0438	-3.661	51.8287
35	21.6707	2.1982	11.4277	3.6757	1.8081	7.8439	0.0205	-0.2979	-0.3718	0.0847	-0.1864	-0.1946	0.2084	-0.1564	0.1659	-0.1535	-0.0029	0.0617	-0.1309	-0.01	-0.162	16.2635	-5.145	56.3009
36	19.3825	-5.6077	-11.0235	19.9017	3.9937	17.8628	-0.0588	-0.9472	0.38	0.8542	0.5552	-1.4104	-0.2707	1.8196	-0.4965	-0.0465	0.0158	-0.0114	0.0927	-0.045	0.0589	30.7406	-4.8259	58.8129
37	21.5467	9.8183	6.0757	6.2552	10.1247	32.092	-0.1772	0.2792	-0.003	-0.0992	0.8192	-0.5246	-1.2059	1.4628	-0.642	-0.0469	0.0497	0.0903	0.0071	-0.0668	0.0474	30.5887	-11.1037	52.5742
38	14.2147	9.3449	4.1708	16.1661	12.1444	15.033	-0.0112	0.252	-0.4861	0.1848	0.2321	-0.5141	0.4357	0.5391	-0.2209	-0.113	0.0938	0.1161	-0.0723	-0.0444	-0.0629	26.5871	-17.3274	49.8829
39	6.1294	0.9301	0.4584	11.4836	9.0292	7.1117	-0.2133	0.0007	-0.566	0.0787	0.1035	-0.0638	0.2968	0.1317	0.1099	-0.0514	0.0713	0.1207	-0.0535	-0.0428	-0.045	19.525	-20.5905	49.1642
40	42.1307	19.355	4.1293	10.5212	8.288	25.4715	0.2095	0.1288	0.0977	-0.5615	-0.3155	0.1451	-0.062	0.2454	0.1059	-0.0151	0.0633	0.0956	-0.0001	-0.1379	0.0521	15.0479	-24.0828	43.8402
41	13.1792	1.7798	-13.8103	18.5038	-0.9727	18.1175	-0.6447	-0.1848	-1.0387	-0.5445	-0.0576	-0.4009	1.2831	0.3562	0.7023	0.0795	0.0227	0.1392	-0.017	-0.1376	0.0683	10.4376	-29.2572	43.6839
42	13.3299	-3.3781	13.7912	15.2665	-10.8452	18.0173	-0.4575	-0.0559	-1.2127	-0.7001	0.074	0.0897	1.2673	0.9593	0.3835	0.1792	0.1165	0.2761	0.0179	-0.077	0.2868	8.8685	-33.3124	49.5061
43	12.4972	0.0923	-4.0089	3.8973	-6.9347	13.5225	-0.5378	-0.1948	-1.6098	-0.2656	-0.4015	-1.0349	0.4098	1.1905	0.9394	0.2271	0.162	0.2942	0.1414	-0.0097	0.5822	12.3301	-34.1124	53.7122
44	16.8971	1.4038	-0.4917	19.9643	-26.2774	73.1962	-0.3131	0.6958	-1.1026	0.7982	-0.2971	-1.5366	0.3136	2.8472	0.6102	0.0751	0.1338	0.0521	0.2137	0.1118	0.4102	11.4223	-37.3212	62.288
45	24.2759	5.3833	5.1882	8.8362	-5.1136	13.2004	-0.2632	-1.6136	-0.7667	0.5436	-0.4097	-0.3857	0.7522	0.8771	0.6729	0.1505	0.148	0.0664	0.0116	0.1043	0.2445	4.3678	-37.8366	65.0157
46	50.6134	-13.8467	-12.9783	30.7603	4.9017	20.8173	-0.2528	0.2449	-1.5225	0.3005	-0.3693	3.029	0.8401	-1.5008	0.6221	0.1567	-0.0829	0.1174	-0.0316	-0.0448	0.6036	-9.9905	-38.7486	62.0612
47	100.3132	-52.0346	-31.5237	31.5299	35.7359	92.6963	1.3252	-2.2442	-2.8141	2.3597	-1.0173	1.0364	3.1369	-3.6252	-0.3079	0.537	-0.2277	0.2695	-0.058	0.2003	0.5099	-9.0831	-39.6036	66.6382

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	5 - 9
2	X-RAY DIFFRACTION	2	A	10 - 14
3	X-RAY DIFFRACTION	3	A	15 - 19
4	X-RAY DIFFRACTION	4	A	20 - 24
5	X-RAY DIFFRACTION	5	A	25 - 29
6	X-RAY DIFFRACTION	6	A	30 - 34
7	X-RAY DIFFRACTION	7	A	35 - 39
8	X-RAY DIFFRACTION	8	A	40 - 44
9	X-RAY DIFFRACTION	9	A	45 - 49
10	X-RAY DIFFRACTION	10	A	50 - 54
11	X-RAY DIFFRACTION	11	A	55 - 59
12	X-RAY DIFFRACTION	12	A	60 - 64
13	X-RAY DIFFRACTION	13	A	65 - 69
14	X-RAY DIFFRACTION	14	A	70 - 74
15	X-RAY DIFFRACTION	15	A	75 - 79
16	X-RAY DIFFRACTION	16	A	80 - 84
17	X-RAY DIFFRACTION	17	A	85 - 89
18	X-RAY DIFFRACTION	18	A	90 - 94
19	X-RAY DIFFRACTION	19	A	95 - 99
20	X-RAY DIFFRACTION	20	A	100 - 104
21	X-RAY DIFFRACTION	21	A	105 - 109
22	X-RAY DIFFRACTION	22	A	110 - 114
23	X-RAY DIFFRACTION	23	A	115 - 119
24	X-RAY DIFFRACTION	24	A	120 - 124
25	X-RAY DIFFRACTION	25	A	125 - 129
26	X-RAY DIFFRACTION	26	A	130 - 134
27	X-RAY DIFFRACTION	27	A	135 - 139
28	X-RAY DIFFRACTION	28	A	140 - 144
29	X-RAY DIFFRACTION	29	A	145 - 149
30	X-RAY DIFFRACTION	30	A	150 - 154
31	X-RAY DIFFRACTION	31	A	155 - 159
32	X-RAY DIFFRACTION	32	A	160 - 164
33	X-RAY DIFFRACTION	33	A	165 - 169
34	X-RAY DIFFRACTION	34	A	170 - 174
35	X-RAY DIFFRACTION	35	A	175 - 179
36	X-RAY DIFFRACTION	36	A	180 - 184
37	X-RAY DIFFRACTION	37	A	185 - 189
38	X-RAY DIFFRACTION	38	A	190 - 194
39	X-RAY DIFFRACTION	39	A	195 - 199
40	X-RAY DIFFRACTION	40	A	200 - 204
41	X-RAY DIFFRACTION	41	A	205 - 209
42	X-RAY DIFFRACTION	42	A	210 - 214
43	X-RAY DIFFRACTION	43	A	215 - 219
44	X-RAY DIFFRACTION	44	A	220 - 224
45	X-RAY DIFFRACTION	45	A	225 - 229
46	X-RAY DIFFRACTION	46	A	230 - 234
47	X-RAY DIFFRACTION	47	A	235 - 239

-
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://pdbjlvh1.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