PDB-2qnk: Crystal structure of human 3-hydroxyanthranilate 3,4-dioxygenase

ID or keywords:

Entry

Database: PDB / ID: 2qnk

Title

Crystal structure of human 3-hydroxyanthranilate 3,4-dioxygenase

Components

3-hydroxyanthranilate 3,4-dioxygenase

Keywords

OXIDOREDUCTASE / Bicupin fold / cupin barrel / extradiol dioxygenase / metalloenzyme / trytophan catabolism / NAD+ synthesis / quinolinate / kynurenine pathway / Structural Genomics Medical Relevance / Protein Structure Initiative / PSI / Center for Eukaryotic Structural Genomics / CESG

Function / homology

Function and homology information

quinolinate metabolic process / 3-hydroxyanthranilate 3,4-dioxygenase / 3-hydroxyanthranilate 3,4-dioxygenase activity / quinolinate biosynthetic process / anthranilate metabolic process / 'de novo' NAD biosynthetic process from tryptophan / tryptophan catabolic process / Tryptophan catabolism / NAD biosynthetic process / response to zinc ion ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.6 Å

Authors

Bitto, E. / Bingman, C.A. / Wesenberg, G.E. / Phillips Jr., G.N. / Center for Eukaryotic Structural Genomics (CESG)

Citation

Journal: to be published
Title: Crystal Structure of Human 3-hydroxyanthranilate 3,4-dioxygenase.
Authors: Bitto, E. / Bingman, C.A. / Wesenberg, G.E. / Phillips Jr., G.N.

History

Deposition	Jul 18, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 14, 2007	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Oct 25, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2qnk.cif.gz	81.4 KB	Display	PDBx/mmCIF format
PDB format	pdb2qnk.ent.gz	63 KB	Display	PDB format
PDBx/mmJSON format	2qnk.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2qnk_validation.pdf.gz	400.9 KB	Display	wwPDB validaton report
Full document	2qnk_full_validation.pdf.gz	401.6 KB	Display
Data in XML	2qnk_validation.xml.gz	7.8 KB	Display
Data in CIF	2qnk_validation.cif.gz	13 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qn/2qnk ftp://data.pdbj.org/pub/pdb/validation_reports/qn/2qnk	HTTPS FTP

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Related structure data

Similar structure data	5tk5-d 5tkq-d 1pv5-d 2fkc-2 5hcf-2 2fl3-d 2aqs-d 5xbi-d 4evq-2 1l5m-d 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	TargetDB: GO.43316

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: 3-hydroxyanthranilate 3,4-dioxygenase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	50.498, 78.227, 85.080
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Details

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

#1: Protein	3-hydroxyanthranilate 3,4-dioxygenase / 3-HAO / 3-hydroxyanthranilic acid dioxygenase / 3-hydroxyanthranilate oxygenase Mass: 32878.234 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Tissue: Brain / Gene: HAAO / Plasmid: pVP16 / Production host: Escherichia coli (E. coli) / Strain (production host): BL834(DE3) P(RARE2) References: UniProt: P46952, 3-hydroxyanthranilate 3,4-dioxygenase
#2: Chemical	ChemComp-NI / NICKEL (II) ION Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 413 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.6 Å³/Da / Density % sol: 52.2 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop Details: Protein solution (10 mg/ml Protein, 0.050 M Sodium chloride, 0.0031 M Sodium azide, 0.0003 M TCEP, 0.005 M Bis-Tris pH 7.0) mixed in a 1:1 ratio with the well solution (50% v/v 2-Methyl-2,4- ...Details: Protein solution (10 mg/ml Protein, 0.050 M Sodium chloride, 0.0031 M Sodium azide, 0.0003 M TCEP, 0.005 M Bis-Tris pH 7.0) mixed in a 1:1 ratio with the well solution (50% v/v 2-Methyl-2,4-pentanediol (MPD), 0.1 M PIPES pH 6.5) and cryoprotected with well solution, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal

Density Matthews: 2.6 Å³/Da / Density % sol: 52.2 %

Crystal grow

Temperature: 277 K / Method: vapor diffusion, hanging drop
Details: Protein solution (10 mg/ml Protein, 0.050 M Sodium chloride, 0.0031 M Sodium azide, 0.0003 M TCEP, 0.005 M Bis-Tris pH 7.0) mixed in a 1:1 ratio with the well solution (50% v/v 2-Methyl-2,4- ...

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 23-ID-B / Wavelength: 0.97943, 0.96420

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 6, 2007 / Details: Adjustable focus K-B pair Si plus Pt, Rh coatings

Radiation

Monochromator: Double crystal cryo-cooled Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97943	1
2	0.9642	1

Reflection

Resolution: 1.6→37.4 Å / Num. obs: 45122 / % possible obs: 99.7 % / Redundancy: 13.7 % / R_merge(I) obs: 0.074 / Χ²: 1.238 / Net I/σ(I): 15.276

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique all	Χ²	% possible all
1.6-1.64	9.3	0.377	4.1037	2860	1.07	96.2
1.64-1.68	10.7	0.36		2929	1.07	99.2
1.68-1.72	12	0.297		2964	1.079	99.9
1.72-1.77	13	0.267		2982	1.143	100
1.77-1.83	13.9	0.237		2982	1.204	100
1.83-1.9	14.3	0.188		2980	1.249	100
1.9-1.97	14.6	0.152		2993	1.393	100
1.97-2.06	14.7	0.126		2996	1.463	100
2.06-2.17	14.8	0.111		3002	1.455	100
2.17-2.31	14.8	0.093		3004	1.305	100
2.31-2.49	14.8	0.084		2995	1.098	100
2.49-2.74	14.8	0.083		3052	1.259	100
2.74-3.13	14.7	0.073		3061	1.336	100
3.13-3.95	14.6	0.05		3086	0.992	100
3.95-37.4	13.9	0.048		3236	1.287	99.6

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Phasing

Phasing

Method:

MAD

Phasing MAD set

Highest resolution: 1.6 Å / Lowest resolution: 32.53 Å

ID	R cullis acentric	R cullis centric	Power acentric	Power centric	Reflection acentric	Reflection centric
ISO_1	0	0	0	0	40550	4460
ISO_2	0.744	0.769	1.745	1.289	40371	4447
ANO_1	0.527	0	2.308	0	40212	0
ANO_2	0.728	0	0.958	0	40185	0

Phasing MAD set shell

ID	Resolution (Å)	R cullis acentric	R cullis centric	Power acentric	Power centric	Reflection acentric	Reflection centric
ISO_1	7-32.53	0	0	0	0	402	217
ISO_1	5.01-7	0	0	0	0	776	219
ISO_1	4.1-5.01	0	0	0	0	1032	228
ISO_1	3.56-4.1	0	0	0	0	1236	215
ISO_1	3.19-3.56	0	0	0	0	1425	230
ISO_1	2.91-3.19	0	0	0	0	1573	223
ISO_1	2.7-2.91	0	0	0	0	1727	221
ISO_1	2.53-2.7	0	0	0	0	1860	223
ISO_1	2.38-2.53	0	0	0	0	1982	231
ISO_1	2.26-2.38	0	0	0	0	2117	230
ISO_1	2.16-2.26	0	0	0	0	2211	225
ISO_1	2.06-2.16	0	0	0	0	2324	219
ISO_1	1.98-2.06	0	0	0	0	2436	229
ISO_1	1.91-1.98	0	0	0	0	2526	228
ISO_1	1.85-1.91	0	0	0	0	2627	231
ISO_1	1.79-1.85	0	0	0	0	2725	224
ISO_1	1.74-1.79	0	0	0	0	2783	222
ISO_1	1.69-1.74	0	0	0	0	2887	227
ISO_1	1.64-1.69	0	0	0	0	2963	216
ISO_1	1.6-1.64	0	0	0	0	2938	202
ANO_1	7-32.53	0.332	0	3.615	0	401	0
ANO_1	5.01-7	0.333	0	3.948	0	776	0
ANO_1	4.1-5.01	0.425	0	2.965	0	1032	0
ANO_1	3.56-4.1	0.427	0	3.107	0	1236	0
ANO_1	3.19-3.56	0.406	0	3.195	0	1425	0
ANO_1	2.91-3.19	0.372	0	3.485	0	1573	0
ANO_1	2.7-2.91	0.368	0	3.65	0	1727	0
ANO_1	2.53-2.7	0.385	0	3.495	0	1860	0
ANO_1	2.38-2.53	0.399	0	3.252	0	1982	0
ANO_1	2.26-2.38	0.433	0	3.016	0	2117	0
ANO_1	2.16-2.26	0.453	0	2.727	0	2211	0
ANO_1	2.06-2.16	0.469	0	2.651	0	2324	0
ANO_1	1.98-2.06	0.532	0	2.283	0	2436	0
ANO_1	1.91-1.98	0.593	0	1.92	0	2526	0
ANO_1	1.85-1.91	0.636	0	1.769	0	2627	0
ANO_1	1.79-1.85	0.715	0	1.495	0	2725	0
ANO_1	1.74-1.79	0.757	0	1.314	0	2783	0
ANO_1	1.69-1.74	0.811	0	1.132	0	2880	0
ANO_1	1.64-1.69	0.861	0	1.018	0	2888	0
ANO_1	1.6-1.64	0.89	0	0.928	0	2683	0
ISO_2	7-32.53	0.5	0.586	2.838	1.939	402	217
ISO_2	5.01-7	0.562	0.67	2.784	1.802	776	219
ISO_2	4.1-5.01	0.692	0.808	2.053	1.37	1032	228
ISO_2	3.56-4.1	0.734	0.833	1.941	1.224	1236	215
ISO_2	3.19-3.56	0.741	0.742	1.907	1.286	1425	230
ISO_2	2.91-3.19	0.735	0.74	2.018	1.36	1573	223
ISO_2	2.7-2.91	0.744	0.771	2.127	1.515	1727	221
ISO_2	2.53-2.7	0.742	0.782	2.122	1.342	1860	223
ISO_2	2.38-2.53	0.729	0.765	2.048	1.339	1982	231
ISO_2	2.26-2.38	0.752	0.724	1.912	1.293	2116	230
ISO_2	2.16-2.26	0.774	0.799	1.816	1.244	2211	225
ISO_2	2.06-2.16	0.758	0.802	1.776	1.109	2324	219
ISO_2	1.98-2.06	0.762	0.815	1.674	1.108	2436	229
ISO_2	1.91-1.98	0.758	0.813	1.544	0.991	2525	228
ISO_2	1.85-1.91	0.752	0.854	1.456	0.892	2625	231
ISO_2	1.79-1.85	0.774	0.781	1.351	0.832	2725	224
ISO_2	1.74-1.79	0.789	0.86	1.207	0.748	2782	222
ISO_2	1.69-1.74	0.805	0.936	1.068	0.658	2882	225
ISO_2	1.64-1.69	0.829	0.917	0.904	0.553	2938	212
ISO_2	1.6-1.64	0.85	0.916	0.762	0.572	2794	195
ANO_2	7-32.53	0.535	0	1.398	0	402	0
ANO_2	5.01-7	0.521	0	1.548	0	776	0
ANO_2	4.1-5.01	0.566	0	1.397	0	1032	0
ANO_2	3.56-4.1	0.562	0	1.491	0	1236	0
ANO_2	3.19-3.56	0.558	0	1.46	0	1425	0
ANO_2	2.91-3.19	0.545	0	1.499	0	1573	0
ANO_2	2.7-2.91	0.551	0	1.536	0	1727	0
ANO_2	2.53-2.7	0.57	0	1.479	0	1860	0
ANO_2	2.38-2.53	0.607	0	1.315	0	1982	0
ANO_2	2.26-2.38	0.646	0	1.24	0	2116	0
ANO_2	2.16-2.26	0.686	0	1.077	0	2211	0
ANO_2	2.06-2.16	0.713	0	1.008	0	2324	0
ANO_2	1.98-2.06	0.758	0	0.901	0	2436	0
ANO_2	1.91-1.98	0.82	0	0.778	0	2525	0
ANO_2	1.85-1.91	0.86	0	0.678	0	2625	0
ANO_2	1.79-1.85	0.893	0	0.588	0	2725	0
ANO_2	1.74-1.79	0.914	0	0.53	0	2782	0
ANO_2	1.69-1.74	0.939	0	0.451	0	2872	0
ANO_2	1.64-1.69	0.959	0	0.392	0	2883	0
ANO_2	1.6-1.64	0.971	0	0.37	0	2673	0

Phasing MAD set site

ID	Cartn x (Å)	Cartn y (Å)	Cartn z (Å)	Atom type symbol	B iso	Occupancy
1	12.27	55.409	52.096	SE	12.69	1.74
2	3.595	48.314	64.75	SE	14.75	1.26
3	7.57	18.939	66.774	SE	27.82	1.24
4	4.079	19.331	61.985	SE	14.54	1.05
5	11.316	10.04	3.444	SE	27.67	1.14
6	11.564	25.893	20.334	SE	20.76	0.51
7	9.929	54.593	70.056	SE	12.79	0.54
8	1.309	51.061	84.287	SE	26.75	0.81

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 45010

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
7.46-100	41.5	0.903	514
5.65-7.46	43.7	0.94	623
4.74-5.65	39.6	0.942	759
4.16-4.74	39.3	0.955	867
3.75-4.16	40.3	0.948	972
3.44-3.75	41.2	0.952	1062
3.2-3.44	40	0.949	1125
3-3.2	40.6	0.943	1199
2.84-3	38.3	0.934	1289
2.7-2.84	41	0.935	1342
2.57-2.7	41.8	0.932	1419
2.47-2.57	42.2	0.928	1470
2.37-2.47	37.7	0.93	1517
2.29-2.37	41.5	0.921	1588
2.21-2.29	43.5	0.927	1641
2.14-2.21	42.9	0.922	1705
2.08-2.14	44	0.916	1736
2.02-2.08	44.9	0.914	1749
1.97-2.02	44.9	0.907	1842
1.92-1.97	47.1	0.899	1910
1.88-1.92	48.8	0.891	1914
1.83-1.88	49.9	0.879	1948
1.79-1.83	52.1	0.864	2009
1.76-1.79	55.8	0.859	2065
1.72-1.76	56.3	0.869	2105
1.69-1.72	59.4	0.855	2118
1.66-1.69	62.4	0.824	2166
1.63-1.66	67.4	0.805	2157
1.6-1.63	65.5	0.738	2199

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SHARP		phasing
DM	5	phasing
REFMAC	5.2.0019	refinement
PDB_EXTRACT	2	data extraction
MAR345	CCD	data collection
HKL-2000		data reduction

Refinement

Method to determine structure:

MAD / Resolution: 1.6→30.92 Å / Cor.coef. F_o:F_c: 0.971 / Cor.coef. F_o:F_c free: 0.967 / WR_factor R_free: 0.188 / WR_factor R_work: 0.163 / SU B: 2.49 / SU ML: 0.047 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.075 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.176	2268	5.036 %	RANDOM
R_work	0.157	-	-	-
obs	0.158	45034	99.476 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 18.034 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.02 Å²	0 Å²	0 Å²
2-	-	1.025 Å²	0 Å²
3-	-	-	-1.004 Å²

Refinement step

Cycle: LAST / Resolution: 1.6→30.92 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2291	0	6	413	2710

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.022	2386
X-RAY DIFFRACTION	r_angle_refined_deg	1.487	1.971	3240
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.412	5	293
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.039	23.565	115
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.889	15	415
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.842	15	21
X-RAY DIFFRACTION	r_chiral_restr	0.113	0.2	346
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	1846
X-RAY DIFFRACTION	r_nbd_refined	0.199	0.2	1007
X-RAY DIFFRACTION	r_nbtor_refined	0.308	0.2	1619
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.133	0.2	318
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.146	0.2	33
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.124	0.2	23
X-RAY DIFFRACTION	r_mcbond_it	1.378	2	1488
X-RAY DIFFRACTION	r_mcangle_it	2.219	4	2346
X-RAY DIFFRACTION	r_scbond_it	3.583	6	1021
X-RAY DIFFRACTION	r_scangle_it	5.116	8	894

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.6-1.641	0.286	126	0.242	2966	3284	94.153
1.641-1.685	0.277	183	0.216	3012	3223	99.131
1.685-1.734	0.232	159	0.191	2960	3125	99.808
1.734-1.787	0.198	147	0.178	2865	3014	99.934
1.787-1.846	0.196	136	0.169	2808	2947	99.898
1.846-1.91	0.202	150	0.16	2719	2871	99.93
1.91-1.982	0.2	142	0.154	2609	2752	99.964
1.982-2.063	0.156	148	0.148	2524	2672	100
2.063-2.154	0.169	120	0.149	2427	2547	100
2.154-2.259	0.164	104	0.151	2339	2443	100
2.259-2.38	0.206	125	0.148	2226	2351	100
2.38-2.523	0.193	95	0.154	2120	2215	100
2.523-2.696	0.171	114	0.161	1967	2081	100
2.696-2.911	0.163	91	0.151	1856	1947	100
2.911-3.186	0.16	101	0.15	1701	1803	99.945
3.186-3.557	0.134	81	0.132	1575	1656	100
3.557-4.098	0.159	80	0.13	1370	1450	100
4.098-4.997	0.126	63	0.127	1205	1268	100
4.997-6.977	0.192	67	0.193	934	1001	100
6.977-30.92	0.181	36	0.223	583	621	99.678

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	0.657	0.0367	0.5118	1.2394	0.9992	1.4099	0.0081	-0.002	0.1877	-0.2195	0.0568	-0.1121	-0.2254	0.2866	-0.0649	-0.0955	-0.0257	0.0156	-0.0456	-0.0037	-0.0731	39.7691	65.8892	30.9319
2	0.9722	0.1565	-0.5492	0.7837	0.1153	3.0765	0.0486	0.0769	0.1673	-0.072	0.0018	0.0939	-0.3327	-0.1529	-0.0504	-0.1184	0.0123	0.0093	-0.1433	0.0031	-0.1288	28.9525	67.0938	16.7434
3	0.3523	0.7891	-1.3054	3.8352	-3.6031	5.0601	-0.0189	0.0436	-0.0183	-0.063	-0.099	-0.0667	0.0519	0.1403	0.1178	-0.1082	0.0209	0.017	-0.086	-0.0119	-0.0933	40.7273	64.2222	4.3275
4	1.5901	0.0039	-2.1863	0.3146	0.8633	5.4048	-0.0211	0.0378	-0.1136	-0.0708	0.0399	0.0661	0.2882	-0.3329	-0.0188	-0.0991	-0.0498	0.0061	-0.05	-0.0018	-0.0825	21.7017	52.6624	28.2523
5	1.2852	-0.3727	-1.589	1.3951	0.6403	4.7161	-0.0501	-0.199	-0.1719	-0.0088	0.014	-0.1272	0.4196	0.1313	0.0361	-0.136	-0.0096	0.0019	-0.1096	0.0166	-0.1009	31.9965	51.9774	35.5161

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

ID	Refine TLS-ID	Auth seq-ID	Label seq-ID
1	1	1 - 36	1 - 36
2	2	37 - 104	37 - 104
3	3	105 - 172	105 - 172
4	4	173 - 225	173 - 225
5	5	226 - 285	226 - 285

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