PDB-3mml: Allophanate Hydrolase Complex from Mycobacterium smegmatis, Msmeg...

ID or keywords:

Entry

Database: PDB / ID: 3mml

Title

Allophanate Hydrolase Complex from Mycobacterium smegmatis, Msmeg0435-Msmeg0436

Components

Allophanate hydrolase subunit 1
Allophanate hydrolase subunit 2

Keywords

HYDROLASE / Structural Genomics / PSI-2 / Protein Structure Initiative / Tuberculosis Structural Genomics Consortium / Integrated Center for Structure and Function Innovation / ISFI / TB Structural Genomics Consortium / TBSGC

Function / homology

Function and homology information

hydrolase activity / ATP binding
Similarity search - Function

Biological species

Mycobacterium smegmatis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.5 Å

Authors

Kaufmann, M. / Chernishof, I. / Shin, A. / Germano, D. / Sawaya, M.R. / Waldo, G.S. / Arbing, M.A. / Perry, J. / Eisenberg, D. / Integrated Center for Structure and Function Innovation (ISFI) / TB Structural Genomics Consortium (TBSGC)

Citation

Journal: To be Published
Title: Crystal Structure of Allphanate Hydrolase Complex from M. smegmatis, Msmeg0435-Msmeg0436
Authors: Kaufmann, M. / Chernishof, I. / Shin, A. / Germano, D. / Sawaya, M.R. / Waldo, G.S. / Arbing, M.A. / Perry, J. / Eisenberg, D.

History

Deposition	Apr 20, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 28, 2010	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

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3mml.cif.gz	774.1 KB	Display	PDBx/mmCIF format
PDB format	pdb3mml.ent.gz	660.4 KB	Display	PDB format
PDBx/mmJSON format	3mml.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3mml_validation.pdf.gz	500.8 KB	Display	wwPDB validaton report
Full document	3mml_full_validation.pdf.gz	521.7 KB	Display
Data in XML	3mml_validation.xml.gz	75.6 KB	Display
Data in CIF	3mml_validation.cif.gz	108.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mm/3mml ftp://data.pdbj.org/pub/pdb/validation_reports/mm/3mml	HTTPS FTP

-
Related structure data

Similar structure data	3edf-d 7bv5-d 5zxd-d 3edd-1 2d2q-d 5iky-d 6niy-d 2jkp-d 1h3a-3 4nry-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) 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	TargetDB: ISFI495 TargetDB: ISFI496

Similar structure data

Other databases

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#163 - Jul 2013 HIV Capsid similarity (1) #245 - May 2020 Spliceosomes similarity (1)

Deposited unit

A: Allophanate hydrolase subunit 2

B: Allophanate hydrolase subunit 1

C: Allophanate hydrolase subunit 2

D: Allophanate hydrolase subunit 1

E: Allophanate hydrolase subunit 2

F: Allophanate hydrolase subunit 1

G: Allophanate hydrolase subunit 2

H: Allophanate hydrolase subunit 1

hetero molecules

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

1

A: Allophanate hydrolase subunit 2

B: Allophanate hydrolase subunit 1

C: Allophanate hydrolase subunit 2

D: Allophanate hydrolase subunit 1

hetero molecules

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

2

E: Allophanate hydrolase subunit 2

F: Allophanate hydrolase subunit 1

G: Allophanate hydrolase subunit 2

H: Allophanate hydrolase subunit 1

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

3

A: Allophanate hydrolase subunit 2

B: Allophanate hydrolase subunit 1

hetero molecules

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

4

C: Allophanate hydrolase subunit 2

D: Allophanate hydrolase subunit 1

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

5

E: Allophanate hydrolase subunit 2

F: Allophanate hydrolase subunit 1

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

6

G: Allophanate hydrolase subunit 2

H: Allophanate hydrolase subunit 1

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

Unit cell

Length a, b, c (Å)	77.483, 84.239, 402.075
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 heterotetramer. There are 2 biological units in the asymmetric unit (chains A,B,C & D, and chains E,F,G, & H).

#1: Protein	Allophanate hydrolase subunit 2 Mass: 34100.336 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: Mc2 155 / Gene: Msmeg0435, MSMEG_0435 / Plasmid: modified pET-DUET-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold (DE3) / References: UniProt: A0QPL0, allophanate hydrolase
#2: Protein	Allophanate hydrolase subunit 1 Mass: 24903.504 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: Mc2 155 / Gene: Msmeg0436, MSMEG_0436 / Plasmid: modified pET-DUET-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold (DE3) / References: UniProt: A0QPL1
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 885 / 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: 2.78 Å³/Da / Density % sol: 55.75 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.17 M ammonium sulfate, 0.085 M tri-sodium citrate pH 5.6, 25.5% (w/v) PEG4000, 15% (v/v) glycerol, vapor diffusion, hanging drop, temperature 277K

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 24-ID-C / Wavelength: 0.97921, 0.97935, 0.97549

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 29, 2008

Radiation

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

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97921	1
2	0.97935	1
3	0.97549	1

Reflection

Redundancy: 3.9 % / Av σ(I) over netI: 12.65 / Number: 604054 / R_merge(I) obs: 0.094 / Χ²: 1.1 / D res high: 2.6 Å / D res low: 500 Å / Num. obs: 155663 / % possible obs: 100

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
5.6	500	99.8	1	0.036	1.044	3.9
4.45	5.6	100	1	0.054	1.142	3.8
3.88	4.45	100	1	0.077	1.034	3.9
3.53	3.88	100	1	0.088	1.078	3.9
3.28	3.53	100	1	0.1	1.057	3.9
3.08	3.28	100	1	0.131	1.075	3.9
2.93	3.08	100	1	0.185	1.027	3.9
2.8	2.93	100	1	0.262	1.088	3.9
2.69	2.8	100	1	0.363	1.166	3.9
2.6	2.69	100	1	0.469	1.292	3.9

Reflection

Resolution: 2.5→90 Å / Num. all: 163304 / Num. obs: 163304 / % possible obs: 93.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4 % / B_iso Wilson estimate: 49.6 Å² / R_merge(I) obs: 0.095 / Χ²: 1.076 / Net I/σ(I): 10

Reflection shell

Resolution: 2.5→2.59 Å / Redundancy: 3.9 % / R_merge(I) obs: 0.488 / Mean I/σ(I) obs: 3 / Num. unique all: 14648 / Χ²: 1.049 / % possible all: 83.6

-
Phasing

Phasing

Method:

MAD

Phasing MAD

D res high: 2.6 Å / D res low: 19.98 Å / FOM : 0.191 / FOM acentric: 0.2 / FOM centric: 0.114 / Reflection: 81487 / Reflection acentric: 73444 / Reflection centric: 8043

Phasing MAD set

Lowest resolution: 20 Å

ID	R cullis acentric	R cullis centric	Highest resolution (Å)	Loc acentric	Loc centric	Power acentric	Power centric	Reflection acentric	Reflection centric
1	0.99	0.96	2.8	23.7	33.4	0.2	0.18	58866	6930
2	1.85	1	2.6	0.1	0.1	0	0	73444	8043

Phasing MAD set shell

ID	Resolution (Å)	R cullis acentric	R cullis centric	Loc acentric	Loc centric	Power acentric	Power centric	Reflection acentric	Reflection centric
1	10.89-19.98	0.89	0.84	25.6	30.8	0.8	0.62	739	322
1	7.48-10.89	0.88	0.81	21.1	26.5	0.84	0.59	1957	523
1	5.7-7.48	0.92	0.92	18.3	24.6	0.69	0.44	3787	711
1	4.6-5.7	0.97	0.95	20.3	29.6	0.42	0.28	6245	911
1	3.86-4.6	0.99	0.99	22	32	0.24	0.15	9236	1102
1	3.32-3.86	1	1	23.4	36.2	0.13	0.08	12912	1310
1	2.92-3.32	1	1	25.5	38.2	0.06	0.04	17091	1483
1	2.6-2.92	1	1	28.1	41.6	0.04	0.02	6899	568
2	10.89-19.98	1.47	1	0.3	0.2	0	0	739	322
2	7.48-10.89	1.73	1	0.3	0.2	0	0	1957	523
2	5.7-7.48	2.25	1	0.3	0.1	0	0	3787	711
2	4.6-5.7	1.53	1	0.2	0.1	0	0	6245	912
2	3.86-4.6	1.28	1	0.1	0.1	0	0	9241	1105
2	3.32-3.86	1.46	1	0.1	0	0	0	12920	1314
2	2.92-3.32	3.19	1	0	0	0	0	17136	1487
2	2.6-2.92	6.9	1	0	0	0	0	21419	1669

Phasing MAD set site

Atom type symbol: Se

ID	B iso	Fract x	Fract y	Fract z	Occupancy	Occupancy iso
1	117.77	0.542	-0.376	0.472	2.989	0.073
2	118.02	0.703	-0.576	0.52	2.963	0.049
3	93.557	0.552	-0.23	0.484	2.776	0.088
4	105.294	0.269	0.388	0.654	2.678	0.096
5	111.165	0.386	0.619	0.892	2.462	0.099
6	115.039	0.299	0.277	0.853	2.446	0.091
7	97.523	1.07	-0.251	0.54	2.58	0.108
8	225.769	0.653	-0.6	0.57	3.224	0.042
9	182.462	0.81	-0.226	0.764	3.018	0.017
10	99.691	0.605	-0.405	0.51	2.225	0.089
11	155.694	0.392	0.33	0.768	2.766	0.053
12	90.228	0.411	0.185	0.629	2.401	0.113
13	118.905	0.118	0.398	0.671	2.492	0.079
14	113.064	0.751	0.02	0.603	2.163	0.075
15	87.087	0.151	0.369	0.643	2.286	0.093
16	112.022	0.35	0.015	0.863	2.296	0.087
17	125.688	0.62	-0.103	0.663	2.491	0.072
18	108.639	0.261	-0.456	0.509	2.408	0.114
19	127.293	0.329	0.092	0.743	1.951	0.055
20	30	0.269	-0.596	0.654	0	0
21	104.526	0.718	0.057	0.626	2.23	0.095
22	109.683	0.202	0.286	0.42	2.128	0.09
23	112.91	0.412	0.316	0.86	2.157	0.092
24	122.366	0.742	-0.153	0.8	2.246	0.074
25	176.867	0.894	-0.513	0.548	2.126	0.064
26	96.021	0.69	-0.198	0.694	1.995	0.082
27	115.418	0.424	0.126	0.75	1.851	0.053
28	118.237	0.366	0.994	0.437	1.958	0.063
29	112.728	1.043	0.016	0.613	1.869	0.079
30	47.016	0.543	-0.376	0.472	3.094	0
31	45.682	0.703	-0.576	0.52	2.513	0
32	50.309	0.552	-0.229	0.484	2.857	0
33	65.309	0.268	0.382	0.654	2.772	0
34	50.044	0.387	0.619	0.892	2.75	0
35	55.932	0.299	0.276	0.853	2.829	0
36	50.319	1.069	-0.25	0.539	2.39	0
37	56.219	0.653	-0.598	0.571	2.22	0
38	59.722	0.809	-0.228	0.764	2.371	0
39	59.991	0.605	-0.405	0.51	2.476	0
40	61.852	0.393	0.329	0.767	2.207	0
41	54.837	0.412	0.185	0.629	2.704	0
42	56.925	0.12	0.397	0.672	2.27	0
43	67.489	0.751	0.019	0.603	2.618	0
44	55.136	0.152	0.37	0.643	2.413	0
45	63.555	0.351	0.017	0.864	2.339	0
46	59.388	0.621	-0.103	0.663	2.283	0
47	60.71	0.261	-0.456	0.509	2.465	0
48	63.929	0.328	0.091	0.743	2.166	0
49	53.911	0.271	-0.599	0.654	1.47	0
50	68.837	0.718	0.057	0.626	2.256	0
51	63.88	0.202	0.286	0.42	2.325	0
52	63.979	0.412	0.317	0.86	2.188	0
53	77.825	0.74	-0.152	0.8	2.132	0
54	63.159	0.895	-0.511	0.547	2.082	0
55	77.96	0.691	-0.198	0.694	2.113	0
56	70.939	0.427	0.125	0.75	2.031	0
57	66.368	0.368	0.995	0.437	2.02	0
58	76.7	1.043	0.019	0.614	1.986	0

Phasing MAD shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
10.89-19.98	0.585	0.677	0.373	1061	739	322
7.48-10.89	0.61	0.669	0.387	2480	1957	523
5.7-7.48	0.543	0.592	0.284	4498	3787	711
4.6-5.7	0.411	0.441	0.202	7157	6245	912
3.86-4.6	0.263	0.282	0.1	10346	9241	1105
3.32-3.86	0.171	0.183	0.049	14234	12920	1314
2.92-3.32	0.098	0.105	0.02	18623	17136	1487
2.6-2.92	0.047	0.05	0.003	23088	21419	1669

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 81487

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
13.16-100	55.6	0.807	525
9.62-13.16	49.8	0.878	1067
7.94-9.62	50.7	0.888	1350
6.92-7.94	50.4	0.879	1547
6.21-6.92	50.7	0.872	1730
5.68-6.21	54.6	0.854	1877
5.27-5.68	56.4	0.864	2043
4.94-5.27	58.7	0.862	2167
4.66-4.94	58.6	0.877	2317
4.42-4.66	62.3	0.867	2421
4.22-4.42	63.9	0.859	2529
4.04-4.22	66.5	0.845	2670
3.89-4.04	69.4	0.827	2775
3.75-3.89	69.1	0.813	2875
3.62-3.75	71.3	0.706	2970
3.51-3.62	73	0.781	3017
3.4-3.51	74	0.777	3169
3.31-3.4	74.5	0.767	3249
3.22-3.31	78.1	0.76	3290
3.14-3.22	77.7	0.768	3416
3.06-3.14	77.5	0.766	3508
2.99-3.06	78.7	0.746	3520
2.93-2.99	80.8	0.749	3645
2.87-2.93	80.8	0.741	3699
2.81-2.87	82.5	0.741	3798
2.76-2.81	84.5	0.733	3873
2.7-2.76	86.4	0.74	3922
2.66-2.7	86.5	0.711	3961
2.6-2.66	86.5	0.645	4557

-
Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
MLPHARE		phasing
DM	6	phasing
TNT		refinement
PDB_EXTRACT	3.1	data extraction
ADSC	Quantum	data collection
BUSTER	2.8.0	refinement

Refinement

Method to determine structure:

MAD / Resolution: 2.5→19.92 Å / Cor.coef. F_o:F_c: 0.951 / Cor.coef. F_o:F_c free: 0.932 / Occupancy max: 1 / Occupancy min: 0.75 / Cross valid method: THROUGHOUT / σ(F): 0

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.202	4507	5.01 %	RANDOM
R_work	0.169	-	-	-
obs	0.17	90043	-	-

Displacement parameters

B_iso max: 194.14 Å² / B_iso mean: 50.543 Å² / B_iso min: 8.83 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.955 Å²	0 Å²	0 Å²
2-	-	0.881 Å²	0 Å²
3-	-	-	0.075 Å²

Refine analyze

Luzzati coordinate error obs: 0.302 Å

Refinement step

Cycle: LAST / Resolution: 2.5→19.92 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15033	0	1	885	15919

Refine LS restraints

Refine-ID	Type	Number	Restraint function	Weight	Dev ideal
X-RAY DIFFRACTION	t_dihedral_angle_d	5030	SINUSOIDAL	2
X-RAY DIFFRACTION	t_trig_c_planes	331	HARMONIC	2
X-RAY DIFFRACTION	t_gen_planes	2321	HARMONIC	5
X-RAY DIFFRACTION	t_it	15405	HARMONIC	20
X-RAY DIFFRACTION	t_nbd	1	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_improper_torsion
X-RAY DIFFRACTION	t_pseud_angle
X-RAY DIFFRACTION	t_chiral_improper_torsion	1983	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_sum_occupancies
X-RAY DIFFRACTION	t_utility_distance
X-RAY DIFFRACTION	t_utility_angle
X-RAY DIFFRACTION	t_utility_torsion
X-RAY DIFFRACTION	t_ideal_dist_contact	17538	SEMIHARMONIC	4
X-RAY DIFFRACTION	t_bond_d	15405	HARMONIC	2	0.01
X-RAY DIFFRACTION	t_angle_deg	21093	HARMONIC	2	1.15
X-RAY DIFFRACTION	t_omega_torsion				3.29
X-RAY DIFFRACTION	t_other_torsion				18.3

LS refinement shell

Resolution: 2.5→2.56 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.265	290	4.96 %
R_work	0.205	5557	-
all	0.208	5847	-

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	1.5406	0.4431	0.0092	0.9322	0.2607	0.5781	-0.0086	0.082	-0.1101	-0.0747	0.0113	-0.032	-0.0366	-0.0088	-0.0027	-0.1025	0.001	-0.0052	-0.0466	0.0131	-0.0194	31.09	49.3959	1.5827
2	1.9057	-2.6187	0.7187	2.9491	-0.8797	0.8198	0.2591	0.1715	-0.6326	-0.294	-0.1148	0.6719	0.0626	0.0349	-0.1443	-0.2245	-0.0193	-0.0725	-0.1679	-0.0812	0.18	23.0712	23.3763	-9.384
3	1.5843	0.7064	-0.4957	1.4251	-0.0451	1.5007	0.0702	-0.2353	-0.0734	0.262	-0.0593	0.0129	0.1103	-0.0748	-0.0109	-0.0912	-0.0447	-0.0382	-0.0465	0.0506	-0.1383	34.6343	56.7481	31.1465
4	3.8719	-0.592	-1.3996	3.9597	-0.7669	3.5799	0.4887	-0.3442	0.9527	0.5779	0.111	0.5054	-0.3937	-0.7139	-0.5998	-0.3468	0.0069	0.293	-0.1324	-0.0751	-0.0362	15.4449	72.1476	47.4296
5	0.8424	0.2868	0.1738	1.7944	0.1473	1.0762	-0.0149	-0.112	0.028	0.1338	-0.0277	-0.0042	0.0075	-0.0789	0.0426	-0.0714	0.0044	-0.0467	-0.0067	-0.006	-0.1439	9.2134	11.2456	110.229
6	2.847	-1.0078	2.2602	0.8927	-0.9699	1.8411	-0.1345	-0.4943	0.0944	0.1229	0.1066	-0.051	-0.0456	-0.2104	0.0279	-0.0225	0.0393	-0.0489	0.0833	-0.0633	-0.2557	15.6244	20.8962	136.997
7	1.1314	0.6835	0.0113	2.0719	-0.0228	1.5151	0.005	0.0723	-0.0579	-0.1029	-0.0637	-0.3619	-0.0005	0.334	0.0587	-0.1629	0.0317	0.0169	-0.011	0.0217	-0.104	28.9902	5.4638	87.404
8	0.8641	-0.8245	1.3604	3.9542	-2.7295	4.6518	0.0739	0.4767	0.1586	-0.3694	-0.2849	-0.3389	0.1898	0.7813	0.2109	-0.1192	-0.0415	0.1876	-0.0033	0.1722	-0.3161	34.0379	22.8307	64.1201

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	{ A\|* }	A	2 - 290
2	X-RAY DIFFRACTION	2	{ B\|* }	B	1 - 210
3	X-RAY DIFFRACTION	3	{ C\|* }	C	2 - 291
4	X-RAY DIFFRACTION	4	{ D\|* }	D	1 - 209
5	X-RAY DIFFRACTION	5	{ E\|* }	E	2 - 293
6	X-RAY DIFFRACTION	6	{ F\|* }	F	1 - 210
7	X-RAY DIFFRACTION	7	{ G\|* }	G	2 - 289
8	X-RAY DIFFRACTION	8	{ H\|* }	H	1 - 209

-
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

-
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