PDB-3i38: Structure of a putative chaperone protein dnaj from klebsiella pn...

ID or keywords:

Entry

Database: PDB / ID: 3i38

Title

Structure of a putative chaperone protein dnaj from klebsiella pneumoniae subsp. pneumoniae mgh 78578

Components

Putative chaperone DnaJ

Keywords

CHAPERONE / DNAJ / KLEBSIELLA PNEUMONIAE / STRUCTURAL GENOMICS / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG

Function / homology

Function and homology information

bent DNA binding / nucleoid / chaperone cofactor-dependent protein refolding / unfolded protein binding / protein refolding / cytoplasm
Similarity search - Function

Biological species

Klebsiella pneumoniae subsp. pneumoniae MGH 78578 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.3 Å

Authors

Filippova, E.V. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Bearden, J. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: Structure of a Putative Chaperone Protein Dnaj from Klebsiella Pneumoniae Subsp. Pneumoniae Mgh 78578
Authors: Filippova, E.V. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Bearden, J. / Joachimiak, A. / Anderson, W.F.

History

Deposition	Jun 30, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 14, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Derived calculations ...Advisory / Derived calculations / Refinement description / Version format compliance
Revision 1.2	Oct 25, 2017	Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.name
Revision 1.3	Oct 16, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3i38.cif.gz	239.9 KB	Display	PDBx/mmCIF format
PDB format	pdb3i38.ent.gz	196.6 KB	Display	PDB format
PDBx/mmJSON format	3i38.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3i38_validation.pdf.gz	517.9 KB	Display	wwPDB validaton report
Full document	3i38_full_validation.pdf.gz	538.6 KB	Display
Data in XML	3i38_validation.xml.gz	51.1 KB	Display
Data in CIF	3i38_validation.cif.gz	67 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/i3/3i38 ftp://data.pdbj.org/pub/pdb/validation_reports/i3/3i38	HTTPS FTP

-
Related structure data

Similar structure data	5j89-1 1t3h-1 1wvl-d 1vhl-1 2eef-d 5niu-1 5n2f-d 5an5-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: apc63096.1

Similar structure data

Other databases

TargetDB: apc63096.1

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#32 - Aug 2002 Chaperones similarity (1) #47 - Nov 2003 Simian Virus 40 similarity (4) #80 - Aug 2006 AAA+ Proteases similarity (4)

Deposited unit

A: Putative chaperone DnaJ

B: Putative chaperone DnaJ

C: Putative chaperone DnaJ

D: Putative chaperone DnaJ

E: Putative chaperone DnaJ

F: Putative chaperone DnaJ

G: Putative chaperone DnaJ

H: Putative chaperone DnaJ

I: Putative chaperone DnaJ

J: Putative chaperone DnaJ

K: Putative chaperone DnaJ

L: Putative chaperone DnaJ

142 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Putative chaperone DnaJ

B: Putative chaperone DnaJ

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

2

C: Putative chaperone DnaJ

D: Putative chaperone DnaJ

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

3

E: Putative chaperone DnaJ

F: Putative chaperone DnaJ

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

4

G: Putative chaperone DnaJ

H: Putative chaperone DnaJ

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

5

I: Putative chaperone DnaJ

J: Putative chaperone DnaJ

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

6

K: Putative chaperone DnaJ

L: Putative chaperone DnaJ

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

7

Idetical with deposited unit
defined by author&software
Evidence: light scattering

Unit cell

Length a, b, c (Å)	61.805, 61.626, 92.907
Angle α, β, γ (deg.)	81.75, 78.71, 83.79
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	4	A	200 - 269
2	1	1	4	B	200 - 269
1	1	2	4	A	270 - 302
2	1	2	4	B	270 - 302
1	1	3	4	C	200 - 269
2	1	3	4	D	200 - 269
1	1	4	4	C	270 - 302
2	1	4	4	D	270 - 302
1	1	5	4	E	200 - 269
2	1	5	4	F	200 - 269
1	1	6	4	E	270 - 302
2	1	6	4	F	270 - 302
1	1	7	4	G	20 - 269
2	1	7	4	H	20 - 269
1	1	8	4	G	270 - 302
2	1	8	4	H	270 - 302
1	1	9	4	I	200 - 269
2	1	9	4	J	200 - 269
1	1	10	4	I	270 - 302
2	1	10	4	J	270 - 302
1	1	11	4	K	200 - 269
2	1	11	4	L	200 - 269
1	1	12	4	K	200 - 302
2	1	12	4	L	200 - 302

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12

Details

AUTHORS HAD THE FOLLOWING COMMENTS ON THE SUPERHELICCAL STRUCTURE IN ASYMMETRIC UNIT: FIRST OF ALL, THE PROTEIN IS A SMALL PART OF A LARGE PROTEIN WHICH CONSISTS OF THREE DOMAINS. THEREFORE IT IS HARD TO PREDICT WHETHER THE FULL LENGTH PROTEIN WILL FORM A SIMILAR SUPERHELICAL STRUCTURE. LIGHT SCATTERING ANALYSIS CONFIRMS THAT THE PROTEIN DOMAIN FORMS A DIMER IN SOLUTION. AUTHORS ASSUME THAT THE SUPERHELICAL STRUCTURE IS AN ARTIFACT AND CREATED BY CRYSTAL PACKING. THIS IS THE VERY INTERESTING PATTERN BUT FROM FUNCTIONAL POINT OF VIEW WE DO NOT KNOW IF IT IS PHYSIOLOGICALLY RELEVANT.

#1: Protein	Putative chaperone DnaJ Mass: 11847.640 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae MGH 78578 (bacteria) Gene: cbpA, KPN78578_44400, KPN_04509 / Plasmid: pMCSG19 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21Magic / References: UniProt: A6TH30
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.48 Å³/Da / Density % sol: 50.4 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.2M Ammonium acetate, 0.1M Bis-Tris, 25% PEG 3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872
Detector	Detector: CCD / Date: Jun 18, 2009 / Details: MIRROR
Radiation	Monochromator: SI-111 CHANNEL / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97872 Å / Relative weight: 1
Reflection	Resolution: 2.2→90.54 Å / Num. obs: 66358 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / R_merge(I) obs: 0.07 / R_sym value: 0.07 / Net I/σ(I): 30.081
Reflection shell	Resolution: 2.2→2.24 Å / Redundancy: 3.4 % / R_merge(I) obs: 0.559 / Mean I/σ(I) obs: 2 / R_sym value: 0.559 / % possible all: 97.6

-
Processing

Software

Name	Version	Classification
Blu-Ice	Max	data collection
HKL-3000		phasing
MLPHARE		phasing
DM		model building
SHELXD		phasing
RESOLVE		model building
CCP4		model building
ARP/wARP		model building
Coot		model building
REFMAC	5.5.0051	refinement
ADSC		data collection
HKL-2000		data scaling
DM		phasing
RESOLVE		phasing
ARP	WARP	model building
CCP4		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.3→90.54 Å / Cor.coef. F_o:F_c: 0.95 / Cor.coef. F_o:F_c free: 0.925 / SU B: 18.451 / SU ML: 0.205 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.384 / ESU R Free: 0.257 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.262	2941	5.1 %	RANDOM
R_work	0.217	-	-	-
obs	0.219	57758	98.09 %	-
all	-	57758	-	-

Solvent computation

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

Displacement parameters

B_iso mean: 25.41 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.83 Å²	-1.77 Å²	1.29 Å²
2-	-	-1.03 Å²	0.8 Å²
3-	-	-	-0.16 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→90.54 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9275	0	0	186	9461

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.022	9541
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	6616
X-RAY DIFFRACTION	r_angle_refined_deg	1.743	1.984	12990
X-RAY DIFFRACTION	r_angle_other_deg	0.893	3	16299
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	2.524	5	1193
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	29.539	24.066	332
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.584	15	1655
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.921	15	49
X-RAY DIFFRACTION	r_chiral_restr	0.098	0.2	1525
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	10195
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1698
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
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	0.986	1.5	6046
X-RAY DIFFRACTION	r_mcbond_other	0.274	1.5	2393
X-RAY DIFFRACTION	r_mcangle_it	1.746	2	9789
X-RAY DIFFRACTION	r_scbond_it	2.594	3	3495
X-RAY DIFFRACTION	r_scangle_it	4.123	4.5	3199
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	845	MEDIUM POSITIONAL	0.44	0.5
1	A	845	MEDIUM THERMAL	0.73	2
2	A	454	MEDIUM POSITIONAL	0.4	0.5
2	A	454	MEDIUM THERMAL	1.11	2
3	C	800	MEDIUM POSITIONAL	0.73	0.5
3	C	800	MEDIUM THERMAL	0.88	2
4	C	474	MEDIUM POSITIONAL	0.49	0.5
4	C	474	MEDIUM THERMAL	0.95	2
5	E	815	MEDIUM POSITIONAL	0.66	0.5
5	E	815	MEDIUM THERMAL	0.78	2
6	E	474	MEDIUM POSITIONAL	0.53	0.5
6	E	474	MEDIUM THERMAL	0.81	2
7	G	826	MEDIUM POSITIONAL	0.44	0.5
7	G	826	MEDIUM THERMAL	0.95	2
8	G	462	MEDIUM POSITIONAL	0.63	0.5
8	G	462	MEDIUM THERMAL	1.2	2
9	I	782	MEDIUM POSITIONAL	0.76	0.5
9	I	782	MEDIUM THERMAL	0.75	2
10	I	474	MEDIUM POSITIONAL	0.42	0.5
10	I	474	MEDIUM THERMAL	0.45	2
11	K	800	MEDIUM POSITIONAL	0.48	0.5
11	K	800	MEDIUM THERMAL	0.72	2
12	K	474	MEDIUM POSITIONAL	0.68	0.5
12	K	474	MEDIUM THERMAL	0.91	2

LS refinement shell

Resolution: 2.3→2.36 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.333	221	-
R_work	0.294	4007	-
obs	-	-	97.6 %

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	4.0797	2.7814	-0.5639	4.5805	-2.6318	2.0349	0.0318	0.3181	0.7055	0.3282	0.159	0.5811	-0.3949	-0.0793	-0.1908	0.2752	0.1422	0.0433	0.1209	0.0482	0.2027	-2.2168	16.74	-2.4215
2	1.5082	-0.0182	-0.6636	3.1033	-0.3936	5.2598	-0.0416	0.0606	-0.0967	0.3249	-0.0636	0.1425	-0.1474	0.0248	0.1051	0.1002	0.0605	-0.0081	0.0827	-0.0285	0.0886	-1.404	-7.2161	7.8213
3	2.0719	1.0233	-1.9207	3.2984	-0.2195	10.0038	-0.1533	0.0088	-0.1734	-0.2878	-0.104	-0.2888	0.6182	0.4644	0.2573	0.1089	0.0827	0.0302	0.0739	0.0112	0.0431	7.8498	-10.6409	-9.5849
4	3.7784	1.5835	-2.6541	1.3125	-0.725	7.6984	-0.0082	0.1489	0.146	0.1617	-0.0736	0.2716	-0.2585	-0.7396	0.0819	0.1912	0.099	0.0207	0.1734	-0.0421	0.1264	-5.8264	-0.1525	9.0767
5	2.4134	-1.653	0.712	8.0514	-3.0008	6.0135	-0.2474	-0.2621	0.1839	0.1528	0.241	0.2714	0.7244	-0.4926	0.0063	0.1625	-0.0119	-0.0222	0.1299	-0.0978	0.3312	13.2311	-26.8622	17.289
6	7.1585	-3.1556	-0.4052	3.0322	-3.134	9.6703	-0.1186	1.04	1.7062	-0.3335	-0.0454	-0.5311	0.4753	-0.5592	0.164	0.1479	-0.1241	-0.1774	0.3541	0.2401	0.9962	27.1161	-10.9363	4.3446
7	7.1107	-1.4954	1.395	5.1011	-1.2906	1.6975	-0.0612	0.194	0.3003	-0.0613	-0.0387	0.1725	0.1306	0.0433	0.1	0.0232	0.0137	-0.0299	0.0469	-0.0489	0.1643	41.761	-24.1557	10.5196
8	5.637	-3.194	0.1174	2.8474	-1.1157	1.0761	-0.1193	-0.0451	0.6125	0.3003	0.092	-0.2659	-0.2412	-0.0621	0.0273	0.0944	0.0603	-0.0738	0.1094	-0.0458	0.6766	19.4291	-11.1693	7.9927
9	2.516	1.8416	0.3878	3.8356	0.1015	2.0423	-0.2841	0.2711	0.5094	0.0326	0.0993	1.1397	0.3746	-0.1064	0.1847	0.2669	-0.0828	0.0801	0.3751	0.1253	0.637	-24.5326	-3.3469	-24.7634
10	5.9263	-2.5988	1.2903	4.837	-4.4357	5.1132	0.1057	0.6101	0.2464	-0.904	0.6538	0.8152	0.363	-0.5815	-0.7596	0.6044	-0.3761	-0.2945	0.5614	0.3513	0.3654	-11.736	12.5554	-38.7666
11	4.7024	-1.7779	2.2663	6.2301	-3.0869	4.4748	-0.1182	0.6771	-0.0318	-0.7718	0.2241	0.1273	0.7249	0.0299	-0.1059	0.3221	-0.1113	-0.0056	0.2929	0.0267	0.0091	3.056	0.8224	-33.6448
12	4.9366	-2.1458	-1.3084	6.8433	0.5951	4.2607	0.1478	0.3388	-0.1216	-0.6464	0.484	1.7537	-0.0691	-0.7995	-0.6318	0.3211	-0.3082	-0.2729	0.6272	0.472	0.6844	-19.0838	12.3672	-34.8683
13	9.1463	-1.4178	-1.2953	2.517	-0.2683	3.0488	0.1825	-0.2359	0.5222	0.301	-0.0689	0.1159	-0.4018	0.0438	-0.1136	0.2236	0.0308	0.0151	0.0341	-0.0332	0.0516	-26.4798	-12.4067	-58.4564
14	5.281	-2.2884	-0.676	3.3345	1.4568	2.7814	0.2359	-0.2808	-0.6427	0.098	-0.3504	-0.0014	0.0773	0.388	0.1146	0.1372	-0.0196	-0.0469	0.2816	0.1395	0.1257	-6.5695	-27.5236	-51.4635
15	4.656	-1.1445	-5.4572	2.9728	2.1729	7.3471	0.1008	-0.6949	0.0959	0.5885	-0.0462	0.2404	-0.283	0.6394	-0.0546	0.3401	-0.0571	0.0188	0.493	0.1369	0.1841	-15.7628	-26.7546	-33.5116
16	8.4808	-0.7763	-0.5594	3.4689	-1.8295	3.8923	0.4999	0.0866	-0.4036	0.2222	-0.6954	-0.1574	-0.2352	0.945	0.1955	0.162	0.007	-0.0345	0.297	0.0522	0.0328	-8.5704	-22.5212	-57.755
17	9.6825	0.8329	-3.2468	3.652	1.106	6.7811	-0.5334	-0.3657	-1.4694	0.4673	0.4794	-0.1112	0.3776	0.4095	0.054	0.5351	0.1423	-0.0243	0.1765	-0.097	0.5059	23.305	-50.5032	11.381
18	1.4337	-1.6273	1.3072	1.888	-1.6759	2.1205	-0.044	-0.079	0.7209	0.0472	-0.0829	-0.7186	-0.2461	0.6228	0.1269	0.3806	-0.2081	0.1712	0.6323	-0.3743	0.6643	31.5413	-49.3705	-11.3846
19	10.0287	-4.3546	1.2424	5.9162	-0.2244	0.6974	-0.1328	0.6791	0.7146	-0.6806	0.2541	-0.3859	-0.3594	0.2422	-0.1214	0.3854	-0.1813	0.1148	0.3391	-0.0436	0.1392	14.3131	-39.4807	-14.0474
20	0.5911	0.3332	-0.9728	0.4099	-0.4056	1.7336	-0.2075	-0.0141	-0.3687	0.0779	-0.0833	-0.46	0.233	0.1207	0.2909	0.4526	-0.1115	0.0373	0.5061	-0.342	0.7808	33.2081	-53.472	-4.3222
21	3.1623	0.5917	-2.1637	1.9493	-1.3421	9.415	-0.1778	-0.2901	-0.4888	-0.0581	-0.2814	-0.5491	0.3458	0.8013	0.4592	0.0857	0.0779	-0.0232	0.174	0.0997	0.2601	-36.9997	-47.2707	-56.5807
22	1.7879	-0.1249	-0.055	3.8207	0.3577	2.3346	0.1574	-0.3436	-0.0966	0.6909	0.0101	0.1871	0.0554	-0.1401	-0.1675	0.342	0.0018	-0.0262	0.3114	0.0607	0.0489	-54.1474	-38.4316	-39.63
23	4.98	2.3269	-0.737	6.2965	-1.2389	2.1497	0.1457	-0.2711	0.4694	0.1444	0.1042	0.2844	-0.1586	-0.1545	-0.2499	0.1467	0.0988	0.0091	0.191	-0.0096	0.0636	-49.661	-21.4845	-47.633
24	1.2504	0.0997	-1.1773	2.4423	0.5054	5.1228	-0.0895	-0.2914	0.0291	0.4625	-0.0455	-0.2039	0.5117	-0.2241	0.135	0.2803	-0.0133	-0.0847	0.3113	0.0791	0.1249	-49.9578	-45.3496	-40.8003

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	200 - 269
2	X-RAY DIFFRACTION	2	A	270 - 302
3	X-RAY DIFFRACTION	3	B	200 - 269
4	X-RAY DIFFRACTION	4	B	270 - 302
5	X-RAY DIFFRACTION	5	C	201 - 269
6	X-RAY DIFFRACTION	6	C	270 - 302
7	X-RAY DIFFRACTION	7	D	200 - 269
8	X-RAY DIFFRACTION	8	D	270 - 302
9	X-RAY DIFFRACTION	9	E	201 - 269
10	X-RAY DIFFRACTION	10	E	270 - 302
11	X-RAY DIFFRACTION	11	F	200 - 269
12	X-RAY DIFFRACTION	12	F	270 - 302
13	X-RAY DIFFRACTION	13	G	200 - 269
14	X-RAY DIFFRACTION	14	G	270 - 302
15	X-RAY DIFFRACTION	15	H	202 - 269
16	X-RAY DIFFRACTION	16	H	270 - 302
17	X-RAY DIFFRACTION	17	I	201 - 269
18	X-RAY DIFFRACTION	18	I	270 - 302
19	X-RAY DIFFRACTION	19	J	200 - 269
20	X-RAY DIFFRACTION	20	J	270 - 302
21	X-RAY DIFFRACTION	21	K	200 - 269
22	X-RAY DIFFRACTION	22	K	270 - 302
23	X-RAY DIFFRACTION	23	L	201 - 269
24	X-RAY DIFFRACTION	24	L	270 - 302

-
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