PDB-3czp: Crystal structure of putative polyphosphate kinase 2 from Pseudom...

ID or keywords:

Entry

Database: PDB / ID: 3czp

Title

Crystal structure of putative polyphosphate kinase 2 from Pseudomonas aeruginosa PA01

Components

Putative polyphosphate kinase 2

Keywords

TRANSFERASE / PPK2 / polyphosphate kinase / kinase / MCSG / PSI-2 / Structural Genomics / Protein Structure Initiative / Midwest Center for Structural Genomics

Function / homology

Function and homology information

AMP-polyphosphate phosphotransferase / polyphosphate:AMP phosphotransferase activity / polyphosphate metabolic process / kinase activity / identical protein binding
Similarity search - Function

Biological species

Pseudomonas aeruginosa PAO1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2 Å

Authors

Nocek, B. / Evdokimova, E. / Osipiuk, J. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: Polyphosphate-dependent synthesis of ATP and ADP by the family-2 polyphosphate kinases in bacteria.
Authors: Nocek, B. / Kochinyan, S. / Proudfoot, M. / Brown, G. / Evdokimova, E. / Osipiuk, J. / Edwards, A.M. / Savchenko, A. / Joachimiak, A. / Yakunin, A.F.

History

Deposition	Apr 29, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 1, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Oct 30, 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 / 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 / _struct_conn.pdbx_leaving_atom_flag / _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	3czp.cif.gz	223.2 KB	Display	PDBx/mmCIF format
PDB format	pdb3czp.ent.gz	180.5 KB	Display	PDB format
PDBx/mmJSON format	3czp.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3czp_validation.pdf.gz	490.3 KB	Display	wwPDB validaton report
Full document	3czp_full_validation.pdf.gz	501.3 KB	Display
Data in XML	3czp_validation.xml.gz	49 KB	Display
Data in CIF	3czp_validation.cif.gz	67.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cz/3czp ftp://data.pdbj.org/pub/pdb/validation_reports/cz/3czp	HTTPS FTP

-
Related structure data

Related structure data	3czqC C: citing same article (ref.)
Similar structure data	2zyd-d 4w8y-1 5ccv-5 2iyp-2 6qau-d 6fqy-d 3qv9-d 1z19-d 6fqz-d 1s2q-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: APC6077

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Putative polyphosphate kinase 2

B: Putative polyphosphate kinase 2

hetero molecules

119 kDa, 2 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)	97.089, 100.735, 120.128
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

-
Protein , 1 types, 2 molecules AB

#1: Protein	Putative polyphosphate kinase 2 Mass: 59028.117 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / 1C / PRS 101 / LMG 12228 / Gene: PA3455 / Plasmid: p11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HYF1

#1: Protein

Putative polyphosphate kinase 2

Mass: 59028.117 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / 1C / PRS 101 / LMG 12228 / Gene: PA3455 / Plasmid: p11 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HYF1

-
Non-polymers , 5 types, 681 molecules

#2: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₂H₃O₂
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-MLI / MALONATE ION Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₂O₄
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 668 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.49 Å³/Da / Density % sol: 50.56 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 5% Tacsimate, 10% PEG MME 5000, 0.1M Hepes pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 3, 2006 / Details: Mirrors
Radiation	Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9794 Å / Relative weight: 1
Reflection	Resolution: 2→40 Å / Num. all: 79999 / Num. obs: 76187 / % possible obs: 95 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / R_merge(I) obs: 0.079 / Net I/σ(I): 20
Reflection shell	Resolution: 2→2.03 Å / Redundancy: 3.8 % / R_merge(I) obs: 0.52 / Mean I/σ(I) obs: 2.1 / % possible all: 72.2

-
Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
SBC-Collect		data collection
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing
SHELXD		phasing
ARP/wARP		model building
Coot		model building
MLPHARE		phasing
CCP4		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2→40 Å / Cor.coef. F_o:F_c: 0.964 / Cor.coef. F_o:F_c free: 0.936 / SU B: 8.068 / SU ML: 0.119 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 / ESU R: 0.169 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2306	3811	5 %	RANDOM
R_work	0.17349	-	-	-
obs	0.17625	72297	94.99 %	-
all	-	76108	-	-

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: 26.17 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.95 Å²	0 Å²	0 Å²
2-	-	2.64 Å²	0 Å²
3-	-	-	-1.69 Å²

Refinement step

Cycle: LAST / Resolution: 2→40 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7692	0	63	668	8423

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.02	0.022	7986
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.02	5747
X-RAY DIFFRACTION	r_angle_refined_deg	1.579	1.951	10769
X-RAY DIFFRACTION	r_angle_other_deg	0.981	3	13755
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.332	5	936
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.301	22.759	435
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.501	15	1416
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.557	15	95
X-RAY DIFFRACTION	r_chiral_restr	0.098	0.2	1102
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	8885
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	1821
X-RAY DIFFRACTION	r_nbd_refined	0.216	0.2	1608
X-RAY DIFFRACTION	r_nbd_other	0.203	0.2	6081
X-RAY DIFFRACTION	r_nbtor_refined	0.184	0.2	3741
X-RAY DIFFRACTION	r_nbtor_other	0.086	0.2	4156
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.187	0.2	463
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	0.166	0.2	13
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.308	0.2	69
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.209	0.2	22
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	1.107	1.5	5754
X-RAY DIFFRACTION	r_mcbond_other	0.252	1.5	1876
X-RAY DIFFRACTION	r_mcangle_it	1.321	2	7437
X-RAY DIFFRACTION	r_scbond_it	2.267	3	3915
X-RAY DIFFRACTION	r_scangle_it	3.177	4.5	3325
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

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

	R_factor	Num. reflection	% reflection
R_free	0.317	212	-
R_work	0.219	4007	-
obs	-	-	72.37 %

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	10.7735	-3.333	11.6767	13.8823	2.9666	39.2282	0.0721	1.1038	0.0084	0.5823	0.4485	-1.458	-0.6414	4.7543	-0.5206	-0.1567	-0.0046	0.0091	0.5433	-0.0281	-0.0233	43.497	47.118	-12.848
2	3.7915	-1.7264	1.3991	1.1845	-1.2138	2.2594	-0.0226	-0.4384	0.1267	0.1072	0.036	0.0063	-0.1849	0.1164	-0.0134	0.0671	-0.0305	-0.0484	0.0933	-0.001	-0.0176	28.111	58.131	4.812
3	2.9567	-0.446	-0.8747	0.6944	0.33	3.1335	-0.0717	-0.0089	-0.1079	0.0675	-0.0193	0.0373	0.2285	0.1921	0.091	0.0454	-0.0001	0.0015	0.0592	-0.0034	0.0129	22.123	49.23	-3.928
4	3.2376	2.5996	2.5094	3.3115	2.1157	3.1314	0.2087	0.1835	-0.2804	0.1132	-0.027	-0.2315	0.2781	-0.0735	-0.1818	0.0696	0.0143	-0.0407	0.0692	0.0084	0.0565	9.795	49.369	-17.438
5	1.7736	-0.6958	-0.8898	1.4989	0.5043	1.4288	-0.0045	0.261	-0.126	-0.035	-0.0885	0.0373	0.082	0.0397	0.0931	0.02	0.0058	-0.0057	0.1362	-0.0245	0.0242	22.785	49.258	-22.574
6	2.5347	-2.8148	0.7628	3.6533	-0.746	1.634	-0.0291	-0.0511	0.1133	-0.0383	0.05	-0.0203	-0.1125	0.3281	-0.0209	0.0034	-0.0101	-0.0109	0.1101	0.0147	0.022	27.352	55.01	-12.71
7	16.4631	-0.1331	4.5294	8.209	7.0104	20.5319	0.1305	-0.6678	-1.5897	0.1235	0.064	-0.0268	2.4409	-0.2844	-0.1945	0.3649	0.1489	-0.0085	0.0549	0.0813	0.0041	34.641	33.754	-14.926
8	0.7824	-0.4651	-0.2694	1.1907	0.8001	2.9716	0.0136	-0.0249	0.0322	0.0229	-0.0303	-0.1365	0.0782	0.2877	0.0167	-0.0371	-0.0049	-0.0005	0.1903	0.0199	-0.0084	33.391	51.511	-12.553
9	3.1221	0.1161	4.3262	0.945	-0.5501	7.2567	-0.5356	1.2085	0.8452	0.2364	-0.1543	-0.1749	-2.1273	1.7748	0.6899	0.2797	0.1062	0.1085	0.1937	0.2824	0.2597	13.37	76.321	-28.675
10	2.8724	1.7683	1.0946	9.0209	-1.6084	2.1452	0.025	0.8099	0.2625	-0.9111	0.1177	1.1506	-0.1094	-0.3893	-0.1427	0.101	0.2294	-0.136	0.3342	-0.0006	-0.0109	-13.772	66.816	-47.179
11	2.6957	-0.5979	-0.1467	1.815	0.3339	1.7265	0.051	0.3655	-0.2122	-0.0943	-0.0365	0.1492	0.1144	-0.137	-0.0145	0.0282	0.0638	-0.0402	0.109	-0.04	-0.0394	-4.069	53.969	-36.143
12	3.8627	1.4369	-0.4977	5.9896	-1.4469	3.3829	0.1147	0.1471	-0.0035	-0.0473	-0.12	0.4495	0.0316	-0.4775	0.0053	0.0019	0.0888	-0.0274	0.1451	-0.0549	0.0105	-12.49	57.472	-31.232
13	3.1775	0.2012	0.4328	0.6441	1.0115	1.5928	-0.0421	-0.2135	0.1586	-0.0332	-0.0221	0.0898	-0.1612	-0.0078	0.0642	0.0973	0.0604	-0.0178	0.0621	0.0082	0.0255	3.737	63.621	-16.772
14	5.5376	-0.3667	1.0576	6.169	2.8911	4.9273	0.0902	-0.1033	-0.1845	0.2089	-0.0113	0.0321	0.1537	-0.2708	-0.0789	0.0197	0.0201	0.006	0.0884	0.002	-0.0297	-1.416	55.604	-26.478
15	6.3968	-0.3263	2.2694	1.5698	1.6868	5.3092	-0.1011	-0.0035	0.7108	0.122	-0.0779	0.0012	-0.474	0.0318	0.1791	0.1175	0.046	-0.0229	0.0214	0.0745	0.097	8.773	74.361	-24.677
16	0.9697	0.0874	0.4595	1.1186	-0.072	0.6314	0.109	0.3306	0.1169	-0.0733	-0.1243	-0.1566	-0.0236	0.0813	0.0153	0.0713	0.0824	0.018	0.1118	0.0414	-0.0028	6.126	64.042	-32.952
17	44.5157	-6.7933	-6.6767	15.5811	13.8691	21.2454	0.1523	-1.0712	1.6686	0.3371	0.092	0.4237	-0.2927	-1.1983	-0.2443	-0.0323	0.2151	0.064	-0.0461	0.1898	0.1389	-14.925	81.687	-32.842
18	19.6196	-1.0042	-7.5363	9.6006	-6.1723	7.3987	0.7235	-1.9555	0.9353	1.1489	-0.7569	0.1733	-1.0103	-0.0859	0.0333	0.4691	0.0606	-0.0022	0.4759	-0.0028	0.4517	-13.74	81.16	-24.844
19	3.991	-0.6402	1.2603	2.4677	-0.3289	2.4364	0.0281	0.6102	0.5166	-0.2328	-0.1851	-0.0173	-0.3339	0.1055	0.1569	0.0732	0.1139	-0.0114	0.0869	0.1381	-0.0355	1.115	72.023	-38.043
20	8.603	-5.3649	-5.3883	14.5632	6.9525	6.2258	0.063	0.2844	-0.0872	-0.7728	-0.0078	-0.1774	-0.1352	0.1272	-0.0552	0.047	0.0559	-0.0373	0.1997	-0.0392	-0.1124	-0.565	52.527	-43.427
21	8.4292	2.4912	2.4422	11.8128	0.4907	6.4038	-0.365	0.4553	0.1711	-0.3798	0.4114	0.2465	-0.0199	-0.9045	-0.0464	-0.2039	-0.0302	-0.1828	0.2305	0.0008	-0.2631	-37.106	55.919	-28.987
22	11.2793	3.6275	8.2506	4.9365	3.5712	13.101	-0.3868	0.296	0.5444	-0.4129	0.1906	0.1507	-0.7217	0.0662	0.1962	-0.0008	0.0755	-0.055	0.0911	-0.0288	0.0008	-21.27	67.857	-19.48
23	3.6576	0.9729	0.9697	3.1587	0.8085	1.86	0.1041	0.0605	-0.033	-0.2658	0.11	0.2102	0.1106	-0.3911	-0.2141	0.0167	0.0115	-0.0933	0.21	0.0218	0.0311	-20.782	53.8	-21.76
24	8.2125	-10.2803	4.3134	14.3038	-5.7824	2.3677	0.3524	0.102	-0.3314	-0.1367	-0.0668	0.6057	0.1026	-0.0691	-0.2856	0.1025	-0.0098	-0.0566	0.2047	-0.0288	0.0175	-7.685	45.665	-17.933
25	1.1954	-0.7238	1.0278	1.3402	-0.8883	1.1101	0.1424	-0.1749	-0.0508	-0.3084	0.0164	0.1134	0.1399	-0.1537	-0.1588	0.0196	-0.0203	-0.0548	0.2178	-0.0017	-0.0045	-10.713	48.158	-11.713
26	14.4099	-0.0531	-4.5741	19.0536	-3.948	2.277	-0.5048	0.6997	-1.3482	-0.5578	0.6354	0.0879	0.9958	0.3858	-0.1306	0.2044	-0.14	-0.1799	0.2104	0.0655	0.1548	-18.653	30.735	-12.151
27	2.7471	-0.0844	1.6487	1.8332	0.6191	4.16	0.2233	-0.5712	-0.4204	-0.0391	-0.0083	0.2974	0.4455	-0.5807	-0.215	-0.0554	-0.1153	-0.0844	0.2917	0.1214	0.0571	-22.81	44.5	-8.089
28	4.6129	-0.2931	3.0838	6.8524	0.5481	10.7635	0.5974	-0.2139	-1.3228	-0.3565	-0.0065	0.6399	1.4443	-0.9739	-0.5909	-0.0243	-0.2381	-0.3036	0.207	0.1761	0.3579	-29.781	35.31	-16.449
29	2.9756	0.674	1.2644	2.6463	-0.8088	1.0618	0.1539	-0.3459	-0.1395	-0.2159	0.0173	0.3973	0.046	-0.6257	-0.1712	-0.0507	-0.0385	-0.1106	0.3681	0.0659	0.0119	-30.343	53.568	-17.233
30	4.1879	-1.0912	5.4406	0.2849	-1.3358	18.6523	-1.0415	-1.2434	-0.2996	0.9138	0.7262	0.5885	-2.2546	-1.7917	0.3153	0.3374	-0.053	-0.0406	0.4408	-0.1918	0.2956	-12.654	57.889	15.15
31	1.1945	0.1316	0.2844	2.1316	1.7365	4.8836	0.0099	-0.1259	-0.139	0.0553	0.16	-0.155	0.3198	0.1458	-0.1699	0.0395	-0.0096	-0.0112	0.0622	0.0075	-0.034	15.068	39.632	20.074
32	0.9636	-0.4785	0.6985	5.3533	2.4401	3.5526	0.0922	-0.144	-0.1707	-0.1262	0.0055	-0.0478	0.3512	-0.3204	-0.0977	0.0705	-0.0976	0.0067	0.0747	0.0198	0.0264	6.701	40.184	5.759
33	2.5288	-0.88	0.1027	3.7985	1.9407	4.4405	0.0562	-0.1556	-0.004	-0.1995	0.1346	-0.1732	0.0046	0.2323	-0.1908	0.0502	-0.043	0.0364	0.0779	-0.0069	0.0149	15.523	45.483	5.301
34	1.4554	-2.3188	1.4275	3.7277	-2.2067	1.5377	-0.0471	0.0153	0.2884	-0.0443	-0.1806	-0.1973	-0.0865	-0.0598	0.2277	0.0358	-0.0049	-0.0188	0.2412	-0.0217	-0.0031	-2.083	58.235	-2.081
35	2.775	-1.0988	0.0504	2.4488	1.4607	4.9	0.1048	0.2355	0.0493	-0.2192	-0.0207	-0.1206	0.036	-0.2042	-0.0841	0.0358	-0.0643	0.0108	0.1027	0.03	-0.0024	2.763	46.91	-0.449
36	1.1608	0.0756	0.9587	0.8753	0.0764	3.1715	-0.0547	-0.2426	0.026	0.0142	0.0409	0.0747	-0.0119	-0.6734	0.0138	-0.0618	-0.01	0.0043	0.2304	0.0065	-0.0304	-4.023	52.181	11.585
37	15.0369	5.9124	-6.8564	8.1338	-2.4834	22.108	0.2301	0.2769	0.3728	0.1883	0.1695	-0.3237	-0.8451	0.8866	-0.3996	0.1174	0.005	-0.0801	0.0707	-0.032	-0.0127	18.811	64.818	19.979
38	40.8258	-3.9667	-26.679	1.2529	5.506	38.0632	0.0364	1.9448	1.212	-0.4072	0.2555	0.1609	-0.2244	-0.9173	-0.2919	0.1084	0.07	-0.0539	0.191	0.1134	0.0193	12.984	66.816	13.806
39	8.8606	4.607	2.1877	5.3319	2.0656	3.7107	-0.1827	-0.3475	0.7603	0.2263	0.0125	0.3765	-0.2148	-0.5046	0.1702	-0.018	0.1202	-0.0213	0.29	-0.0286	-0.0547	-2.289	59.973	20.953
40	0.8255	-0.4151	0.4857	1.1751	0.259	2.8928	0.0442	-0.2721	-0.2056	0.1256	0.1107	0.066	0.4189	-0.3825	-0.1549	0.0594	-0.0911	0.0013	0.1334	0.0299	0.0164	4.366	39.208	14.903

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	2 - 8	4 - 10
2	X-RAY DIFFRACTION	2	A	A	9 - 40	11 - 42
3	X-RAY DIFFRACTION	3	A	A	41 - 75	43 - 77
4	X-RAY DIFFRACTION	4	A	A	76 - 99	78 - 101
5	X-RAY DIFFRACTION	5	A	A	100 - 139	102 - 141
6	X-RAY DIFFRACTION	6	A	A	140 - 155	142 - 157
7	X-RAY DIFFRACTION	7	A	A	156 - 185	158 - 187
8	X-RAY DIFFRACTION	8	A	A	186 - 232	188 - 234
9	X-RAY DIFFRACTION	9	A	A	233 - 261	235 - 263
10	X-RAY DIFFRACTION	10	A	A	262 - 282	264 - 284
11	X-RAY DIFFRACTION	11	A	A	283 - 310	285 - 312
12	X-RAY DIFFRACTION	12	A	A	311 - 328	313 - 330
13	X-RAY DIFFRACTION	13	A	A	329 - 349	331 - 351
14	X-RAY DIFFRACTION	14	A	A	350 - 363	352 - 365
15	X-RAY DIFFRACTION	15	A	A	364 - 384	366 - 386
16	X-RAY DIFFRACTION	16	A	A	385 - 414	387 - 416
17	X-RAY DIFFRACTION	17	A	A	415 - 424	417 - 426
18	X-RAY DIFFRACTION	18	A	A	425 - 442	427 - 444
19	X-RAY DIFFRACTION	19	A	A	443 - 480	445 - 482
20	X-RAY DIFFRACTION	20	A	A	481 - 496	483 - 498
21	X-RAY DIFFRACTION	21	B	B	6 - 21	8 - 23
22	X-RAY DIFFRACTION	22	B	B	22 - 38	24 - 40
23	X-RAY DIFFRACTION	23	B	B	39 - 68	41 - 70
24	X-RAY DIFFRACTION	24	B	B	69 - 83	71 - 85
25	X-RAY DIFFRACTION	25	B	B	84 - 110	86 - 112
26	X-RAY DIFFRACTION	26	B	B	111 - 122	113 - 124
27	X-RAY DIFFRACTION	27	B	B	123 - 157	125 - 159
28	X-RAY DIFFRACTION	28	B	B	158 - 202	160 - 204
29	X-RAY DIFFRACTION	29	B	B	203 - 234	205 - 236
30	X-RAY DIFFRACTION	30	B	B	235 - 260	237 - 262
31	X-RAY DIFFRACTION	31	B	B	261 - 289	263 - 291
32	X-RAY DIFFRACTION	32	B	B	290 - 310	292 - 312
33	X-RAY DIFFRACTION	33	B	B	311 - 328	313 - 330
34	X-RAY DIFFRACTION	34	B	B	329 - 346	331 - 348
35	X-RAY DIFFRACTION	35	B	B	347 - 363	349 - 365
36	X-RAY DIFFRACTION	36	B	B	364 - 419	366 - 421
37	X-RAY DIFFRACTION	37	B	B	420 - 428	422 - 430
38	X-RAY DIFFRACTION	38	B	B	429 - 437	431 - 439
39	X-RAY DIFFRACTION	39	B	B	438 - 456	440 - 458
40	X-RAY DIFFRACTION	40	B	B	457 - 496	459 - 498

-
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

-
Protein , 1 types, 2 molecules AB

-
Non-polymers , 5 types, 681 molecules

-
Details

-
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

-Protein , 1 types, 2 molecules AB

-Non-polymers , 5 types, 681 molecules

-Details

-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

-
Protein , 1 types, 2 molecules AB

-
Non-polymers , 5 types, 681 molecules

-
Details

-
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