PDB-6czp: 2.2 Angstrom Resolution Crystal Structure Oxygen-Insensitive NAD(...

ID or keywords:

Entry

Database: PDB / ID: 6czp

Title

2.2 Angstrom Resolution Crystal Structure Oxygen-Insensitive NAD(P)H-dependent Nitroreductase NfsB from Vibrio vulnificus in Complex with FMN

Components

Oxygen-insensitive NAD(P)H nitroreductase

Keywords

OXIDOREDUCTASE /

Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / oxygen-insensitive nitroreductase

Function / homology

Function and homology information

oxidoreductase activity
Similarity search - Function

Biological species

Vibrio vulnificus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.24 Å

Authors

Minasov, G. / Wawrzak, Z. / Skarina, T. / Grimshaw, S. / Kwon, K. / Savchenko, A. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To Be Published
Title: 2.2 Angstrom Resolution Crystal Structure Oxygen-Insensitive NAD(P)H-dependent Nitroreductase NfsB from Vibrio vulnificus in Complex with FMN.
Authors: Minasov, G. / Wawrzak, Z. / Skarina, T. / Grimshaw, S. / Kwon, K. / Savchenko, A. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Apr 9, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 25, 2018	Provider: repository / Type: Initial release
Revision 1.1	Oct 4, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6czp.cif.gz	712 KB	Display	PDBx/mmCIF format
PDB format	pdb6czp.ent.gz	591.7 KB	Display	PDB format
PDBx/mmJSON format	6czp.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cz/6czp ftp://data.pdbj.org/pub/pdb/validation_reports/cz/6czp	HTTPS FTP

-
Related structure data

Related structure data	1icrS S: Starting model for refinement
Similar structure data	1oo5-d 1v5y-d 3x21-4 1kqb-1 1kqd-1 1oo6-d 1icu-2 1oon-d 1nec-1 1icv-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) 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	TargetTrack: CSGID-IDP07377

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Oxygen-insensitive NAD(P)H nitroreductase

B: Oxygen-insensitive NAD(P)H nitroreductase

C: Oxygen-insensitive NAD(P)H nitroreductase

D: Oxygen-insensitive NAD(P)H nitroreductase

E: Oxygen-insensitive NAD(P)H nitroreductase

F: Oxygen-insensitive NAD(P)H nitroreductase

G: Oxygen-insensitive NAD(P)H nitroreductase

H: Oxygen-insensitive NAD(P)H nitroreductase

hetero molecules

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

1

A: Oxygen-insensitive NAD(P)H nitroreductase

B: Oxygen-insensitive NAD(P)H nitroreductase

hetero molecules

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

2

C: Oxygen-insensitive NAD(P)H nitroreductase

D: Oxygen-insensitive NAD(P)H nitroreductase

hetero molecules

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

3

E: Oxygen-insensitive NAD(P)H nitroreductase

F: Oxygen-insensitive NAD(P)H nitroreductase

hetero molecules

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

4

G: Oxygen-insensitive NAD(P)H nitroreductase

H: Oxygen-insensitive NAD(P)H nitroreductase

hetero molecules

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

Unit cell

Length a, b, c (Å)	118.769, 119.659, 131.175
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

-
Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein	Oxygen-insensitive NAD(P)H nitroreductase Mass: 24481.701 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio vulnificus (bacteria) / Gene: FORC36_4330 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-Magic / References: UniProt: A0A1W6MCC0, UniProt: Q7MCD2*PLUS

#1: Protein

Oxygen-insensitive NAD(P)H nitroreductase

Mass: 24481.701 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Vibrio vulnificus (bacteria) / Gene: FORC36_4330 / Plasmid: pMCSG53 / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-Magic / References: UniProt: A0A1W6MCC0, UniProt: Q7MCD2*PLUS

-
Non-polymers , 6 types, 647 molecules

#2: Chemical	ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide Mass: 456.344 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₁₇H₂₁N₄O₉P
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#5: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#7: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 627 / 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: 2.35 Å³/Da / Density % sol: 47.8 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Protein: 17.0 mg/ml, 0.3M Sodium chloride, 0.01M HEPES pH 7.5, Screen: 0.2M Magnesium chloride, 0.1M Tris pH 8.5, 25% (w/v) PEG3350, Cryo: paratone

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 14, 2018 / Details: C(111)
Radiation	Monochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97872 Å / Relative weight: 1
Reflection	Resolution: 2.2→30 Å / Num. obs: 88464 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.8 % / B_iso Wilson estimate: 48.5 Å² / R_merge(I) obs: 0.129 / R_pim(I) all: 0.048 / R_rim(I) all: 0.138 / R_sym value: 0.129 / Χ²: 1.02 / Net I/σ(I): 38.3
Reflection shell	Resolution: 2.2→2.24 Å / Redundancy: 7.3 % / R_merge(I) obs: 0.768 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 4360 / CC_1/2: 0.852 / R_pim(I) all: 0.3 / R_rim(I) all: 0.826 / R_sym value: 0.768 / Χ²: 1.025 / % possible all: 100

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0222	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1ICR

1icr

Resolution: 2.24→29.91 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c free: 0.937 / SU B: 12.513 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.311 / ESU R Free: 0.215 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22392	4434	5 %	RANDOM
R_work	0.17733	-	-	-
obs	0.17962	83952	97.58 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 49.134 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.72 Å²	0 Å²	0 Å²
2-	-	3.56 Å²	0 Å²
3-	-	-	-1.84 Å²

Refinement step

Cycle: 1 / Resolution: 2.24→29.91 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13691	0	320	627	14638

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.015	14335
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	12899
X-RAY DIFFRACTION	r_angle_refined_deg	1.249	1.747	19356
X-RAY DIFFRACTION	r_angle_other_deg	0.438	1.732	30137
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	2.165	5	1746
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	18.525	18.547	475
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	9.108	15	2019
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.85	15	80
X-RAY DIFFRACTION	r_chiral_restr	0.052	0.2	1825
X-RAY DIFFRACTION	r_gen_planes_refined	0.022	0.02	16058
X-RAY DIFFRACTION	r_gen_planes_other	0.019	0.02	2754
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	1.592	2.851	6996
X-RAY DIFFRACTION	r_mcbond_other	1.592	2.852	6997
X-RAY DIFFRACTION	r_mcangle_it	2.458	4.268	8738
X-RAY DIFFRACTION	r_mcangle_other	2.458	4.269	8739
X-RAY DIFFRACTION	r_scbond_it	2.136	3.215	7339
X-RAY DIFFRACTION	r_scbond_other	2.136	3.215	7339
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	3.343	4.723	10619
X-RAY DIFFRACTION	r_long_range_B_refined	6.633	36.795	17018
X-RAY DIFFRACTION	r_long_range_B_other	6.606	36.652	16937
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.239→2.296 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.298	207	-
R_work	0.237	4278	-
obs	-	-	68.02 %

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	2.098	0.2539	-1.2119	1.1782	-0.2231	1.8857	-0.0484	0.1953	0.0257	-0.1941	0.0894	-0.1198	0.1253	-0.0177	-0.041	0.0877	0.0121	0.0267	0.0482	-0.0191	0.0412	16.278	39.2739	24.1432
2	9.943	-4.1746	-2.6406	5.9311	-0.4063	1.4301	-0.2627	-0.41	-0.4866	-0.0339	0.2848	-0.1308	0.2667	0.1218	-0.0222	0.3863	0.0707	-0.0298	0.04	-0.0629	0.5425	15.7494	11.6549	33.7818
3	2.2471	0.7318	-1.1447	1.3198	-0.5949	1.6859	-0.0887	0.1463	-0.0971	-0.0987	0.0695	-0.0467	0.1384	-0.0281	0.0192	0.1043	0.0046	0.019	0.0299	-0.0373	0.0641	10.3489	35.9513	30.2747
4	1.8998	-0.6885	0.2055	5.1918	-4.0568	9.6207	-0.0668	-0.1012	0.234	0.338	0.1167	-0.7158	-0.9984	0.1283	-0.05	0.1135	-0.0377	0.0261	0.13	-0.0793	0.1751	23.6703	51.5865	40.9502
5	1.3547	-0.5989	0.9812	2.4208	-1.0572	3.8899	0.4074	0.3476	0.0088	-0.3161	-0.094	-0.5916	1.1587	1.2944	-0.3134	0.431	0.2899	-0.0776	0.688	-0.0361	0.6211	33.2053	27.9957	37.9835
6	1.7862	-0.0592	-0.2957	3.1667	-0.3534	1.9338	-0.0178	-0.3993	-0.1642	0.1336	0.0709	-0.5403	0.0691	0.3838	-0.0531	0.1036	0.0097	-0.0526	0.1706	-0.0031	0.1295	19.8246	42.2297	47.2416
7	2.3031	-0.1751	0.0586	1.9261	-0.1876	1.3706	-0.0059	-0.2791	-0.4324	0.2274	0.004	-0.3713	0.1451	0.2809	0.0019	0.1495	0.0276	-0.0371	0.1362	0.0336	0.175	16.9687	34.4073	45.8135
8	3.5709	-2.6878	1.7618	4.7059	-3.5221	5.52	-0.262	0.1779	-0.3044	-0.4778	-0.0844	-0.5366	0.4837	0.3605	0.3464	0.231	0.016	0.1713	0.0791	-0.0731	0.2976	21.0256	22.245	26.7425
9	1.7587	-1.9894	1.0563	2.4495	-1.4694	4.0614	0.2144	0.0221	-0.497	-0.2331	-0.1005	0.8308	0.1691	-0.3704	-0.1139	0.077	0.0017	-0.0034	0.3087	-0.1328	0.6302	-34.6253	36.8502	46.672
10	1.9845	-0.2642	0.2126	1.4826	0.1464	1.3947	0.103	-0.0692	0.1044	0.2314	-0.1692	0.2793	-0.0795	-0.0891	0.0662	0.156	-0.0232	0.076	0.0624	-0.0245	0.0767	-15.2725	41.7998	53.4871
11	5.8038	-0.5141	1.2565	0.7197	-0.7811	0.9622	0.1367	-0.0562	0.3231	0.2052	-0.1705	0.0618	-0.2037	0.1178	0.0338	0.208	0.0138	0.0712	0.1723	-0.0702	0.214	-20.3829	45.4934	46.9272
12	3.728	-1.0184	0.5681	2.1284	-0.7721	4.0224	0.0581	0.0238	-0.0407	-0.3926	-0.0183	0.3035	0.34	-0.7736	-0.0397	0.16	-0.0662	-0.0382	0.2535	-0.1331	0.2589	-27.9843	24.7621	38.0761
13	2.8441	-0.1691	1.3616	8.6753	-5.5314	4.1394	-0.355	-0.8463	0.3266	0.9297	0.4488	0.4193	-0.5943	-0.7689	-0.0938	0.5392	-0.0048	0.1755	0.6796	0.0276	0.2107	-25.8854	29.167	63.8935
14	1.5793	-0.0643	0.3345	1.9688	-0.6733	3.4182	0.0249	-0.0852	-0.5515	0.051	-0.1707	0.2586	0.5592	-0.3017	0.1458	0.2158	-0.1018	0.0578	0.0681	-0.0277	0.2584	-18.5142	18.7006	48.257
15	3.0581	0.6177	-0.1978	2.2445	-0.7681	2.3165	0.0131	-0.1248	-0.2646	0.1078	-0.0611	0.322	0.2883	-0.2193	0.048	0.1207	-0.022	0.0449	0.0393	-0.0139	0.1021	-14.4041	25.477	46.1557
16	1.8972	1.8703	-1.7223	5.3285	-5.7394	6.2817	-0.1744	-0.4851	-0.0341	0.1019	-0.0416	-0.1725	-0.1176	-0.1337	0.216	0.3449	-0.0395	0.1533	0.3133	-0.0722	0.1415	-19.041	40.4567	65.359
17	0.9887	0.1701	-0.3087	1.6198	-0.8106	1.6987	0.0831	-0.1498	-0.0274	0.2225	-0.1744	-0.0932	0.009	0.2688	0.0914	0.1178	0.032	-0.0187	0.0894	0.0142	0.0151	-6.0813	15.1224	8.0329
18	2.3119	1.1655	-1.1721	2.3648	-1.2994	1.8232	0.0641	-0.0087	-0.2026	-0.0247	-0.3184	-0.4528	0.2389	0.5194	0.2543	0.1064	0.1231	-0.025	0.2929	0.1033	0.1455	9.9841	17.0543	-3.0841
19	0.7965	-0.231	-0.4013	2.5883	-0.6854	2.2104	0.1123	-0.0672	0.0338	0.3647	-0.0054	0.0438	-0.0908	0.1027	-0.1069	0.1225	0.0144	-0.0104	0.0674	-0.006	0.019	-8.4995	21.3628	7.4448
20	4.3667	-1.1817	-3.0445	2.0187	0.8135	6.9651	0.1509	0.0446	-0.1871	-0.1147	-0.0148	0.1989	0.3912	-0.3207	-0.1361	0.1297	-0.0018	-0.0698	0.0293	0.0021	0.0482	-18.6793	5.6051	-8.1261
21	3.0165	-1.0272	0.4018	2.3121	-0.9275	1.1702	0.166	0.0605	-0.7882	-0.4125	-0.1776	-0.244	0.824	0.3597	0.0116	0.6221	0.2475	-0.0097	0.3909	0.0187	0.437	0.472	-2.5204	-5.546
22	2.0194	-0.3545	0.8148	1.7991	-0.3872	1.6027	0.1782	0.3427	-0.1295	-0.3077	-0.1947	-0.2285	0.3854	0.3104	0.0165	0.1999	0.1057	0.0154	0.1651	-0.0121	0.0519	-6.6291	12.3072	-13.8465
23	1.9497	-1.4027	0.3562	6.0069	-3.745	2.9647	0.4667	0.5343	-0.2785	-0.5065	-0.5887	-0.2657	0.3095	0.5944	0.122	0.3004	0.2217	-0.0133	0.4468	-0.1316	0.2346	0.962	6.7625	-15.7995
24	4.674	-1.8841	-4.1714	1.9983	1.6212	5.2534	-0.1908	-0.3141	-0.3887	0.3788	-0.3452	-0.328	0.3449	0.6231	0.536	0.2288	0.0669	-0.0914	0.4219	0.194	0.3237	10.7456	9.0566	5.7602
25	1.2776	-0.3089	0.0556	0.9995	0.9388	2.4034	-0.0549	0.3622	0.2662	-0.2459	0.0527	-0.4519	-0.2791	0.4791	0.0021	0.2064	-0.0527	0.1084	0.3956	0.1243	0.3272	12.8837	47.6899	-23.1721
26	0.1223	-0.6795	-0.335	7.4461	1.7265	0.957	-0.0245	-0.0059	-0.0222	0.5158	-0.0845	0.3339	0.0167	0.0264	0.109	0.0976	0.0037	-0.0154	0.0552	0.0188	0.1347	2.5466	54.8266	2.8981
27	1.4407	0.5867	-0.1988	1.4242	0.1519	1.9419	-0.1066	0.3145	0.0915	-0.1731	0.0383	-0.2716	-0.1073	0.396	0.0683	0.0604	-0.0009	0.0407	0.2276	0.0999	0.1108	8.6085	42.2102	-19.3597
28	3.7268	1.5283	-3.6308	1.6781	-1.302	5.3308	-0.2919	0.176	0.0904	-0.6046	-0.0546	0.0233	0.0998	0.175	0.3465	0.2524	0.0152	-0.0273	0.2832	0.1379	0.1194	-6.7095	45.7672	-36.1288
29	3.6197	-1.4877	0.6351	1.443	-0.0431	3.7648	-0.1642	0.0152	0.7369	-0.1495	-0.2075	-0.0407	-0.3873	0.0884	0.3717	0.1399	0.07	-0.0758	0.1528	0.0633	0.3773	-4.8826	63.4153	-17.8576
30	1.5877	-0.2452	-0.3954	2.7274	1.0891	2.1663	-0.0555	0.1237	0.365	-0.2706	-0.07	0.2533	-0.0995	-0.1104	0.1255	0.0865	0.0573	-0.0575	0.2054	0.0745	0.1618	-13.0071	47.4177	-21.7132
31	1.1485	-0.4384	0.4607	1.9981	0.7569	1.0239	-0.0117	0.3322	0.246	-0.3222	-0.0664	0.0113	-0.0124	0.2041	0.0781	0.2311	0.0289	0.0139	0.3467	0.1138	0.1182	-2.0858	39.3515	-28.7116
32	1.3377	0.1775	0.4662	1.101	-0.0146	0.9169	-0.118	-0.0021	0.4007	-0.0551	-0.0274	0.0929	-0.1313	-0.073	0.1454	0.0715	0.0428	-0.0257	0.1454	0.034	0.1316	-5.8381	50.7843	-12.7647

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	-1 - 95
2	X-RAY DIFFRACTION	2	A	96 - 124
3	X-RAY DIFFRACTION	3	A	125 - 195
4	X-RAY DIFFRACTION	4	A	196 - 217
5	X-RAY DIFFRACTION	5	B	0 - 24
6	X-RAY DIFFRACTION	6	B	25 - 124
7	X-RAY DIFFRACTION	7	B	125 - 197
8	X-RAY DIFFRACTION	8	B	198 - 217
9	X-RAY DIFFRACTION	9	C	-1 - 25
10	X-RAY DIFFRACTION	10	C	26 - 179
11	X-RAY DIFFRACTION	11	C	180 - 195
12	X-RAY DIFFRACTION	12	C	196 - 217
13	X-RAY DIFFRACTION	13	D	0 - 17
14	X-RAY DIFFRACTION	14	D	18 - 109
15	X-RAY DIFFRACTION	15	D	110 - 198
16	X-RAY DIFFRACTION	16	D	199 - 217
17	X-RAY DIFFRACTION	17	E	-1 - 99
18	X-RAY DIFFRACTION	18	E	100 - 156
19	X-RAY DIFFRACTION	19	E	157 - 195
20	X-RAY DIFFRACTION	20	E	196 - 217
21	X-RAY DIFFRACTION	21	F	0 - 36
22	X-RAY DIFFRACTION	22	F	37 - 179
23	X-RAY DIFFRACTION	23	F	180 - 195
24	X-RAY DIFFRACTION	24	F	196 - 217
25	X-RAY DIFFRACTION	25	G	1 - 98
26	X-RAY DIFFRACTION	26	G	99 - 124
27	X-RAY DIFFRACTION	27	G	125 - 197
28	X-RAY DIFFRACTION	28	G	198 - 217
29	X-RAY DIFFRACTION	29	H	0 - 24
30	X-RAY DIFFRACTION	30	H	25 - 99
31	X-RAY DIFFRACTION	31	H	100 - 163
32	X-RAY DIFFRACTION	32	H	164 - 217

-
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, 8 molecules ABCDEFGH

-
Non-polymers , 6 types, 647 molecules

-
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, 8 molecules ABCDEFGH

-Non-polymers , 6 types, 647 molecules

-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, 8 molecules ABCDEFGH

-
Non-polymers , 6 types, 647 molecules

-
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