PDB-4r7u: Structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase fr...

ID or keywords:

Entry

Database: PDB / ID: 4r7u

Title

Structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase from Vibrio cholerae in complex with substrate UDP-N-acetylglucosamine and the drug fosfomycin

Components

UDP-N-acetylglucosamine 1-carboxyvinyltransferase

Keywords

TRANSFERASE/ANTIBIOTIC / MURA / FOSFOMYCIN / PEPTIDOGLYCAN / AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM / PEPTIDOGLYCAN BIOSYNTHESIS / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / UDP-N-acetylglucosamine 1-carboxyvinyltransferase / TRANSFERASE-ANTIBIOTIC complex

Function / homology

Function and homology information

UDP-N-acetylglucosamine 1-carboxyvinyltransferase / UDP-N-acetylglucosamine 1-carboxyvinyltransferase activity / UDP-N-acetylgalactosamine biosynthetic process / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell cycle / cell division / cytoplasm
Similarity search - Function

Biological species

Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.45 Å

Authors

Nocek, B. / Maltseva, N. / Anderson, W. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To be Published
Title: Structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase from Vibrio cholerae in complex with substrate UDP-N-acetylglucosamine and the drug fosfomycin
Authors: Nocek, B. / Maltseva, N. / Anderson, W. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Aug 28, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 24, 2014	Provider: repository / Type: Initial release
Revision 1.1	Nov 22, 2017	Group: Refinement description / Category: software

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4r7u.cif.gz	615 KB	Display	PDBx/mmCIF format
PDB format	pdb4r7u.ent.gz	530.9 KB	Display	PDB format
PDBx/mmJSON format	4r7u.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4r7u_validation.pdf.gz	1.7 MB	Display	wwPDB validaton report
Full document	4r7u_full_validation.pdf.gz	1.7 MB	Display
Data in XML	4r7u_validation.xml.gz	60.4 KB	Display
Data in CIF	4r7u_validation.cif.gz	83.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/r7/4r7u ftp://data.pdbj.org/pub/pdb/validation_reports/r7/4r7u	HTTPS FTP

-
Related structure data

Similar structure data	3vcy-d 3v4t-1 1q3g-3 3swd-15 6cn1-1 3swd-13 2z2c-d 1ryw-1 3v4t-2 1ryw-2 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-IDP01463

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#218 - Feb 2018 EPSP Synthase and Weedkillers similarity (4)

Deposited unit

A: UDP-N-acetylglucosamine 1-carboxyvinyltransferase

B: UDP-N-acetylglucosamine 1-carboxyvinyltransferase

C: UDP-N-acetylglucosamine 1-carboxyvinyltransferase

D: UDP-N-acetylglucosamine 1-carboxyvinyltransferase

hetero molecules

183 kDa, 4 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)	204.283, 204.283, 118.878
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	146
Space group name H-M	H3

-
Protein , 1 types, 4 molecules ABCD

#1: Protein	UDP-N-acetylglucosamine 1-carboxyvinyltransferase / Enoylpyruvate transferase / UDP-N-acetylglucosamine enolpyruvyl transferase / EPT Mass: 45011.582 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria) Strain: N16961 / Gene: murA, VC_2514 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9KP62, UDP-N-acetylglucosamine 1-carboxyvinyltransferase

#1: Protein

UDP-N-acetylglucosamine 1-carboxyvinyltransferase / Enoylpyruvate transferase / UDP-N-acetylglucosamine enolpyruvyl transferase / EPT

Mass: 45011.582 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Strain: N16961 / Gene: murA, VC_2514 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9KP62, UDP-N-acetylglucosamine 1-carboxyvinyltransferase

-
Non-polymers , 5 types, 309 molecules

#2: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#3: Chemical	ChemComp-FFQ / [(1R)-1-hydroxypropyl]phosphonic acid / Fosfomycin, bound form Mass: 140.075 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₉O₄P / Comment: antibiotic*YM
#4: Chemical	ChemComp-UD1 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE Mass: 607.354 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₇H₂₇N₃O₁₇P₂
#5: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 295 / 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: 2.65 Å³/Da / Density % sol: 53.61 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 30.0 % w/v PEG 2000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 29, 2012 / Details: mirrors
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9794 Å / Relative weight: 1
Reflection	Resolution: 2.45→38.64 Å / Num. all: 67896 / Num. obs: 67896 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.1 % / R_merge(I) obs: 0.102 / Net I/σ(I): 12.8
Reflection shell	Resolution: 2.45→2.49 Å / % possible all: 100

-
Processing

Software

Name	Version	Classification
SBC-Collect		data collection
REFMAC	5.7.0029	refinement
HKL-3000		data reduction
HKL-3000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.45→38.64 Å / Cor.coef. F_o:F_c: 0.94 / Cor.coef. F_o:F_c free: 0.896 / SU B: 16.122 / SU ML: 0.192 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.82 / ESU R Free: 0.294 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23372	2986	5.1 %	RANDOM
R_work	0.17767	-	-	-
obs	0.1805	55981	86.72 %	-
all	-	58967	-	-

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: 31.492 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.25 Å²	-0.25 Å²	0 Å²
2-	-	-0.25 Å²	0 Å²
3-	-	-	0.81 Å²

Refinement step

Cycle: LAST / Resolution: 2.45→38.64 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12460	0	206	295	12961

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.019	12840
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	12612
X-RAY DIFFRACTION	r_angle_refined_deg	1.45	1.986	17413
X-RAY DIFFRACTION	r_angle_other_deg	0.739	3	28964
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.221	5	1669
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.652	23.968	504
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.468	15	2169
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.644	15	94
X-RAY DIFFRACTION	r_chiral_restr	0.074	0.2	2069
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	14429
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2693
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
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.45→2.513 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.229	43	-
R_work	0.187	811	-
obs	-	-	17.04 %

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	1.3354	0.0563	0.3533	0.3899	0.1213	0.2209	-0.1609	0.0127	0.183	-0.0198	0.1263	-0.0632	-0.1271	0.003	0.0346	0.1176	0.0145	0.0057	0.1023	-0.014	0.0725	-45.4452	2.5884	-21.5121
2	2.345	-0.7921	0.0592	1.7812	0.0995	0.2644	-0.0914	-0.0366	0.1656	0.0056	0.0992	-0.0769	-0.0178	0.0079	-0.0078	0.105	-0.0203	-0.0033	0.0824	-0.0624	0.1012	-28.1369	4.6172	-14.6124
3	8.29	-3.0477	0.0069	2.466	-0.9112	0.6257	-0.0833	-0.2499	-0.3477	0.1719	0.1569	0.2236	-0.1327	-0.0213	-0.0736	0.1466	-0.032	-0.0163	0.1329	-0.041	0.0687	-31.9439	-6.7377	-5.8574
4	0.2085	-0.2261	-0.0957	0.3677	-0.084	0.3376	-0.0316	-0.045	-0.0301	0.007	0.0388	0.0251	0.0261	0.0171	-0.0072	0.0987	0.0242	-0.0151	0.1414	-0.0628	0.1465	-27.5784	-15.2472	-11.9191
5	2.2812	0.4224	-0.0616	0.1026	0.1634	3.4299	0.0926	-0.1911	-0.061	0.0671	-0.026	-0.0475	0.2527	0.2667	-0.0665	0.1149	0.0255	-0.0568	0.0478	-0.0059	0.1763	-21.1727	-18.2861	-11.1685
6	0.1054	-0.0198	-0.2823	1.0485	-0.291	0.9746	-0.0396	-0.0027	0.0307	-0.0816	0.0607	-0.0952	0.0485	0.0072	-0.0211	0.1097	-0.0106	0.0074	0.0932	-0.0367	0.1254	-25.5414	-12.8281	-26.6827
7	5.9121	-3.138	1.0023	20.7206	-1.7514	0.25	-0.4561	-0.4205	0.1908	-0.3996	0.3595	-1.4992	-0.0434	-0.0625	0.0966	0.1013	-0.0337	0.0918	0.2417	-0.1432	0.1978	-13.4491	-5.2249	-23.8623
8	1.0427	-0.6875	0.6926	0.4681	-0.4732	0.4806	-0.1207	-0.1417	0.2244	0.0275	0.0439	-0.1167	-0.0352	-0.0644	0.0767	0.1549	0.0199	-0.0501	0.1349	-0.0482	0.2033	-44.764	-0.2255	-29.0406
9	3.5879	-0.5412	-1.193	0.7039	-0.9884	2.7368	0.1635	0.2873	0.1487	-0.1805	-0.1058	-0.0431	0.0932	0.0789	-0.0577	0.1896	-0.0307	0.0181	0.1064	-0.0286	0.1377	-47.1242	0.6895	-36.0412
10	3.4567	1.6332	-0.4379	1.7068	-0.2657	0.0631	-0.0866	0.4034	-0.0358	-0.3242	0.0817	-0.1308	0.0238	-0.0649	0.0049	0.1232	0.0392	0.0161	0.1684	0.0036	0.0749	-51.3019	-2.684	-39.5793
11	2.6573	0.3776	0.3265	0.8305	0.2819	0.1212	-0.0594	-0.0159	0.1512	-0.0126	0.0388	-0.0433	0	-0.0153	0.0206	0.1314	0.0074	-0.0103	0.1301	-0.0103	0.0687	-54.0213	-11.6816	-30.0617
12	5.7409	-0.2607	2.872	0.0942	0.3408	4.2209	-0.1193	0.0313	-0.122	-0.0024	0.021	0.0351	-0.02	0.0142	0.0982	0.1378	-0.0401	-0.0264	0.0863	0.0101	0.121	-52.8272	-17.5415	-23.5499
13	0.2463	-0.1298	-0.1229	1.591	0.0511	0.3585	-0.0657	-0.0699	-0.0993	0.0852	0.0725	0.14	0.0989	-0.0431	-0.0068	0.1004	-0.02	-0.0278	0.1065	-0.0011	0.1477	-63.2568	-12.0193	-19.4074
14	0.1571	0.3216	-0.1139	1.502	0.4661	0.6631	0.0393	-0.0153	-0.0012	0.0761	-0.0089	-0.0311	-0.0177	0.0304	-0.0304	0.1285	0.0275	-0.0195	0.1211	0.0009	0.0892	-55.6497	-1.3521	-15.5328
15	0.7305	-0.3299	0.5875	0.8891	-0.1325	0.4967	-0.099	-0.0171	0.1724	-0.0159	-0.0308	-0.1433	-0.099	-0.0217	0.1298	0.1226	0.0263	-0.0253	0.1218	-0.0147	0.11	-53.0612	8.2225	-18.9305
16	1.7841	0.2749	-0.2654	0.06	-0.0339	0.1847	-0.0403	-0.1256	0.1103	0.0436	-0.011	0.0078	0.0577	-0.0158	0.0513	0.1494	0.0146	-0.0028	0.1064	-0.0496	0.0944	-55.6992	-21.1994	12.3369
17	1.5359	-0.1672	-0.0231	0.5451	0.586	0.6634	-0.1556	-0.1713	0.1974	0.0574	0.0761	0.035	0.0142	0.0302	0.0795	0.1413	0.0188	0.0142	0.1196	-0.0639	0.1025	-73.2141	-13.0556	12.9061
18	7.8617	4.3877	-2.9205	2.4489	-1.63	1.1073	-0.1645	0.2749	0.3125	-0.1067	0.1874	0.1729	0.0945	-0.0712	-0.0229	0.1698	0.0392	-0.0164	0.1275	0.0422	0.218	-69.6822	-8.6884	-0.8884
19	1.6967	0.1884	0.1929	0.1175	0.1288	0.1453	0.0425	0.0669	0.0472	0.0216	-0.021	-0.0318	0.0196	-0.0146	-0.0216	0.0979	0.0212	0.0094	0.1037	-0.0098	0.1485	-74.9287	-16.331	-7.0938
20	1.3101	0.7623	-0.1809	0.4874	-0.0486	1.8506	0.1057	0.0329	0.3136	0.0189	-0.0629	0.2184	-0.1044	-0.244	-0.0428	0.0585	0.084	-0.0125	0.156	-0.0258	0.1593	-82.0234	-17.2023	-9.06
21	0.0448	-0.0996	-0.0928	0.7173	0.0813	0.2259	-0.0251	0.0015	-0.0252	0.0023	-0.0141	0.0816	0.087	-0.0041	0.0391	0.1221	-0.0288	-0.0017	0.1173	-0.0338	0.1223	-76.103	-28.6661	-1.1259
22	2.0077	-2.8793	-0.1858	6.0731	2.3271	2.2139	0.0676	-0.0222	-0.2401	0.0747	-0.0635	0.352	0.2023	-0.0333	-0.0041	0.0873	-0.0545	0.0387	0.1193	-0.0231	0.1465	-80.6986	-32.0896	3.8561
23	3.4366	-1.8716	-0.256	5.9587	-3.1843	2.2584	0.0786	-0.4025	-0.3254	0.4194	0.2401	0.7235	-0.3203	-0.0119	-0.3187	0.0914	0.0426	0.078	0.3196	-0.1709	0.3985	-87.532	-23.6533	8.9346
24	0.5218	0.2538	-0.116	0.7373	-0.3943	0.212	0.0547	-0.0661	0.02	0.0132	-0.0598	-0.0089	0.0017	0.03	0.0051	0.1625	0.0282	0.0025	0.1458	-0.0051	0.0548	-56.1228	-32.9232	12.6001
25	5.124	-0.927	-6.5567	3.5888	2.3702	8.8053	-0.2179	0.0818	-0.1827	0.1634	0.0112	0.0333	0.3294	-0.1041	0.2067	0.1459	0.0533	-0.0452	0.1077	0.0429	0.083	-52.8193	-40.6832	13.4213
26	2.688	1.6968	-4.1057	2.9933	1.6908	15.813	-0.2264	-0.5329	-0.3152	-0.0583	-0.3258	-0.1594	0.4508	0.896	0.5522	0.1647	0.1002	-0.0484	0.1716	0.0961	0.1677	-40.984	-40.5918	9.6236
27	1.5843	0.3118	-0.3235	0.6778	0.0639	0.2696	-0.0706	-0.049	0.0125	-0.0473	0.049	-0.0625	0.0454	-0.0201	0.0216	0.1189	0.0372	-0.0083	0.1093	-0.0097	0.0767	-50.0968	-30.2756	-2.7818
28	1.2219	-0.0767	0.9374	1.8671	0.0838	0.9802	-0.07	0.1307	0.0181	-0.0532	0.0497	-0.2344	0.1123	0.0993	0.0203	0.1265	0.0036	0.0328	0.1406	-0.0095	0.0597	-39.9692	-27.3774	-6.2603
29	2.1968	0.3835	0.0149	1.0129	-0.3017	0.6913	0.1108	-0.0399	0.0411	0.0772	-0.0922	-0.0079	-0.0096	0.0126	-0.0186	0.1281	0.0493	-0.0364	0.1088	-0.0154	0.0744	-41.9264	-21.515	5.2777
30	2.4125	0.6742	0.3167	2.2051	-0.3872	0.9413	0.0151	-0.2001	0.3557	0.1104	0.0083	0.0001	-0.0003	-0.0598	-0.0234	0.1108	0.0274	-0.0295	0.1135	-0.0723	0.0884	-47.2881	-16.1742	12.5371
31	0.4281	-0.0125	-0.044	1.4614	0.1564	1.661	0.0277	0.1261	-0.1071	-0.0892	0.0581	0.16	0.064	-0.0999	-0.0858	0.0742	0.0076	-0.0517	0.0604	0.0009	0.1239	-77.3658	-47.9883	-37.6611
32	0.4627	1.4148	-0.3969	4.4807	-1.8052	3.6048	-0.0007	0.0389	-0.0288	0.0473	0.0294	-0.0075	-0.0532	0.1748	-0.0287	0.1443	-0.006	0.0471	0.0887	-0.0431	0.1521	-67.3977	-62.4253	-12.6322
33	1.6008	-0.6179	0.4185	0.657	-0.3495	1.3759	0.0781	0.0544	-0.1302	-0.0363	-0.0224	0.1123	0.1385	0.0357	-0.0557	0.1548	-0.0391	0.0039	0.0504	-0.0161	0.1161	-68.0008	-67.8798	-19.2243
34	2.248	-0.4067	-0.1263	0.9172	-1.7118	3.6015	-0.0349	0.1426	-0.0471	0.0722	0.0024	-0.0091	-0.0615	-0.0145	0.0325	0.1783	0.0157	-0.0351	0.0788	-0.0262	0.0973	-55.6705	-63.457	-14.5391
35	0.7334	-0.4951	-0.0208	0.8598	-0.6466	1.6803	0.0042	-0.042	0.1264	0.0645	-0.0152	-0.1342	-0.0183	0.154	0.011	0.1514	0.0237	-0.0195	0.0963	0.0044	0.0624	-50.6242	-57.0703	-9.1164
36	0.543	-0.6101	-0.0355	1.3265	-0.7535	0.992	-0.0214	-0.0745	0.0937	-0.1731	-0.009	-0.1567	0.1939	0.0716	0.0305	0.1826	0.0334	-0.0106	0.1086	0.0245	0.0665	-60.3056	-51.6666	-3.3094
37	2.1374	-0.0936	0.3287	2.2109	0.283	0.1511	-0.1794	-0.0849	0.0539	0.0692	0.1064	0.304	0.0483	0.0658	0.073	0.1792	0.0445	0.0396	0.0971	0.0267	0.0525	-68.6894	-54.4203	-3.4781
38	2.9247	-3.244	0.1063	19.2132	-2.8147	1.5043	-0.1166	-0.3441	-0.0845	0.4091	0.0988	0.3939	0.0438	-0.0564	0.0178	0.1531	-0.0213	0.0633	0.1139	0.0114	0.0381	-68.307	-56.2693	2.2147
39	0.3393	-0.1567	0.107	0.1262	0.1057	0.5244	-0.0505	0.003	-0.1067	0.053	0.0103	0.0582	-0.0137	-0.0961	0.0402	0.1379	-0.0058	0.0196	0.1228	-0.0008	0.1496	-76.8529	-50.5452	-20.8141
40	2.0895	-1.0574	1.226	1.302	0.4291	2.202	-0.016	-0.1598	-0.1661	0.0738	0.0951	0.1323	0.0306	-0.1196	-0.079	0.1033	-0.0031	0.0122	0.1032	0.0204	0.1573	-82.7175	-42.9067	-21.7316
41	1.6018	0.1587	0.0184	1.2445	0.7099	0.4369	0.0925	-0.096	0.2598	0.0642	-0.0944	0.1236	-0.0113	-0.0824	0.0018	0.1109	0.0281	0.0547	0.1303	0.0324	0.1774	-82.7025	-34.9685	-24.0958
42	0.3776	-0.129	-0.104	0.4863	0.3793	0.9043	-0.0136	-0.0136	0.0669	-0.0035	-0.0283	0.0082	0.134	0.0367	0.0419	0.128	-0.0136	-0.0251	0.0941	-0.0032	0.1008	-65.8154	-36.3523	-26.9839
43	1.6563	1.1556	-0.0355	1.0146	-0.0405	0.0083	-0.1504	0.1927	0.1633	-0.0696	0.1681	0.0612	-0.0263	0.0128	-0.0177	0.1785	-0.0689	-0.0012	0.1185	-0.0143	0.1189	-64.9519	-31.4648	-35.6346
44	1.6754	-2.5266	0.4211	5.7244	-1.3944	4.5041	0.0858	0.1283	0.32	0.2231	0.1429	-0.2	0.2039	0.1267	-0.2287	0.1726	0.0611	-0.0192	0.1015	0.0426	0.1932	-64.8028	-45.8882	-32.3255
45	1.2237	0.5676	0.0265	0.4131	0.0129	0.4556	-0.0154	-0.0033	-0.2029	-0.1006	0.0357	-0.0586	0.0774	-0.0469	-0.0203	0.1291	-0.0028	-0.0235	0.1017	-0.0019	0.1174	-71.5349	-50.2267	-38.2703
46	8.2162	-0.2558	6.3397	2.0865	0.053	4.9392	0.1462	-0.0916	-0.2645	-0.0744	0.0381	0.0651	0.1416	-0.0399	-0.1843	0.1564	0.0694	-0.0159	0.1275	-0.0201	0.0356	-32.9694	-59.3849	-29.6267
47	1.3856	-0.7431	1.8663	0.5745	-1.2758	3.0024	0.083	0.0934	-0.0539	-0.0881	0.0068	-0.0037	0.1134	0.0633	-0.0898	0.1633	-0.0154	0.0359	0.1003	-0.0241	0.1334	-33.2078	-39.1408	-46.6153
48	1.2791	0.7771	1.0713	1.1367	0.3651	1.131	-0.0538	0.0874	-0.0724	-0.1114	0.0829	-0.0185	0.1092	0.0936	-0.0291	0.1435	0.0108	0.0465	0.1078	-0.0321	0.0924	-38.1588	-42.822	-55.6591
49	2.0452	0.8606	0.2843	0.6556	-0.4594	1.1991	-0.1217	0.0106	-0.139	-0.0539	0.0051	-0.1107	-0.0328	-0.0248	0.1167	0.1571	0.0307	0.0122	0.076	-0.0316	0.1025	-51.1069	-40.0007	-54.1288
50	0.2435	0.3629	-0.0218	1.282	-0.5737	0.4024	-0.0299	0.0032	-0.0078	-0.0162	0.0826	0.0526	0.0118	-0.0594	-0.0527	0.1444	-0.0079	-0.0113	0.111	-0.0084	0.0905	-51.6375	-29.5959	-48.232
51	0.7817	0.6796	0.8337	2.2186	0.3174	1.0606	-0.0578	0.0032	0.1239	-0.1515	0.0295	0.2196	-0.0006	-0.0336	0.0283	0.1152	0.0152	-0.0343	0.1241	0.0196	0.0985	-54.5383	-23.9596	-52.3247
52	0.6194	-0.0366	0.2401	0.7294	0.6908	0.7803	-0.0393	-0.0479	0.1436	-0.0134	0.0612	-0.0826	-0.0108	0.0248	-0.0218	0.1425	-0.0243	-0.0024	0.1015	0.0214	0.0935	-40.0191	-23.4621	-46.1887
53	0.8997	0.2845	-0.2706	1.2781	0.0001	0.7125	0.0093	0.084	0.2399	-0.1444	0.0765	-0.2025	-0.0428	0.2254	-0.0858	0.1551	-0.0466	0.0302	0.1142	0.0147	0.1295	-34.9243	-22.0106	-54.4542
54	0.0882	0.238	-0.2416	0.6534	-0.6146	1.3281	0.0072	0.007	-0.0387	-0.0036	0.0376	-0.1293	-0.0115	-0.0382	-0.0448	0.0977	0.0215	0.0004	0.1267	-0.0442	0.112	-25.5782	-39.2249	-33.8969
55	0.866	-0.1474	-1.9948	0.9584	-1.829	9.7114	-0.037	0.0767	0.1022	0.1112	-0.1426	-0.2337	-0.2023	0.1714	0.1796	0.0672	-0.0167	-0.0333	0.1001	-0.0474	0.1851	-18.3964	-38.5374	-28.2849
56	66.2672	-6.1271	-0.0733	0.5747	0.0056	0.0025	0.0357	-1.2283	-0.2822	-0.0292	0.0153	0.0293	0.0275	0.0025	-0.051	0.3361	0.0696	-0.1196	0.398	0.016	0.1782	-21.7714	-42.9018	-16.0658
57	0.304	0.1651	0.3467	1.6667	-1.2902	1.8626	-0.0011	-0.0799	0.0172	-0.0995	0.0326	-0.0288	0.0625	-0.0737	-0.0315	0.1192	0.0087	-0.0022	0.1337	-0.0842	0.1441	-37.3136	-36.3946	-24.2608
58	0.4653	-0.5784	-0.5174	1.9325	0.8336	0.9689	-0.0202	-0.0198	-0.0548	0.155	0.0104	0.1175	0.0136	-0.0672	0.0097	0.125	-0.0045	-0.002	0.1155	-0.0145	0.0795	-41.5872	-47.7912	-18.7846
59	1.3999	-0.4454	0.4753	0.3451	-0.53	0.8805	0.0496	-0.0613	0.0608	-0.0272	0.0427	0.0239	0.0183	-0.0459	-0.0923	0.1301	0.007	0.0028	0.0827	-0.0303	0.1232	-35.9273	-52.4365	-33.1465
60	23.4541	-6.632	4.3606	1.8885	-1.5115	16.7153	0.9036	1.461	-1.9081	-0.2784	-0.3963	0.5005	0.0559	0.6681	-0.5073	0.3314	0.0148	0.0107	0.1102	-0.164	0.3882	-36.2461	-61.8388	-36.1626

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 36
2	X-RAY DIFFRACTION	2	A	37 - 79
3	X-RAY DIFFRACTION	3	A	80 - 95
4	X-RAY DIFFRACTION	4	A	96 - 137
5	X-RAY DIFFRACTION	5	A	138 - 159
6	X-RAY DIFFRACTION	6	A	160 - 216
7	X-RAY DIFFRACTION	7	A	217 - 225
8	X-RAY DIFFRACTION	8	A	226 - 246
9	X-RAY DIFFRACTION	9	A	247 - 261
10	X-RAY DIFFRACTION	10	A	262 - 286
11	X-RAY DIFFRACTION	11	A	287 - 318
12	X-RAY DIFFRACTION	12	A	319 - 332
13	X-RAY DIFFRACTION	13	A	333 - 366
14	X-RAY DIFFRACTION	14	A	367 - 398
15	X-RAY DIFFRACTION	15	A	399 - 418
16	X-RAY DIFFRACTION	16	B	1 - 35
17	X-RAY DIFFRACTION	17	B	36 - 79
18	X-RAY DIFFRACTION	18	B	80 - 95
19	X-RAY DIFFRACTION	19	B	96 - 139
20	X-RAY DIFFRACTION	20	B	140 - 159
21	X-RAY DIFFRACTION	21	B	160 - 198
22	X-RAY DIFFRACTION	22	B	199 - 216
23	X-RAY DIFFRACTION	23	B	217 - 226
24	X-RAY DIFFRACTION	24	B	227 - 265
25	X-RAY DIFFRACTION	25	B	266 - 283
26	X-RAY DIFFRACTION	26	B	284 - 293
27	X-RAY DIFFRACTION	27	B	294 - 338
28	X-RAY DIFFRACTION	28	B	339 - 357
29	X-RAY DIFFRACTION	29	B	358 - 384
30	X-RAY DIFFRACTION	30	B	385 - 418
31	X-RAY DIFFRACTION	31	C	1 - 21
32	X-RAY DIFFRACTION	32	C	22 - 38
33	X-RAY DIFFRACTION	33	C	39 - 79
34	X-RAY DIFFRACTION	34	C	80 - 108
35	X-RAY DIFFRACTION	35	C	109 - 153
36	X-RAY DIFFRACTION	36	C	154 - 176
37	X-RAY DIFFRACTION	37	C	177 - 204
38	X-RAY DIFFRACTION	38	C	205 - 221
39	X-RAY DIFFRACTION	39	C	222 - 246
40	X-RAY DIFFRACTION	40	C	247 - 265
41	X-RAY DIFFRACTION	41	C	266 - 296
42	X-RAY DIFFRACTION	42	C	297 - 344
43	X-RAY DIFFRACTION	43	C	345 - 366
44	X-RAY DIFFRACTION	44	C	367 - 377
45	X-RAY DIFFRACTION	45	C	378 - 419
46	X-RAY DIFFRACTION	46	D	1 - 12
47	X-RAY DIFFRACTION	47	D	13 - 37
48	X-RAY DIFFRACTION	48	D	38 - 74
49	X-RAY DIFFRACTION	49	D	75 - 92
50	X-RAY DIFFRACTION	50	D	93 - 137
51	X-RAY DIFFRACTION	51	D	138 - 159
52	X-RAY DIFFRACTION	52	D	160 - 198
53	X-RAY DIFFRACTION	53	D	199 - 226
54	X-RAY DIFFRACTION	54	D	227 - 267
55	X-RAY DIFFRACTION	55	D	268 - 286
56	X-RAY DIFFRACTION	56	D	287 - 291
57	X-RAY DIFFRACTION	57	D	292 - 332
58	X-RAY DIFFRACTION	58	D	333 - 367
59	X-RAY DIFFRACTION	59	D	368 - 412
60	X-RAY DIFFRACTION	60	D	413 - 418

-
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

-
Protein , 1 types, 4 molecules ABCD

-
Non-polymers , 5 types, 309 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, 4 molecules ABCD

-Non-polymers , 5 types, 309 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, 4 molecules ABCD

-
Non-polymers , 5 types, 309 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