PDB-2j58: The structure of Wza

ID or keywords:

Entry

Database: PDB / ID: 2j58

Title

The structure of Wza

Components

OUTER MEMBRANE LIPOPROTEIN WZA

Keywords

MEMBRANE PROTEIN

Function / homology

Function and homology information

polysaccharide transmembrane transporter activity / porin activity / pore complex / monoatomic ion transport / cell outer membrane
Similarity search - Function

Biological species

ESCHERICHIA COLI (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.25 Å

Authors

Dong, C. / Naismith, J.H.

Citation

Journal: Nature / Year: 2006
Title: Wza the Translocon for E. Coli Capsular Polysaccharides Defines a New Class of Membrane Protein.
Authors: Dong, C. / Beis, K. / Nesper, J. / Brunkan-Lamontagne, A.L. / Clarke, B.R. / Whitfield, C. / Naismith, J.H.

History

Deposition	Sep 12, 2006	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 6, 2006	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Refinement description / Version format compliance

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	2j58.cif.gz	572.6 KB	Display	PDBx/mmCIF format
PDB format	pdb2j58.ent.gz	497 KB	Display	PDB format
PDBx/mmJSON format	2j58.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	2j58_validation.pdf.gz	535.5 KB	Display	wwPDB validaton report
Full document	2j58_full_validation.pdf.gz	598.3 KB	Display
Data in XML	2j58_validation.xml.gz	123 KB	Display
Data in CIF	2j58_validation.cif.gz	167.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/j5/2j58 ftp://data.pdbj.org/pub/pdb/validation_reports/j5/2j58	HTTPS FTP

-
Related structure data

Similar structure data	20953 6qnw-1 6qpf-1 2hv7-d 6qpf-2 6qpg-1 1pn0-d 6qpf-4 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#144 - Dec 2011 Complex I similarity (1) #152 - Aug 2012 cAMP-dependent Protein Kinase similarity (1) #191 - Nov 2015 Glutamate-gated Chloride Receptors similarity (1) #261 - Sep 2021 DNA-Sequencing Nanopores similarity (1) #22 - Oct 2001 Photosystem I similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #29 - May 2002 Penicillin-binding Proteins similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#144 - Dec 2011
Complex I
similarity (1)
#152 - Aug 2012
cAMP-dependent Protein Kinase
similarity (1)
#191 - Nov 2015
Glutamate-gated Chloride Receptors
similarity (1)
#261 - Sep 2021
DNA-Sequencing Nanopores
similarity (1)
#22 - Oct 2001
Photosystem I
similarity (1)
#262 - Oct 2021
Fifty Years of Open Access to PDB Structures
similarity (1)
#29 - May 2002
Penicillin-binding Proteins
similarity (1)
#95 - Nov 2007
Multidrug Resistance Transporters
similarity (1)

Deposited unit

A: OUTER MEMBRANE LIPOPROTEIN WZA

B: OUTER MEMBRANE LIPOPROTEIN WZA

C: OUTER MEMBRANE LIPOPROTEIN WZA

D: OUTER MEMBRANE LIPOPROTEIN WZA

E: OUTER MEMBRANE LIPOPROTEIN WZA

F: OUTER MEMBRANE LIPOPROTEIN WZA

G: OUTER MEMBRANE LIPOPROTEIN WZA

H: OUTER MEMBRANE LIPOPROTEIN WZA

hetero molecules

324 kDa, 8 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)	94.719, 215.268, 220.892
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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	2	A	89 - 169
2	1	1	2	B	89 - 169
3	1	1	2	C	89 - 169
4	1	1	2	D	89 - 169
5	1	1	2	E	89 - 169
6	1	1	2	F	89 - 169
7	1	1	2	G	89 - 169
8	1	1	2	H	89 - 169
1	1	2	2	A	172 - 249
2	1	2	2	B	172 - 249
3	1	2	2	C	172 - 249
4	1	2	2	D	172 - 249
5	1	2	2	E	172 - 249
6	1	2	2	F	172 - 249
7	1	2	2	G	172 - 249
8	1	2	2	H	172 - 249
1	1	3	2	A	256 - 342
2	1	3	2	B	256 - 342
3	1	3	2	C	256 - 342
4	1	3	2	D	256 - 342
5	1	3	2	E	256 - 342
6	1	3	2	F	256 - 342
7	1	3	2	G	256 - 342
8	1	3	2	H	256 - 342
1	1	4	2	A	346 - 373
2	1	4	2	B	346 - 373
3	1	4	2	C	346 - 373
4	1	4	2	D	346 - 373
5	1	4	2	E	346 - 373
6	1	4	2	F	346 - 373
7	1	4	2	G	346 - 373
8	1	4	2	H	346 - 373

NCS ensembles :

ID
1
2
3
4

#1: Protein	OUTER MEMBRANE LIPOPROTEIN WZA / WZA Mass: 40100.812 Da / Num. of mol.: 8 / Fragment: MATURE PROTEIN, RESIDUES 21-379 Source method: isolated from a genetically manipulated source Details: ACYLATED AT CYS 21 SELENOMETHIONINE DERIVATIVE. / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: O9A\:K30 / Plasmid: PWQ126 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): LE392 / References: UniProt: Q9X4B7
#2: Chemical	ChemComp-OCT / N-OCTANE Mass: 114.229 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₈H₁₈
#3: Chemical	ChemComp-HEX / HEXANE Mass: 86.175 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₆H₁₄
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1634 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	THE MATURE PROTEIN IS CLEAVED AND ACYLATED AT RESIDUE 21 (CYS). THE PROTEIN IS ALSO CLEAVED IN THE ...THE MATURE PROTEIN IS CLEAVED AND ACYLATED AT RESIDUE 21 (CYS). THE PROTEIN IS ALSO CLEAVED IN THE EXPRESSION STRAIN.

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.39 Å³/Da / Density % sol: 63.41 %

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979
Detector	Type: ADSC CCD / Detector: CCD / Date: Nov 19, 2005
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 2.26→108 Å / Num. obs: 200359 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 5 % / R_merge(I) obs: 0.08 / Net I/σ(I): 18.4
Reflection shell	Resolution: 2.26→2.32 Å / Redundancy: 2.6 % / R_merge(I) obs: 0.35 / Mean I/σ(I) obs: 1.8 / % possible all: 94.9

-
Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
MOSFLM		data reduction
SCALA		data scaling
SHELX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.25→107.83 Å / Cor.coef. F_o:F_c: 0.943 / Cor.coef. F_o:F_c free: 0.923 / SU B: 9.911 / SU ML: 0.131 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.226	10587	5 %	RANDOM
R_work	0.188	-	-	-
obs	0.19	200359	99.2 %	-

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: 36.1 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.46 Å²	0 Å²	0 Å²
2-	-	0.09 Å²	0 Å²
3-	-	-	0.37 Å²

Refinement step

Cycle: LAST / Resolution: 2.25→107.83 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	22040	0	192	1634	23866

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.022	22584
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.292	1.97	30688
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.194	5	2832
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.975	24.918	976
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.887	15	3808
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.923	15	128
X-RAY DIFFRACTION	r_chiral_restr	0.085	0.2	3576
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	16808
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.233	0.3	10758
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.325	0.5	15411
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.194	0.5	3161
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	0.24	0.3	40
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.259	0.5	11
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	1.17	1.5	14406
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.165	2	22992
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	2.282	3	9123
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	3.245	4.5	7696
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

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	324	tight positional	0.03	0.05
1	2	B	324	tight positional	0.03	0.05
1	3	C	324	tight positional	0.03	0.05
1	4	D	324	tight positional	0.03	0.05
1	5	E	324	tight positional	0.03	0.05
1	6	F	324	tight positional	0.03	0.05
1	7	G	324	tight positional	0.03	0.05
1	8	H	324	tight positional	0.04	0.05
2	1	A	312	tight positional	0.03	0.05
2	2	B	312	tight positional	0.03	0.05
2	3	C	312	tight positional	0.04	0.05
2	4	D	312	tight positional	0.03	0.05
2	5	E	312	tight positional	0.04	0.05
2	6	F	312	tight positional	0.04	0.05
2	7	G	312	tight positional	0.04	0.05
2	8	H	312	tight positional	0.04	0.05
3	1	A	348	tight positional	0.04	0.05
3	2	B	348	tight positional	0.04	0.05
3	3	C	348	tight positional	0.04	0.05
3	4	D	348	tight positional	0.05	0.05
3	5	E	348	tight positional	0.04	0.05
3	6	F	348	tight positional	0.04	0.05
3	7	G	348	tight positional	0.05	0.05
3	8	H	348	tight positional	0.04	0.05
4	1	A	112	tight positional	0.04	0.05
4	2	B	112	tight positional	0.03	0.05
4	3	C	112	tight positional	0.04	0.05
4	4	D	112	tight positional	0.03	0.05
4	5	E	112	tight positional	0.04	0.05
4	6	F	112	tight positional	0.04	0.05
4	7	G	112	tight positional	0.04	0.05
4	8	H	112	tight positional	0.04	0.05
1	1	A	304	medium positional	0.45	0.5
1	2	B	304	medium positional	0.42	0.5
1	3	C	304	medium positional	0.55	0.5
1	4	D	304	medium positional	0.43	0.5
1	5	E	304	medium positional	0.44	0.5
1	6	F	304	medium positional	0.47	0.5
1	7	G	304	medium positional	0.37	0.5
1	8	H	304	medium positional	0.45	0.5
2	1	A	279	medium positional	0.35	0.5
2	2	B	279	medium positional	0.45	0.5
2	3	C	279	medium positional	0.41	0.5
2	4	D	279	medium positional	0.36	0.5
2	5	E	279	medium positional	0.51	0.5
2	6	F	279	medium positional	0.48	0.5
2	7	G	279	medium positional	0.37	0.5
2	8	H	279	medium positional	0.44	0.5
3	1	A	311	medium positional	0.27	0.5
3	2	B	311	medium positional	0.51	0.5
3	3	C	311	medium positional	0.38	0.5
3	4	D	311	medium positional	0.44	0.5
3	5	E	311	medium positional	0.52	0.5
3	6	F	311	medium positional	0.33	0.5
3	7	G	311	medium positional	0.52	0.5
3	8	H	311	medium positional	0.41	0.5
4	1	A	117	medium positional	0.48	0.5
4	2	B	117	medium positional	0.21	0.5
4	3	C	117	medium positional	0.35	0.5
4	4	D	117	medium positional	0.28	0.5
4	5	E	117	medium positional	0.45	0.5
4	6	F	117	medium positional	0.22	0.5
4	7	G	117	medium positional	0.32	0.5
4	8	H	117	medium positional	0.34	0.5
1	1	A	324	tight thermal	0.08	0.5
1	2	B	324	tight thermal	0.07	0.5
1	3	C	324	tight thermal	0.08	0.5
1	4	D	324	tight thermal	0.07	0.5
1	5	E	324	tight thermal	0.08	0.5
1	6	F	324	tight thermal	0.08	0.5
1	7	G	324	tight thermal	0.07	0.5
1	8	H	324	tight thermal	0.09	0.5
2	1	A	312	tight thermal	0.09	0.5
2	2	B	312	tight thermal	0.09	0.5
2	3	C	312	tight thermal	0.11	0.5
2	4	D	312	tight thermal	0.09	0.5
2	5	E	312	tight thermal	0.1	0.5
2	6	F	312	tight thermal	0.11	0.5
2	7	G	312	tight thermal	0.11	0.5
2	8	H	312	tight thermal	0.11	0.5
3	1	A	348	tight thermal	0.12	0.5
3	2	B	348	tight thermal	0.12	0.5
3	3	C	348	tight thermal	0.13	0.5
3	4	D	348	tight thermal	0.11	0.5
3	5	E	348	tight thermal	0.12	0.5
3	6	F	348	tight thermal	0.13	0.5
3	7	G	348	tight thermal	0.13	0.5
3	8	H	348	tight thermal	0.12	0.5
4	1	A	112	tight thermal	0.08	0.5
4	2	B	112	tight thermal	0.09	0.5
4	3	C	112	tight thermal	0.08	0.5
4	4	D	112	tight thermal	0.08	0.5
4	5	E	112	tight thermal	0.07	0.5
4	6	F	112	tight thermal	0.08	0.5
4	7	G	112	tight thermal	0.09	0.5
4	8	H	112	tight thermal	0.08	0.5
1	1	A	304	medium thermal	0.53	2
1	2	B	304	medium thermal	0.55	2
1	3	C	304	medium thermal	0.64	2
1	4	D	304	medium thermal	0.44	2
1	5	E	304	medium thermal	0.51	2
1	6	F	304	medium thermal	0.52	2
1	7	G	304	medium thermal	0.53	2
1	8	H	304	medium thermal	0.54	2
2	1	A	279	medium thermal	0.68	2
2	2	B	279	medium thermal	0.63	2
2	3	C	279	medium thermal	0.71	2
2	4	D	279	medium thermal	0.65	2
2	5	E	279	medium thermal	0.66	2
2	6	F	279	medium thermal	0.8	2
2	7	G	279	medium thermal	0.69	2
2	8	H	279	medium thermal	0.71	2
3	1	A	311	medium thermal	0.7	2
3	2	B	311	medium thermal	0.79	2
3	3	C	311	medium thermal	0.79	2
3	4	D	311	medium thermal	0.74	2
3	5	E	311	medium thermal	0.82	2
3	6	F	311	medium thermal	0.77	2
3	7	G	311	medium thermal	0.87	2
3	8	H	311	medium thermal	0.84	2
4	1	A	117	medium thermal	0.51	2
4	2	B	117	medium thermal	0.54	2
4	3	C	117	medium thermal	0.74	2
4	4	D	117	medium thermal	0.53	2
4	5	E	117	medium thermal	0.66	2
4	6	F	117	medium thermal	0.49	2
4	7	G	117	medium thermal	0.56	2
4	8	H	117	medium thermal	0.52	2

LS refinement shell

Resolution: 2.25→2.31 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.335	701	-
R_work	0.25	13871	-
obs	-	-	94.82 %

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	1.6643	-0.0779	0.056	0.6811	-0.2459	0.1737	0.0007	-0.2006	0.5094	0.1103	0.0188	-0.0469	-0.1149	-0.0093	-0.0195	-0.0493	-0.0039	0.0103	-0.1514	-0.1112	0.0713	59.875	114.699	31.156
2	1.3625	-0.2482	-0.3358	0.9193	0.1321	0.5173	0.0319	-0.084	0.3134	0.0346	0.0084	-0.1615	-0.0753	0.0803	-0.0402	-0.1129	-0.0217	0.0015	-0.1669	-0.018	-0.0389	75.902	103.049	21.993
3	1.6712	-0.0629	-0.0537	0.1378	0.0225	0.7224	0.0151	0.2807	-0.1464	-0.0941	-0.0103	0.0182	0.0925	-0.0365	-0.0048	-0.0687	0.0032	-0.0011	-0.1038	-0.0305	-0.1832	40.145	72.435	-2.097
4	1.1245	0.0328	0.48	0.8571	0.0648	0.5289	-0.0194	-0.149	0.4123	0.0683	0.0266	0.059	-0.1093	-0.1242	-0.0071	-0.0824	0.0076	0.0322	-0.1485	-0.0871	0.0545	38.05	114.077	30.473
5	0.9241	-0.0532	0.2237	0.6643	0.2655	0.3743	-0.0011	-0.0242	0.2748	-0.0158	0.0326	0.0938	-0.0293	-0.0777	-0.0316	-0.1087	0.0031	0.0193	-0.1482	-0.0012	-0.058	23.241	101.423	20.402
6	1.1316	-0.3916	-0.2654	0.6527	0.13	0.9869	-0.0092	0.1466	0.0071	-0.0578	-0.0261	0.1231	0.0534	-0.1035	0.0352	-0.1202	-0.0082	-0.0186	-0.1342	0.006	-0.1514	24.132	84.158	7.001
7	0.9551	0.3743	-0.0123	0.596	0.2298	0.4584	-0.0017	0.1424	0.0843	-0.011	-0.008	-0.152	0.0039	0.0464	0.0097	-0.1062	0.004	0.0203	-0.132	0.0065	-0.1419	76.778	85.941	8.414
8	1.6675	0.6836	0.0614	0.7832	0.011	0.6699	-0.0075	0.2572	-0.1334	-0.0749	0.0109	-0.126	0.0722	0.0728	-0.0033	-0.097	0.0149	0.0261	-0.102	-0.0364	-0.1777	61.974	73.165	-1.535
9	1	0.0831	-0.6485	2.0315	-1.4941	3.1159	0.0117	-0.4758	0.2349	0.2632	-0.0902	-0.213	-0.3419	0.1063	0.0786	0.0304	-0.0418	-0.0569	0.0926	-0.1197	-0.1162	63.261	91.526	59.893
10	1.3295	-0.6012	-0.1936	3.1871	-0.6803	1.7597	0.0169	-0.702	-0.2198	0.3514	0.0136	-0.0409	-0.0547	0.0314	-0.0304	0.1829	-0.0842	-0.0359	0.5367	0.0369	-0.1951	53.404	71.177	83.793
11	0.6949	0.3699	0.1307	1.3996	-1.4174	3.9211	-0.0491	-0.1941	0.0255	0.0905	-0.1962	-0.3537	-0.0716	0.3649	0.2452	-0.0687	-0.0197	-0.0505	-0.0137	0.0298	-0.0969	78.085	77.977	49.298
12	1.0163	0.3381	-0.5415	3.9468	-0.9998	1.8854	-0.0248	-0.5827	-0.2506	0.4235	0.0233	-0.1198	0.0704	0.0213	0.0015	0.1117	-0.0545	-0.1058	0.3862	0.1388	-0.1267	70.249	63.271	77.668
13	1.7904	-0.4088	0.6504	1.8489	-1.2398	2.3358	0.0012	0.0122	-0.2417	-0.2561	0.0246	0.0554	0.1975	-0.1744	-0.0259	-0.0622	-0.0299	-0.0064	-0.1918	0.041	-0.1099	36.488	50.006	27.114
14	2.2958	-0.711	0.1019	0.9325	-0.6243	2.008	0.0807	-0.5009	-0.4478	0.0884	-0.0337	0.0885	-0.0443	-0.012	-0.0471	-0.0203	-0.0448	-0.0327	-0.0372	0.2645	0.1227	46.179	31.512	52.551
15	1.3755	0.2892	-1.0123	2.1945	-1.904	2.7895	0.1214	-0.4057	0.3178	0.4162	-0.0638	-0.024	-0.4186	-0.0388	-0.0575	0.0605	-0.0265	0.0187	0.1116	-0.1343	-0.1419	40.59	92.956	60.893
16	2.0054	-0.6986	0.9687	3.2196	-1.2722	1.0345	0.0251	-0.7453	-0.1215	0.3662	0.0113	-0.0336	-0.0334	-0.0574	-0.0364	0.1595	-0.0668	0.0822	0.487	0.0737	-0.1805	34.432	67.472	80.758
17	1.423	0.4107	-0.2554	2.893	-2.2262	1.8931	0.0184	-0.2758	0.257	0.2894	0.1149	0.293	-0.2479	-0.2785	-0.1334	-0.0118	-0.0018	0.0666	0.0499	-0.0487	-0.1705	23.363	81.411	51.707
18	1.7153	-0.8091	1.2788	2.1987	-1.1776	2.5443	0.0429	-0.6783	-0.1566	0.3191	0.0456	-0.0102	0.033	-0.0351	-0.0884	0.0464	-0.044	0.0908	0.315	0.1763	-0.0839	24.463	54.292	70.367
19	0.8913	0.0077	0.3604	2.6886	-1.8412	2.2163	-0.0488	-0.1453	-0.0777	0.0213	0.241	0.3206	-0.0765	-0.3362	-0.1922	-0.1027	-0.0155	0.0342	-0.0906	0.0585	-0.136	21.713	63.542	37.698
20	1.5849	-0.4039	-0.1018	1.8519	-0.7951	3.6617	0.0378	-0.5691	-0.3433	0.2739	0.0012	0.1352	-0.0041	0.0286	-0.0389	-0.0347	-0.0464	0.0254	0.0708	0.2561	0.041	29.33	39.416	58.666
21	1.6654	-0.3679	0.8255	1.3748	-1.8734	3.4636	0.045	-0.004	-0.1906	-0.2093	-0.2104	-0.3434	0.3035	0.2299	0.1654	-0.0566	0.0144	0.005	-0.1564	0.0753	-0.0436	76.436	60.216	35.308
22	1.3136	0.7572	-0.1784	2.1972	-0.833	2.4676	0.1123	-0.4834	-0.411	0.2829	-0.0966	-0.1344	0.0739	-0.0723	-0.0158	0.0148	-0.0487	-0.1228	0.1948	0.259	0.0335	75.147	48.382	65.97
23	1.355	-0.4649	0.6654	1.9032	-1.8463	3.1028	0.0928	0.073	-0.3628	-0.3596	-0.0572	-0.046	0.3565	-0.0234	-0.0357	-0.0399	0.0032	0.009	-0.2106	0.0195	-0.0544	59.222	48.553	26.125
24	2.6206	0.9019	-0.4013	1.0475	-0.4828	3.1213	0.1064	-0.4786	-0.4279	0.2067	-0.1053	-0.1479	0.12	-0.1109	-0.0012	-0.0163	-0.0319	-0.0489	0.011	0.2664	0.1047	65.155	35.182	55.512
25	14.624	-4.9348	22.6616	5.0337	-13.4623	47.1447	-0.2371	0.1376	0.5855	-0.9066	0.1548	0.1952	0.9095	-0.6232	0.0823	0.1932	0.0169	-0.0068	-0.0061	0.2752	0.3076	41.345	124.001	-6.422
26	18.9645	-17.0957	18.5114	22.9696	-23.9313	26.2445	0.1634	0.2616	0.4155	-0.4635	0.1519	0.4895	0.2232	-0.4813	-0.3153	0.0985	0.0108	0.0237	0.0218	0.2401	0.3348	51.674	126.57	-4.61
27	15.2257	18.8386	-8.6072	51.4484	-27.3338	16.4249	-0.5827	0.9277	0.4711	0.3634	0.7549	-0.4912	-0.9294	0.0375	-0.1722	0.2005	-0.0431	0.0134	0.2558	0.1978	-0.0222	58.789	106.589	-19.99
28	0.1928	0.4314	-1.1423	2.2562	-7.9402	70.3745	-0.2561	0.3436	0.073	-0.5038	-0.5903	-0.0686	-0.2247	0.3664	0.8464	0.1392	0.046	-0.0357	0.1156	0.2436	0.3008	36.166	116.669	-12.241
29	13.3885	6.3606	-22.457	4.884	-15.0986	55.4958	0.497	0.7578	0.3203	-0.1593	-0.2264	-0.0618	-0.03	0.187	-0.2705	0.1205	0.0413	-0.048	0.1591	0.274	0.1073	39.187	108.463	-18.675
30	17.1628	14.7968	-18.9249	17.3085	-20.2361	26.9583	0.0314	1.0465	0.1851	0.0998	0.1258	-0.181	-0.4122	-0.0119	-0.1572	0.0828	0.0249	-0.0202	0.2499	0.2175	0.0119	48.464	104.303	-22.012
31	7.815	-16.6412	8.0509	49.6282	-24.2679	12.5808	0.3186	0.1233	0.6592	-0.5375	-0.0431	-0.2344	-0.002	-0.1455	-0.2755	0.1394	-0.0228	0.0289	0.0562	0.2483	0.2775	61.048	122.301	-7.666
32	0.2192	-0.7955	-0.5514	57.5537	-15.6298	7.073	-0.0873	0.1984	0.4715	-0.4141	0.6073	-0.2164	-0.3992	-0.368	-0.52	0.105	-0.0009	0.0517	0.2193	0.2942	0.1817	64.124	114.077	-14.052

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	21 - 64
2	X-RAY DIFFRACTION	1	A	252 - 354
3	X-RAY DIFFRACTION	2	B	21 - 64
4	X-RAY DIFFRACTION	2	B	252 - 354
5	X-RAY DIFFRACTION	3	C	21 - 64
6	X-RAY DIFFRACTION	3	C	252 - 354
7	X-RAY DIFFRACTION	4	D	21 - 64
8	X-RAY DIFFRACTION	4	D	252 - 354
9	X-RAY DIFFRACTION	5	E	21 - 64
10	X-RAY DIFFRACTION	5	E	252 - 354
11	X-RAY DIFFRACTION	6	F	21 - 64
12	X-RAY DIFFRACTION	6	F	252 - 354
13	X-RAY DIFFRACTION	7	G	21 - 64
14	X-RAY DIFFRACTION	7	G	252 - 354
15	X-RAY DIFFRACTION	8	H	21 - 64
16	X-RAY DIFFRACTION	8	H	252 - 354
17	X-RAY DIFFRACTION	9	A	65 - 85
18	X-RAY DIFFRACTION	9	A	168 - 251
19	X-RAY DIFFRACTION	10	A	86 - 167
20	X-RAY DIFFRACTION	11	B	65 - 85
21	X-RAY DIFFRACTION	11	B	168 - 251
22	X-RAY DIFFRACTION	12	B	86 - 167
23	X-RAY DIFFRACTION	13	C	65 - 85
24	X-RAY DIFFRACTION	13	C	168 - 251
25	X-RAY DIFFRACTION	14	C	86 - 167
26	X-RAY DIFFRACTION	15	D	65 - 85
27	X-RAY DIFFRACTION	15	D	168 - 251
28	X-RAY DIFFRACTION	16	D	86 - 167
29	X-RAY DIFFRACTION	17	E	65 - 85
30	X-RAY DIFFRACTION	17	E	168 - 251
31	X-RAY DIFFRACTION	18	E	86 - 167
32	X-RAY DIFFRACTION	19	F	65 - 85
33	X-RAY DIFFRACTION	19	F	168 - 251
34	X-RAY DIFFRACTION	20	F	86 - 167
35	X-RAY DIFFRACTION	21	G	65 - 85
36	X-RAY DIFFRACTION	21	G	168 - 251
37	X-RAY DIFFRACTION	22	G	86 - 167
38	X-RAY DIFFRACTION	23	H	65 - 85
39	X-RAY DIFFRACTION	23	H	168 - 251
40	X-RAY DIFFRACTION	24	H	86 - 167
41	X-RAY DIFFRACTION	25	A	355 - 376
42	X-RAY DIFFRACTION	26	B	355 - 376
43	X-RAY DIFFRACTION	27	C	355 - 376
44	X-RAY DIFFRACTION	28	D	355 - 376
45	X-RAY DIFFRACTION	29	E	355 - 376
46	X-RAY DIFFRACTION	30	F	355 - 376
47	X-RAY DIFFRACTION	31	G	355 - 376
48	X-RAY DIFFRACTION	32	H	355 - 376

-
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