PDB-2rce: DFP modified DegS delta PDZ

ID or keywords:

Entry

Database: PDB / ID: 2rce

Title

DFP modified DegS delta PDZ

Components

Protease degS

Keywords

HYDROLASE / dfp modified active site serine /

Protease /

Serine protease

Function / homology

Function and homology information

peptidase Do / cellular response to misfolded protein / serine-type peptidase activity / outer membrane-bounded periplasmic space /

peptidase activity / serine-type endopeptidase activity /

proteolysis / identical protein binding /

plasma membrane
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.35 Å

Authors

Sohn, J. / Grant, R.A. / Sauer, R.T.

Citation

Journal: To be Published
Title: DFP modified DegS delta PDZ
Authors: Sohn, J. / Grant, R.A. / Sauer, R.T.

History

Deposition	Sep 19, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 11, 2007	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Refinement description / Version format compliance
Revision 1.2	Oct 25, 2017	Group: Refinement description / Category: software

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	2rce.cif.gz	359.9 KB	Display	PDBx/mmCIF format
PDB format	pdb2rce.ent.gz	304.3 KB	Display	PDB format
PDBx/mmJSON format	2rce.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rc/2rce ftp://data.pdbj.org/pub/pdb/validation_reports/rc/2rce	HTTPS FTP

-
Related structure data

Related structure data	2qf0 2qf3 2qgr
Similar structure data	3lh3-1 3lh3-2 3lgv-1 1dc1-d 2qf0-2 4l39-1 3q3i-1 5aij-d 2cg2-d 3eh2-2 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

Related structure data

2qf0

2qf3

2qgr

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#232 - Apr 2019 Proteins and Biominerals similarity (1)

Deposited unit

A: Protease degS

B: Protease degS

C: Protease degS

D: Protease degS

E: Protease degS

F: Protease degS

G: Protease degS

H: Protease degS

I: Protease degS

236 kDa, 9 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Protease degS

B: Protease degS

C: Protease degS

defined by author&software
78.8 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: Protease degS

E: Protease degS

F: Protease degS

defined by author&software
78.8 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

G: Protease degS

H: Protease degS

I: Protease degS

defined by author&software
78.8 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	71.531, 132.745, 231.200
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	Beg label comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	PRO	TYR	2	A	A	44 - 62	31 - 49
2	1	1	PRO	TYR	2	B	B	44 - 62	31 - 49
3	1	1	PRO	TYR	2	C	C	44 - 62	31 - 49
4	1	1	PRO	TYR	2	D	D	44 - 62	31 - 49
5	1	1	PRO	TYR	2	E	E	44 - 62	31 - 49
6	1	1	PRO	TYR	2	F	F	44 - 62	31 - 49
7	1	1	PRO	TYR	2	H	H	44 - 62	31 - 49
8	1	1	PRO	TYR	2	I	I	44 - 62	31 - 49
9	2	1	THR	ASP	2	A	A	78 - 86	65 - 73
10	2	1	THR	ASP	2	B	B	78 - 86	65 - 73
11	2	1	THR	ASP	2	C	C	78 - 86	65 - 73
12	2	1	THR	ASP	2	D	D	78 - 86	65 - 73
13	2	1	THR	ASP	2	E	E	78 - 86	65 - 73
14	2	1	THR	ASP	2	F	F	78 - 86	65 - 73
15	2	1	THR	ASP	2	H	H	78 - 86	65 - 73
16	2	1	THR	ASP	2	I	I	78 - 86	65 - 73
17	3	1	ILE	THR	2	A	A	91 - 93	78 - 80
18	3	1	ILE	THR	2	B	B	91 - 93	78 - 80
19	3	1	ILE	THR	2	C	C	91 - 93	78 - 80
20	3	1	ILE	THR	2	D	D	91 - 93	78 - 80
21	3	1	ILE	THR	2	E	E	91 - 93	78 - 80
22	3	1	ILE	THR	2	F	F	91 - 93	78 - 80
23	3	1	ILE	THR	2	H	H	91 - 93	78 - 80
24	3	1	ILE	THR	2	I	I	91 - 93	78 - 80
25	4	1	GLN	ILE	2	A	A	103 - 132	90 - 119
26	4	1	GLN	ILE	2	B	B	103 - 132	90 - 119
27	4	1	GLN	ILE	2	C	C	103 - 132	90 - 119
28	4	1	GLN	ILE	2	D	D	103 - 132	90 - 119
29	4	1	GLN	ILE	2	E	E	103 - 132	90 - 119
30	4	1	GLN	ILE	2	F	F	103 - 132	90 - 119
31	4	1	GLN	ILE	2	H	H	103 - 132	90 - 119
32	4	1	GLN	ILE	2	I	I	103 - 132	90 - 119
33	5	1	LEU	SER	2	A	A	138 - 174	125 - 161
34	5	1	LEU	SER	2	B	B	138 - 174	125 - 161
35	5	1	LEU	SER	2	C	C	138 - 174	125 - 161
36	5	1	LEU	SER	2	D	D	138 - 174	125 - 161
37	5	1	LEU	SER	2	E	E	138 - 174	125 - 161
38	5	1	LEU	SER	2	F	F	138 - 174	125 - 161
39	5	1	LEU	SER	2	H	H	138 - 174	125 - 161
40	5	1	LEU	SER	2	I	I	138 - 174	125 - 161
41	6	1	GLN	SER	2	A	A	191 - 219	178 - 206
42	6	1	GLN	SER	2	B	B	191 - 219	178 - 206
43	6	1	GLN	SER	2	C	C	191 - 219	178 - 206
44	6	1	GLN	SER	2	D	D	191 - 219	178 - 206
45	6	1	GLN	SER	2	E	E	191 - 219	178 - 206
46	6	1	GLN	SER	2	F	F	191 - 219	178 - 206
47	6	1	GLN	SER	2	H	H	191 - 219	178 - 206
48	6	1	GLN	SER	2	I	I	191 - 219	178 - 206
49	7	1	PRO	PHE	2	A	A	229 - 238	216 - 225
50	7	1	PRO	PHE	2	B	B	229 - 238	216 - 225
51	7	1	PRO	PHE	2	C	C	229 - 238	216 - 225
52	7	1	PRO	PHE	2	D	D	229 - 238	216 - 225
53	7	1	PRO	PHE	2	E	E	229 - 238	216 - 225
54	7	1	PRO	PHE	2	F	F	229 - 238	216 - 225
55	7	1	PRO	PHE	2	H	H	229 - 238	216 - 225
56	7	1	PRO	PHE	2	I	I	229 - 238	216 - 225
1	1	2	GLN	TYR	5	A	A	87 - 90	74 - 77
2	1	2	GLN	TYR	5	B	B	87 - 90	74 - 77
3	1	2	GLN	TYR	5	C	C	87 - 90	74 - 77
4	1	2	GLN	TYR	5	D	D	87 - 90	74 - 77
5	1	2	GLN	TYR	5	E	E	87 - 90	74 - 77
6	1	2	GLN	TYR	5	F	F	87 - 90	74 - 77
7	1	2	GLN	TYR	5	G	G	87 - 90	74 - 77
8	1	2	GLN	TYR	5	H	H	87 - 90	74 - 77
9	1	2	GLN	TYR	5	I	I	87 - 90	74 - 77
10	2	2	ASN	ASP	5	A	A	94 - 102	81 - 89
11	2	2	ASN	ASP	5	B	B	94 - 102	81 - 89
12	2	2	ASN	ASP	5	C	C	94 - 102	81 - 89
13	2	2	ASN	ASP	5	D	D	94 - 102	81 - 89
14	2	2	ASN	ASP	5	E	E	94 - 102	81 - 89
15	2	2	ASN	ASP	5	F	F	94 - 102	81 - 89
16	2	2	ASN	ASP	5	G	G	94 - 102	81 - 89
17	2	2	ASN	ASP	5	H	H	94 - 102	81 - 89
18	2	2	ASN	ASP	5	I	I	94 - 102	81 - 89
19	3	2	GLN	ILE	5	A	A	239 - 249	226 - 236
20	3	2	GLN	ILE	5	B	B	239 - 249	226 - 236
21	3	2	GLN	ILE	5	C	C	239 - 249	226 - 236
22	3	2	GLN	ILE	5	D	D	239 - 249	226 - 236
23	3	2	GLN	ILE	5	E	E	239 - 249	226 - 236
24	3	2	GLN	ILE	5	F	F	239 - 249	226 - 236
25	3	2	GLN	ILE	5	G	G	239 - 249	226 - 236
26	3	2	GLN	ILE	5	H	H	239 - 249	226 - 236
27	3	2	GLN	ILE	5	I	I	239 - 249	226 - 236
1	1	3	ALA	LEU	5	B	B	175 - 190	162 - 177
2	1	3	ALA	LEU	5	C	C	175 - 190	162 - 177
3	1	3	ALA	LEU	5	F	F	175 - 190	162 - 177
4	1	3	ALA	LEU	5	G	G	175 - 190	162 - 177
5	1	3	ALA	LEU	5	H	H	175 - 190	162 - 177

NCS ensembles :

ID
1
2
3

Details

Trimers consisting of chains ABC, DEF, and GHI are the biological assembly

#1: Protein	Protease degS Mass: 26256.508 Da / Num. of mol.: 9 / Fragment: RESIDUES 27-256 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: degS, hhoB, htrH / Production host: Escherichia coli (E. coli) References: UniProt: P0AEE3, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 679 / 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: 2.32 Å³/Da / Density % sol: 47.04 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 50 MM NA CACODYLATE PH 6.5, 100 MM NA CITRATE, 20% ISOPROPANOL, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97949 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 5, 2007
Radiation	Monochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97949 Å / Relative weight: 1
Reflection	Resolution: 2.35→50 Å / Num. obs: 90170 / % possible obs: 97.6 % / Redundancy: 6.4 % / R_merge(I) obs: 0.07 / Net I/σ(I): 8.9
Reflection shell	Resolution: 2.35→2.43 Å / Redundancy: 5.5 % / R_merge(I) obs: 0.401 / % possible all: 97.2

-
Phasing

Phasing	Method: molecular replacement

-
Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHASER		phasing
REFMAC	5.2.0019	refinement
PDB_EXTRACT	3	data extraction
ADSC	Quantum	data collection

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.35→37.22 Å / Cor.coef. F_o:F_c: 0.947 / Cor.coef. F_o:F_c free: 0.925 / SU B: 10.251 / SU ML: 0.148 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.388 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23635	4127	4.9 %	RANDOM
R_work	0.19432	-	-	-
obs	0.19633	80387	91.01 %	-

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: 37.883 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.2 Å²	0 Å²	0 Å²
2-	-	0.27 Å²	0 Å²
3-	-	-	-0.47 Å²

Refinement step

Cycle: LAST / Resolution: 2.35→37.22 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13877	0	0	679	14556

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	14047
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.115	1.972	19090
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.474	5	1823
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.572	24.869	612
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.473	15	2289
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.434	15	98
X-RAY DIFFRACTION	r_chiral_restr	0.067	0.2	2298
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	10505
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.188	0.2	5957
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.297	0.2	9667
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.12	0.2	952
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	0.216	0.2	104
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.132	0.2	17
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	2.203	2	9334
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	3.414	3	14643
X-RAY DIFFRACTION	r_scbond_it	2.724	2	5116
X-RAY DIFFRACTION	r_scangle_it	3.891	3	4447
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	548	tight positional	0.04	0.05
1	2	B	548	tight positional	0.03	0.05
1	3	C	548	tight positional	0.04	0.05
1	4	D	548	tight positional	0.03	0.05
1	5	E	548	tight positional	0.03	0.05
1	6	F	548	tight positional	0.03	0.05
1	7	H	548	tight positional	0.02	0.05
1	8	I	548	tight positional	0.02	0.05
1	1	A	458	medium positional	0.19	0.5
1	2	B	458	medium positional	0.23	0.5
1	3	C	458	medium positional	0.18	0.5
1	4	D	458	medium positional	0.17	0.5
1	5	E	458	medium positional	0.16	0.5
1	6	F	458	medium positional	0.19	0.5
1	7	H	458	medium positional	0.17	0.5
1	8	I	458	medium positional	0.2	0.5
2	1	A	96	medium positional	0.16	0.5
2	2	B	96	medium positional	0.1	0.5
2	3	C	96	medium positional	0.12	0.5
2	4	D	96	medium positional	0.16	0.5
2	5	E	96	medium positional	0.12	0.5
2	6	F	96	medium positional	0.11	0.5
2	7	G	96	medium positional	0.15	0.5
2	8	H	96	medium positional	0.14	0.5
2	9	I	96	medium positional	0.18	0.5
3	1	B	64	medium positional	0.12	0.5
3	2	C	64	medium positional	0.12	0.5
3	3	F	64	medium positional	0.15	0.5
3	4	G	64	medium positional	0.11	0.5
3	5	H	64	medium positional	0.14	0.5
2	1	A	98	loose positional	0.87	5
2	2	B	98	loose positional	0.73	5
2	3	C	98	loose positional	0.91	5
2	4	D	98	loose positional	0.76	5
2	5	E	98	loose positional	0.95	5
2	6	F	98	loose positional	1.01	5
2	7	G	98	loose positional	1.05	5
2	8	H	98	loose positional	0.87	5
2	9	I	98	loose positional	0.93	5
3	1	B	56	loose positional	0.23	5
3	2	C	56	loose positional	0.2	5
3	3	F	56	loose positional	0.22	5
3	4	G	56	loose positional	0.16	5
3	5	H	56	loose positional	0.31	5
1	1	A	548	tight thermal	0.08	0.5
1	2	B	548	tight thermal	0.07	0.5
1	3	C	548	tight thermal	0.07	0.5
1	4	D	548	tight thermal	0.07	0.5
1	5	E	548	tight thermal	0.06	0.5
1	6	F	548	tight thermal	0.07	0.5
1	7	H	548	tight thermal	0.05	0.5
1	8	I	548	tight thermal	0.05	0.5
1	1	A	458	medium thermal	0.71	2
1	2	B	458	medium thermal	0.64	2
1	3	C	458	medium thermal	0.67	2
1	4	D	458	medium thermal	0.76	2
1	5	E	458	medium thermal	0.55	2
1	6	F	458	medium thermal	0.62	2
1	7	H	458	medium thermal	0.5	2
1	8	I	458	medium thermal	0.5	2
2	1	A	96	medium thermal	0.69	2
2	2	B	96	medium thermal	0.47	2
2	3	C	96	medium thermal	0.49	2
2	4	D	96	medium thermal	0.73	2
2	5	E	96	medium thermal	0.36	2
2	6	F	96	medium thermal	0.6	2
2	7	G	96	medium thermal	0.62	2
2	8	H	96	medium thermal	0.42	2
2	9	I	96	medium thermal	0.36	2
3	1	B	64	medium thermal	0.66	2
3	2	C	64	medium thermal	0.83	2
3	3	F	64	medium thermal	0.54	2
3	4	G	64	medium thermal	0.74	2
3	5	H	64	medium thermal	0.62	2
2	1	A	98	loose thermal	3.56	10
2	2	B	98	loose thermal	2.72	10
2	3	C	98	loose thermal	2.29	10
2	4	D	98	loose thermal	4.54	10
2	5	E	98	loose thermal	2.96	10
2	6	F	98	loose thermal	3.08	10
2	7	G	98	loose thermal	2.51	10
2	8	H	98	loose thermal	2.1	10
2	9	I	98	loose thermal	1.98	10
3	1	B	56	loose thermal	2	10
3	2	C	56	loose thermal	2.81	10
3	3	F	56	loose thermal	2.2	10
3	4	G	56	loose thermal	3.01	10
3	5	H	56	loose thermal	2.21	10

LS refinement shell

Resolution: 2.347→2.408 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.279	260	-
R_work	0.223	4779	-
obs	-	-	74.41 %

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	1.2432	0.0809	0.7022	0.7742	-0.116	1.0471	0.0207	-0.0477	-0.014	-0.0318	0.0451	0.022	0.0656	-0.1002	-0.0659	-0.0914	-0.008	0.0135	-0.0777	0.0477	-0.116	-7.828	88.05	8.002
2	1.178	0.0045	0.3863	0.5293	0.1133	1.0505	-0.0883	-0.1626	0.1296	0.0865	0.0308	0.002	-0.0624	-0.1485	0.0575	-0.0307	0.0263	-0.0017	-0.0845	-0.0107	-0.0746	8.233	97.596	33.793
3	0.7744	0.2232	-0.0136	1.0006	0.0874	0.5186	0.004	0.0221	-0.1765	0.0819	0.0096	-0.1466	0.0771	0.0273	-0.0136	-0.0679	0.028	0.0082	-0.0991	0.0071	-0.0332	17.465	70.423	18.107
4	1.7138	0.2261	0.1194	0.807	-0.0314	1.3571	-0.0277	0.3106	0.0722	-0.2876	-0.0301	-0.1605	-0.0457	0.3291	0.0578	0.0432	-0.0349	0.0383	0.1384	0.081	-0.0673	44.189	43.24	45.092
5	58.0322	80.2237	-46.2022	117.3254	-73.9274	52.5298	0.2907	3.2073	-0.5621	3.4607	0.2407	1.694	-1.4163	-1.6707	-0.5314	0.0259	0.0102	-0.0573	0.0027	-0.0016	0.0139	14.407	23.176	59.869
6	0.86	0.0266	-0.1208	0.8366	-0.2571	0.9825	-0.021	0.0269	-0.0207	0.0273	0.0489	0.0495	0.012	0.1079	-0.0279	-0.0546	-0.0178	-0.0083	-0.0633	0.0531	-0.0894	27.166	34.086	71.211
7	2.041	-0.04	0.4673	0.9446	-0.0505	1.6574	-0.0373	0.257	0.1523	0.0423	-0.0346	-0.0249	-0.1314	0.2774	0.0718	-0.0198	-0.0411	0.0334	-0.0042	-0.0264	-0.0617	63.509	31.802	5.995
8	1.4496	0.63	0.1819	0.8478	-0.2771	1.7736	0.1109	-0.138	-0.3846	0.0738	-0.0139	-0.0707	0.3935	0.0728	-0.097	0.1582	0.0179	-0.0135	-0.019	-0.0005	0.1185	53.017	3.82	17.433
9	2.0343	-0.2542	0.6787	0.6791	-0.1439	1.1762	0.1261	-0.2862	-0.1827	0.2676	-0.1178	-0.1582	0.0386	0.3466	-0.0083	0.1506	-0.0133	-0.0458	0.2812	0.0129	0.0254	79.184	19.916	30.342

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	38 - 252
2	X-RAY DIFFRACTION	2	B	37 - 252
3	X-RAY DIFFRACTION	3	C	37 - 253
4	X-RAY DIFFRACTION	4	E	40 - 251
5	X-RAY DIFFRACTION	5	E	37 - 39
6	X-RAY DIFFRACTION	6	F	37 - 252
7	X-RAY DIFFRACTION	7	G	37 - 253
8	X-RAY DIFFRACTION	8	H	41 - 251
9	X-RAY DIFFRACTION	9	I	37 - 251

-
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

-
Phasing

-
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

-Phasing

-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

-
Phasing

-
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