PDB-2h5n: Crystal Structure of Protein of Unknown Function PG1108 from Porp...

ID or keywords:

Entry

Database: PDB / ID: 2h5n

Title

Crystal Structure of Protein of Unknown Function PG1108 from Porphyromonas gingivalis W83

Components

Hypothetical protein PG_1108

Keywords

STRUCTURAL GENOMICS / UNKNOWN FUNCTION / hypothetical protein / SAD / MCSG / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics

Function / homology

Co-chaperone DjlA, N-terminal / TerB-like / Tellurite resistance protein TerB / TerB-like / TerB-like / Orthogonal Bundle / Mainly Alpha / metal ion binding / TerB domain-containing protein

Function and homology information

Biological species

Porphyromonas gingivalis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.01 Å

Authors

Nocek, B. / Bigelow, L. / Moy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: Crystal structure of hypothetical protein PG_1108 from Porphyromonas gingivalis W83
Authors: Nocek, B. / Bigelow, L. / Moy, S. / Joachimiak, A.

History

Deposition	May 26, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 25, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Feb 14, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_related / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_related.db_name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Remark 300

BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S) ...

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	2h5n.cif.gz	119.5 KB	Display	PDBx/mmCIF format
PDB format	pdb2h5n.ent.gz	96.8 KB	Display	PDB format
PDBx/mmJSON format	2h5n.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	2h5n_validation.pdf.gz	457.2 KB	Display	wwPDB validaton report
Full document	2h5n_full_validation.pdf.gz	464.8 KB	Display
Data in XML	2h5n_validation.xml.gz	23.9 KB	Display
Data in CIF	2h5n_validation.cif.gz	34.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/h5/2h5n ftp://data.pdbj.org/pub/pdb/validation_reports/h5/2h5n	HTTPS FTP

-
Related structure data

Similar structure data	3tpz-d 2q7v-d 1p3r-d 3h0d-d 3f8r-1 3f8d-2 4jnq-1 3f8p-2 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	TargetDB: apc80971

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Hypothetical protein PG_1108

B: Hypothetical protein PG_1108

C: Hypothetical protein PG_1108

D: Hypothetical protein PG_1108

hetero molecules

58.6 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

2

D: Hypothetical protein PG_1108

B: Hypothetical protein PG_1108

hetero molecules

B: Hypothetical protein PG_1108

hetero molecules

A: Hypothetical protein PG_1108

C: Hypothetical protein PG_1108

hetero molecules

A: Hypothetical protein PG_1108

C: Hypothetical protein PG_1108

hetero molecules

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

Type	Name	Symmetry operation	Number
crystal symmetry operation	1_455	x-1,y,z	1
crystal symmetry operation	3_655	-x+1,y,-z+1/2	1
crystal symmetry operation	5_455	x-1/2,y+1/2,z	1
crystal symmetry operation	7_555	-x+1/2,y+1/2,-z+1/2	1
identity operation	1_555	x,y,z	1
crystal symmetry operation	3_555	-x,y,-z+1/2	1

Unit cell

Length a, b, c (Å)	79.961, 84.826, 164.535
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	B-1056- HOH
2	1	D-211- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Refine code: 4

Dom-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	ILE	ILE	ASN	ASN	A	A	10 - 132	10 - 132
2	ILE	ILE	LYS	LYS	B	B	10 - 131	10 - 131
3	ILE	ILE	ASN	ASN	C	C	10 - 132	10 - 132
4	MET	MET	ASN	ASN	D	D	11 - 132	11 - 132

#1: Protein	Hypothetical protein PG_1108 Mass: 14635.183 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q7MVF6
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 331 / 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: 2.38 Å³/Da / Density % sol: 48.38 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 20% 1,4 butanediol, 0.1 imidazole pH 8.0, 0.1 M Zn(oAC)2, 0.1M MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 25, 2006
Radiation	Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 2.01→40 Å / Num. all: 35653 / Num. obs: 35476 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / R_merge(I) obs: 0.095 / Net I/σ(I): 15.1
Reflection shell	Resolution: 2.01→2.08 Å / Redundancy: 2.8 % / R_merge(I) obs: 0.466 / Mean I/σ(I) obs: 2 / % possible all: 97.5

-
Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
SBC-Collect		data collection
HKL-2000		data scaling
HKL-3000		phasing
SHELXD		phasing
SHELXE		model building
MLPHARE		phasing
DM		phasing
SOLVE		phasing
RESOLVE		phasing
Coot		model building
CCP4		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.01→40 Å / Cor.coef. F_o:F_c: 0.95 / Cor.coef. F_o:F_c free: 0.917 / SU B: 8.443 / SU ML: 0.121 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.184 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24365	1869	5 %	RANDOM
R_work	0.18825	-	-	-
obs	0.19094	35476	99.5 %	-
all	-	37345	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 26.528 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.47 Å²	0 Å²	0 Å²
2-	-	2.12 Å²	0 Å²
3-	-	-	0.36 Å²

Refinement step

Cycle: LAST / Resolution: 2.01→40 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3822	0	3	331	4156

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.022	3942
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.621	1.987	5306
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.142	5	514
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	41.399	25.973	149
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.358	15	792
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.695	15	18
X-RAY DIFFRACTION	r_chiral_restr	0.115	0.2	641
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	2798
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.207	0.2	1939
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.291	0.2	2857
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.25	0.2	285
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	0.266	0.2	80
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.312	0.2	20
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	0.851	1.5	2655
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.161	2	4087
X-RAY DIFFRACTION	r_scbond_it	2.027	3	1478
X-RAY DIFFRACTION	r_scangle_it	3.129	4.5	1219
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Ens-ID: 1 / Number: 836 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Type	Rms dev position (Å)	Weight position
1	A	medium positional	0.7	0.5
2	B	medium positional	0.7	0.5
3	C	medium positional	0.48	0.5
4	D	medium positional	0.57	0.5
1	A	medium thermal	1.15	2
2	B	medium thermal	1.33	2
3	C	medium thermal	0.95	2
4	D	medium thermal	1.11	2

LS refinement shell

Resolution: 2.01→2.063 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.286	119	-
R_work	0.223	2492	-
obs	-	-	95.99 %

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	52.3657	-9.3812	-5.815	1.8706	1.619	2.3999	-0.0682	-0.4913	0.638	-0.0046	0.0964	-0.035	-0.0283	0.2351	-0.0283	0.0535	-0.0258	-0.054	-0.0147	0.0494	0.0869	-4.5967	18.7166	44.1471
2	0.3968	-0.2046	-0.027	1.9183	1.3058	0.9226	-0.0153	0.0376	0.102	-0.0541	0.0598	-0.083	0.0354	0.1271	-0.0445	0.0502	0.028	-0.0124	0.0193	0.0218	0.0557	22.3808	11.543	33.3357
3	6.7635	-10.4404	0.6487	25.1364	-6.2124	3.0727	0.7298	0.1227	0.322	-1.4354	-0.6568	-0.4079	0.4465	0.4244	-0.0729	0.1519	-0.0048	0.04	0.0816	0.0353	-0.019	28.2907	7.1849	15.7309
4	4.9783	-1.2767	-4.4284	1.6028	-1.5293	9.5078	0.0302	-0.1045	-0.1424	-0.3295	-0.0441	0.1653	-0.1066	0.151	0.0139	0.0383	-0.0023	-0.0121	0.0486	0.0738	0.0662	21.4656	15.0558	18.9871
5	7.567	-4.3328	-8.727	5.0165	6.3703	10.8085	-0.1561	0.5446	0.5102	0.0822	-0.0694	0.3972	-0.384	0.1031	0.2255	-0.0285	0.0214	-0.0265	0.0583	0.0643	0.1323	15.3082	17.9001	27.7171
6	19.8412	-7.4947	-2.9968	11.3118	1.3678	0.9104	0.7653	0.5009	1.3507	-0.8647	-0.3058	-0.8303	-0.6506	0.1124	-0.4595	0.1573	0.0105	0.0716	0.0471	0.0608	0.1142	24.868	22.0966	31.4028
7	3.6444	1.9078	1.5311	24.7386	-8.3022	10.7889	0.1197	-0.1683	0.4212	0.2357	-0.3719	-1.5307	-0.107	0.4103	0.2522	0.0037	0.038	0.0162	-0.0109	-0.008	0.2113	32.3877	8.7294	34.1406
8	10.0705	1.0867	-4.0675	1.4197	-0.3905	1.6446	0.0391	-0.1466	0.2202	0.2507	0.0677	0.0063	0.0408	-0.0254	-0.1069	0.0787	0.059	-0.0017	0.0345	0.0375	0.0485	21.312	4.9018	39.0562
9	2.9348	-0.4593	4.6843	8.9375	3.2379	9.2727	-0.0425	-0.0835	-0.1592	0.2519	-0.1506	0.823	0.2372	-0.618	0.1931	0.0242	0.0402	0.0488	0.0158	0.0043	0.0972	10.94	5.8012	36.2903
10	3.8089	1.6055	-3.9116	1.6127	-4.1481	10.6907	-0.1142	0.0463	0.3141	-0.1977	-0.0444	0.5465	-0.1012	-0.0595	0.1585	0.0388	0.0345	-0.0513	0.0436	0.0249	0.0726	15.2243	8.8099	25.6811
11	23.5069	-7.5564	-19.0068	23.7902	8.3688	15.6071	0.1352	1.0276	0.4539	-1.176	-1.029	0.9581	-0.2121	0.0372	0.8937	0.1667	-0.0011	-0.259	0.0635	0.0587	0.0185	12.9037	6.0272	13.451
12	2.9049	-1.4124	0.5814	2.8393	-0.1852	4.6208	0.0607	0.2735	-0.1446	-0.1067	-0.1758	0.066	-0.092	-0.0561	0.1151	0.0423	0.0251	-0.0562	0.054	-0.017	0.0384	18.7358	-0.9498	21.928
13	10.6895	-1.8445	6.3811	6.9847	-5.7549	7.058	0.2499	-0.3079	-0.4763	-0.02	0.3526	0.49	0.2369	-0.3319	-0.6025	0.0074	0.0187	-0.0295	0.0289	-0.0279	0.0461	14.0723	-0.2174	29.4575
14	0.0922	1.0923	-0.0502	13.0054	0.009	5.8602	-0.1245	0.1216	0.2305	-0.349	0.1545	1.124	-0.4404	-0.7444	-0.03	-0.0898	0.0859	-0.0783	0.1584	0.0849	0.2142	6.1293	9.1166	23.82
15	2.0169	-0.6949	1.5881	0.6105	-0.4827	2.4397	0.143	0.0568	-0.2028	0.0453	0.0339	-0.0007	-0.0301	-0.0122	-0.1768	0.0251	-0.0223	-0.0346	0.0213	-0.0137	0.0585	29.92	-13.7469	34.1435
16	1.2037	-3.9631	-1.2264	17.7019	4.7666	1.3636	0.0943	-0.0129	-0.1025	-0.373	-0.237	0.505	-0.1219	-0.0462	0.1426	0.0439	0.0031	-0.081	0.0581	-0.0055	0.0127	20.0285	-13.9189	19.3043
17	9.4662	2.065	4.7434	0.4504	1.0347	2.3768	0.1264	0.031	0.4087	-0.1849	0.0998	-0.2707	0.2708	0.0731	-0.2262	0.0538	-0.0236	-0.0108	0.0268	-0.0217	0.0228	29.5427	-20.9756	23.3752
18	1.8476	5.1987	-2.1188	14.628	-5.9619	2.4299	0.1589	-0.2452	-0.3135	-0.1079	-0.3406	-0.8044	0.0942	0.421	0.1817	0.0329	-0.0192	-0.0532	0.1285	-0.0212	0.0173	34.3549	-22.1195	31.7615
19	4.047	-6.0687	-1.9034	11.2113	5.0957	4.1385	-0.0087	-0.0008	-0.184	-0.027	0.0318	0.3818	0.186	-0.0821	-0.0232	0.0463	-0.0324	-0.0252	-0.0182	0.0081	-0.0254	24.2964	-22.8998	34.2836
20	0.0308	-0.6649	-0.0462	15.9404	-1.6612	4.502	-0.1749	-0.0896	0.1267	0.7077	0.4229	0.6587	-0.3994	-0.4823	-0.2481	-0.0019	0.0154	0.001	0.026	0.0293	0.0444	20.3118	-9.6312	38.4106
21	7.2136	5.9936	2.9368	5.6616	1.3031	3.0918	-0.015	-0.2284	0.0628	0.0058	-0.2337	-0.2019	0.0248	-0.3959	0.2487	0.0764	0.0066	-0.0358	0.0239	-0.0086	0.0323	27.7488	-5.8958	38.763
22	6.0236	-2.4808	-3.1504	1.533	1.8017	2.1449	0.0615	-0.0973	0.1248	-0.2726	0.1122	-0.1698	-0.1095	-0.0675	-0.1737	0.0242	-0.0032	-0.0449	0.0068	0.0069	0.0611	37.9847	-4.9626	38.0644
23	2.8341	0.7923	4.107	1.4127	0.4625	6.3463	0.3486	0.0462	-0.2157	-0.3381	-0.134	-0.1377	0.1288	0.3575	-0.2145	-0.0072	0.0404	-0.017	0.0404	0.0064	0.0793	41.248	-9.6491	32.6827
24	3.2302	3.0324	3.1772	3.423	3.5733	3.7305	-0.0497	0.089	-0.026	-0.0733	-0.0597	-0.2089	-0.0872	0.0051	0.1095	0.0168	0.0021	-0.0334	0.0613	-0.0059	0.0208	33.0883	-12.1578	24.4965
25	31.8308	-15.6271	8.7046	15.1823	-4.0727	10.1968	0.5539	1.6795	-0.3999	-1.5112	-0.8629	-0.3832	0.1859	0.3829	0.309	0.066	-0.0124	0.0274	0.128	-0.0903	-0.1634	32.7503	-11.4577	12.5
26	2.4397	0.429	0.6809	4.216	1.7511	3.6282	0.0173	0.1562	0.1683	-0.2257	-0.0793	0.0077	-0.1195	-0.1073	0.062	0.0788	0.0287	-0.0169	0.0193	0.0135	0.0093	29.5432	-3.4638	20.6483
27	6.2544	-1.7048	-4.272	4.8454	4.3909	5.2942	0.0662	0.3304	0.3098	0.0135	0.084	-0.1296	-0.218	0.0323	-0.1501	0.034	0.007	-0.0407	0.0147	0.036	0.0073	36.1331	-2.7857	26.7337
28	4.62	0.8185	3.7499	15.2982	-6.2491	16.4721	-0.0258	0.5759	-0.5283	-0.4398	0.1775	-1.0048	0.3781	0.7329	-0.1517	-0.1024	0.0005	0.0485	0.1141	-0.0818	0.0527	41.9411	-12.9471	20.7028
29	7.398	1.8643	3.2262	19.7753	-2.9578	2.1435	-0.1285	0.0826	0.1945	-0.585	-0.2109	0.3004	-0.1063	-0.0836	0.3394	0.0954	0.0384	-0.0277	0.1511	0.071	-0.0194	34.2378	25.8681	-3.0456
30	3.2546	-1.0761	3.1313	0.714	-0.0026	5.9908	0.0978	0.0658	-0.2959	0.0094	-0.1057	0.1086	0.0567	-0.2257	0.0079	0.0156	0.0056	-0.0087	0.027	0.0343	0.0981	35.8854	17.4761	8.0962
31	9.1033	-3.594	-4.0688	3.2929	-2.2393	9.7099	-0.0748	-0.8792	-0.2866	0.1487	0.2006	0.4589	-0.4502	0.5085	-0.1258	-0.0367	-0.0312	0.0283	0.0958	0.0645	0.1139	35.2509	13.9263	21.3015
32	8.1991	-3.3545	2.3756	13.8271	-7.1174	3.7207	0.2633	-0.0465	0.1258	0.2881	0.2146	0.3842	-0.1484	-0.0574	-0.4779	0.0202	0.0143	0.0149	0.0759	0.0078	0.0324	29.3062	21.2219	18.4468
33	6.3866	-2.6783	1.2735	5.2644	-4.888	4.8316	-0.2115	0.155	0.2723	0.2464	-0.1557	-0.0372	-0.0945	-0.1909	0.3672	0.0115	0.023	-0.0271	0.01	0.0199	0.0536	28.3777	26.4577	8.4065
34	13.2745	-2.4782	5.3137	30.2899	-2.6802	2.2226	0.0702	0.0211	-0.5825	0.553	0.2806	0.9824	0.2569	-0.2232	-0.3508	0.0183	0.0281	-0.0121	0.0662	0.0188	0.0158	24.182	18.7659	3.5626
35	27.9438	-9.1396	-6.8097	3.9348	5.4547	12.6769	0.5123	0.531	-2.4522	0.1429	-0.54	0.4475	0.3524	-0.0454	0.0277	0.0071	-0.014	-0.143	-0.0519	0.0093	0.384	34.8891	9.6615	3.0222
36	6.3609	2.9177	-2.3978	15.0487	-8.0656	4.4429	0.1235	0.546	-0.2518	-0.2714	-0.1934	0.058	0.0165	0.1916	0.0698	0.0369	0.0284	-0.0295	0.109	0.0337	-0.0133	43.3813	18.2542	0.2301
37	21.6946	5.9262	-11.0211	7.6742	1.2691	8.6237	0.0912	0.2749	1.017	-0.4527	0.2648	-0.0071	-0.2045	-0.1919	-0.356	0.0946	0.0288	0.0024	0.012	0.0755	0.0593	42.7334	30.445	0.366
38	5.1998	1.9815	-3.7393	1.3858	-2.5591	4.7286	0.1016	0.1639	0.4086	0.1132	0.0941	0.0705	-0.2311	-0.2729	-0.1957	0.0696	0.0093	-0.0062	0.0059	0.0603	0.0623	37.4868	28.2729	9.9975
39	4.804	-2.7055	3.5336	10.8713	-2.0774	3.4359	-0.3134	-1.0799	0.2913	0.8498	0.289	0.563	-0.1106	-0.2805	0.0244	0.0815	0.0329	0.0302	0.1033	-0.0826	-0.0086	38.5559	27.3376	23.8245
40	1.9517	-1.2452	-3.2997	1.9813	0.7278	7.1779	-0.0082	-0.0835	0.0562	0.1156	0.0032	-0.0154	0.1139	0.2748	0.0051	0.0185	-0.0159	-0.0161	0.0427	0.0373	0.0489	45.5375	22.4144	14.3722
41	7.188	2.5501	-3.7186	1.8588	-2.6211	3.7002	0.1944	-0.0263	0.4221	0.2818	-0.194	-0.1702	-0.6267	0.5268	-0.0004	0.0522	0.0111	-0.044	0.0041	0.0225	0.0956	44.8161	31.0408	12.4786
42	6.1629	-5.4985	8.1951	9.1026	-2.3733	16.7077	-0.119	-0.1929	0.4789	0.4222	0.1792	0.7527	-0.9966	0.0113	-0.0602	0.1567	0.0455	0.0958	-0.072	0.0512	0.1474	35.7736	36.1689	11.6951
43	2.6015	0.1236	-0.9433	1.1877	0.5645	0.6561	-0.153	0.077	-0.2032	0.007	0.0698	-0.021	0.07	0.0256	0.0832	0.033	-0.0197	-0.0108	0.0937	0.0535	0.0667	60.8711	9.7281	6.0743
44	3.6862	1.4652	1.5625	3.7602	1.5013	0.9061	0.0105	-0.1177	-0.0642	-0.0729	-0.1418	0.1128	0.0203	-0.0137	0.1312	0.0224	-0.0177	-0.0257	0.0461	0.051	0.0265	54.4358	20.1453	18.8431
45	2.1186	-0.1563	0.0293	2.2012	-0.0616	0.002	0.0528	-0.2554	-0.1275	0.0304	0.0731	-0.0564	0.095	-0.0538	-0.1258	0.0656	-0.0173	-0.0587	0.0629	0.0107	0.0003	60.2146	17.9522	25.0003
46	9.9678	-3.2201	-4.5014	1.6804	2.7013	4.4624	-0.0855	0.0467	0.1141	0.1936	0.1595	-0.1478	0.0481	0.4325	-0.074	0.0545	0.0035	-0.0254	0.0604	0.0704	0.0434	64.8046	9.1167	17.9808
47	38.2485	30.6276	-15.6704	28.16	-8.0715	11.9335	-0.5081	-0.1207	-2.1879	0.0972	-0.2107	-0.6853	0.7542	1.008	0.7188	0.0362	0.0859	-0.0293	0.0182	0.0447	0.1696	68.3938	6.2747	13.901
48	9.5122	-2.2557	0.7579	3.4697	-2.9986	8.1121	-0.0916	-0.1623	0.3333	-0.1799	-0.0629	0.0247	-0.0157	0.4913	0.1545	-0.0283	-0.0162	0.0064	0.0452	0.0204	0.0028	69.0632	16.2172	10.7686
49	8.6084	5.8257	2.418	10.3062	-3.1292	4.248	-0.2445	-0.6585	0.5124	-0.2634	0.0781	0.3175	-0.3193	-0.1901	0.1664	0.0238	-0.0001	0.0461	0.091	0.0183	0.0119	58.8721	21.5522	5.4567
50	4.8668	2.8787	4.6579	12.5239	3.1166	4.47	0.1707	0.4877	-0.2301	-0.1863	-0.2446	-0.0629	-0.1312	0.2514	0.0739	0.0152	0.0047	0.0263	0.0916	0.0568	0.0421	52.8555	13.4504	2.7961
51	4.6884	-3.4264	-1.1991	6.1037	6.567	9.3032	-0.1125	0.4889	-0.6236	-0.0866	-0.0937	0.0544	0.3274	0.1874	0.2062	0.0366	-0.025	-0.0561	0.0206	-0.0084	0.1512	52.8913	1.5828	3.4407
52	3.4307	2.3407	2.9844	2.554	2.0836	8.565	-0.0233	-0.1325	-0.5316	0.0124	0.0898	-0.1076	0.0986	0.0895	-0.0665	0.0262	-0.0051	-0.0118	-0.0233	0.0702	0.1127	55.4901	4.5437	13.6791
53	5.3786	-6.7647	0.2252	10.236	-2.4991	12.5385	0.4398	-0.4495	-0.0745	0.302	-0.3221	0.053	0.0949	0.0624	-0.1177	0.05	-0.0514	-0.0077	0.1299	0.1205	-0.0575	50.1117	10.8682	27.3151
54	1.6435	-0.4855	1.4381	1.6171	1.0371	5.2319	0.067	-0.1875	-0.1708	-0.0735	-0.0265	0.026	0.0961	-0.2909	-0.0405	0.0064	-0.0215	-0.0161	0.0324	0.0794	0.1001	46.4427	11.0037	14.8224
55	8.9412	1.5374	0.7249	0.6491	-1.3936	9.1597	0.1362	-0.2076	-0.774	0.0504	0.5108	0.373	0.076	-0.4904	-0.647	-0.0027	-0.012	-0.0127	-0.001	0.1075	0.1521	47.9507	2.6683	16.7196
56	28.1953	-1.1062	-10.9571	5.5224	3.1002	5.5595	-0.1991	-0.7354	-1.9303	0.2624	-0.0692	-0.2166	0.3598	0.276	0.2684	0.0646	-0.0116	-0.0989	0.0285	0.2082	0.1799	57.0327	-1.6631	20.0238

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	1 - 10	1 - 10
2	X-RAY DIFFRACTION	2	A	A	11 - 29	11 - 29
3	X-RAY DIFFRACTION	3	A	A	30 - 36	30 - 36
4	X-RAY DIFFRACTION	4	A	A	37 - 44	37 - 44
5	X-RAY DIFFRACTION	5	A	A	45 - 51	45 - 51
6	X-RAY DIFFRACTION	6	A	A	52 - 64	52 - 64
7	X-RAY DIFFRACTION	7	A	A	65 - 70	65 - 70
8	X-RAY DIFFRACTION	8	A	A	71 - 80	71 - 80
9	X-RAY DIFFRACTION	9	A	A	81 - 85	81 - 85
10	X-RAY DIFFRACTION	10	A	A	86 - 95	86 - 95
11	X-RAY DIFFRACTION	11	A	A	96 - 102	96 - 102
12	X-RAY DIFFRACTION	12	A	A	103 - 114	103 - 114
13	X-RAY DIFFRACTION	13	A	A	115 - 122	115 - 122
14	X-RAY DIFFRACTION	14	A	A	123 - 132	123 - 132
15	X-RAY DIFFRACTION	15	B	B	10 - 29	10 - 29
16	X-RAY DIFFRACTION	16	B	B	30 - 38	30 - 38
17	X-RAY DIFFRACTION	17	B	B	39 - 46	39 - 46
18	X-RAY DIFFRACTION	18	B	B	47 - 53	47 - 53
19	X-RAY DIFFRACTION	19	B	B	54 - 64	54 - 64
20	X-RAY DIFFRACTION	20	B	B	65 - 70	65 - 70
21	X-RAY DIFFRACTION	21	B	B	71 - 76	71 - 76
22	X-RAY DIFFRACTION	22	B	B	77 - 81	77 - 81
23	X-RAY DIFFRACTION	23	B	B	82 - 86	82 - 86
24	X-RAY DIFFRACTION	24	B	B	87 - 95	87 - 95
25	X-RAY DIFFRACTION	25	B	B	96 - 102	96 - 102
26	X-RAY DIFFRACTION	26	B	B	103 - 114	103 - 114
27	X-RAY DIFFRACTION	27	B	B	115 - 122	115 - 122
28	X-RAY DIFFRACTION	28	B	B	123 - 131	123 - 131
29	X-RAY DIFFRACTION	29	C	C	10 - 17	10 - 17
30	X-RAY DIFFRACTION	30	C	C	18 - 29	18 - 29
31	X-RAY DIFFRACTION	31	C	C	30 - 36	30 - 36
32	X-RAY DIFFRACTION	32	C	C	37 - 42	37 - 42
33	X-RAY DIFFRACTION	33	C	C	43 - 51	43 - 51
34	X-RAY DIFFRACTION	34	C	C	52 - 62	52 - 62
35	X-RAY DIFFRACTION	35	C	C	63 - 68	63 - 68
36	X-RAY DIFFRACTION	36	C	C	69 - 79	69 - 79
37	X-RAY DIFFRACTION	37	C	C	80 - 84	80 - 84
38	X-RAY DIFFRACTION	38	C	C	85 - 94	85 - 94
39	X-RAY DIFFRACTION	39	C	C	95 - 104	95 - 104
40	X-RAY DIFFRACTION	40	C	C	105 - 117	105 - 117
41	X-RAY DIFFRACTION	41	C	C	118 - 123	118 - 123
42	X-RAY DIFFRACTION	42	C	C	124 - 133	124 - 133
43	X-RAY DIFFRACTION	43	D	D	11 - 24	11 - 24
44	X-RAY DIFFRACTION	44	D	D	25 - 34	25 - 34
45	X-RAY DIFFRACTION	45	D	D	35 - 42	35 - 42
46	X-RAY DIFFRACTION	46	D	D	43 - 48	43 - 48
47	X-RAY DIFFRACTION	47	D	D	49 - 54	49 - 54
48	X-RAY DIFFRACTION	48	D	D	55 - 63	55 - 63
49	X-RAY DIFFRACTION	49	D	D	64 - 69	64 - 69
50	X-RAY DIFFRACTION	50	D	D	70 - 77	70 - 77
51	X-RAY DIFFRACTION	51	D	D	78 - 82	78 - 82
52	X-RAY DIFFRACTION	52	D	D	83 - 94	83 - 94
53	X-RAY DIFFRACTION	53	D	D	95 - 105	95 - 105
54	X-RAY DIFFRACTION	54	D	D	106 - 117	106 - 117
55	X-RAY DIFFRACTION	55	D	D	118 - 123	118 - 123
56	X-RAY DIFFRACTION	56	D	D	124 - 133	124 - 133

-
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

-
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