PDB-3ic3: Structure of a putative pyruvate dehydrogenase from the photosynt...

ID or keywords:

Entry

Database: PDB / ID: 3ic3

Title

Structure of a putative pyruvate dehydrogenase from the photosynthetic bacterium Rhodopseudomonas palustrus CGA009

Components

putative pyruvate dehydrogenase

Keywords

OXIDOREDUCTASE / Rhodopseudomonas palustris / pyruvate dehydrogenase / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG

Function / homology

Function and homology information

putative pyruvate dehydrogenase fold / putative pyruvate dehydrogenase / Protein of unknown function DUF5076 / Domain of unknown function (DUF5076) / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology

Biological species

Rhodopseudomonas palustris (phototrophic)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.8 Å

Authors

Cuff, M.E. / Tesar, C. / Jedrzejczak, R. / Mckinlay, J.B. / Harwood, C.S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: TO BE PUBLISHED
Title: Structure of a putative pyruvate dehydrogenase from the photosynthetic bacterium Rhodopseudomonas palustrus CGA009
Authors: Cuff, M.E. / Tesar, C. / Jedrzejczak, R. / Mckinlay, J.B. / Harwood, C.S. / Joachimiak, A.

History

Deposition	Jul 17, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 22, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Refinement description / Version format compliance
Revision 1.2	Nov 1, 2017	Group: Refinement description / Category: software
Revision 1.3	Jul 29, 2020	Group: Data collection / Derived calculations / Structure summary Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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 Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4	Nov 6, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3ic3.cif.gz	105 KB	Display	PDBx/mmCIF format
PDB format	pdb3ic3.ent.gz	81 KB	Display	PDB format
PDBx/mmJSON format	3ic3.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3ic3_validation.pdf.gz	495.6 KB	Display	wwPDB validaton report
Full document	3ic3_full_validation.pdf.gz	499.8 KB	Display
Data in XML	3ic3_validation.xml.gz	24.6 KB	Display
Data in CIF	3ic3_validation.cif.gz	32.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ic/3ic3 ftp://data.pdbj.org/pub/pdb/validation_reports/ic/3ic3	HTTPS FTP

-
Related structure data

Similar structure data	2ltd-d 6ax1-2 6r0j-d 6bvc-d 5l9b-1 1yus-d 3jwe-1 5wl3-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: apc92224

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#198 - Jun 2016 Beta-galactosidase similarity (1) #75 - Mar 2006 Tissue Factor similarity (1) #77 - May 2006 Glucose Oxidase similarity (1)

Deposited unit

A: putative pyruvate dehydrogenase

B: putative pyruvate dehydrogenase

C: putative pyruvate dehydrogenase

D: putative pyruvate dehydrogenase

hetero molecules

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

1

A: putative pyruvate dehydrogenase

D: putative pyruvate dehydrogenase

hetero molecules

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

2

B: putative pyruvate dehydrogenase

C: putative pyruvate dehydrogenase

hetero molecules

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

3

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	64.700, 64.995, 116.890
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Details

authors state that the biological unit is unknown, and possibly a dimer.

-
Protein / Sugars , 2 types, 5 molecules ABCD

#1: Protein

putative pyruvate dehydrogenase

Mass: 11513.149 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Rhodopseudomonas palustris (phototrophic)
Strain: CGA009 / Gene: JGI_07::RPA2865, RPA2865 / Plasmid: pMCSG19 / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q6N5V5

#3: Sugar

ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose

Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C₆H₁₂O₆

-
Non-polymers , 5 types, 364 molecules

#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO₄
#6: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 355 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.67 Å³/Da / Density % sol: 53.9 %
Crystal grow	Temperature: 278 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 0.1M phosphate critrate pH 4.2 1.6M NaH2PO4, 0.4M K2HPO4, VAPOR DIFFUSION, SITTING DROP, temperature 278K

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.97948, 0.97935

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 21, 2009

Radiation

Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97948	1
2	0.97935	1

Reflection

Redundancy: 8 % / Av σ(I) over netI: 32.22 / Number: 371122 / R_merge(I) obs: 0.09 / Χ²: 1.93 / D res high: 1.8 Å / D res low: 50 Å / Num. obs: 46379 / % possible obs: 99.6

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
4.88	50	96	1	0.073	6.576	7.7
3.88	4.88	98.7	1	0.059	4.026	7.9
3.39	3.88	99.3	1	0.07	3.644	8
3.08	3.39	99.7	1	0.076	3.034	8.1
2.86	3.08	99.8	1	0.087	2.612	8.2
2.69	2.86	99.9	1	0.09	2.14	8.1
2.55	2.69	100	1	0.097	1.947	8.2
2.44	2.55	100	1	0.1	1.681	8.2
2.35	2.44	100	1	0.113	1.51	8.2
2.27	2.35	100	1	0.119	1.352	8.2
2.2	2.27	100	1	0.128	1.252	8.2
2.13	2.2	100	1	0.141	1.154	8.2
2.08	2.13	100	1	0.167	1.076	8.2
2.03	2.08	100	1	0.213	0.994	8.2
1.98	2.03	100	1	0.242	0.933	8.2
1.94	1.98	100	1	0.28	0.912	8.3
1.9	1.94	100	1	0.321	0.876	8.1
1.86	1.9	100	1	0.409	0.855	8
1.83	1.86	100	1	0.509	0.852	7.3
1.8	1.83	100	1	0.596	0.815	6.8

Reflection

Resolution: 1.8→50 Å / Num. all: 46379 / Num. obs: 46379 / % possible obs: 99.6 % / Observed criterion σ(F): -3 / Redundancy: 8 % / R_merge(I) obs: 0.09 / Net I/σ(I): 8.4

Reflection shell

Resolution: 1.8→1.83 Å / Redundancy: 6.8 % / R_merge(I) obs: 0.596 / % possible all: 100

-
Phasing

Phasing

Method:

MAD

Phasing MAD

D res high: 1.8 Å / D res low: 50 Å / FOM : 0.423 / FOM acentric: 0.438 / FOM centric: 0.284 / Reflection: 46232 / Reflection acentric: 41753 / Reflection centric: 4479

Phasing MAD set

Highest resolution: 1.8 Å / Lowest resolution: 50 Å

ID	R cullis acentric	R cullis centric	Loc acentric	Loc centric	Power acentric	Power centric	Reflection acentric	Reflection centric
1	1.66	1	0.2	0.2	0	0	41753	4479
2	0.94	0.86	14.6	20.8	0.63	0.52	35559	4017

Phasing MAD set shell

ID	Resolution (Å)	R cullis acentric	R cullis centric	Loc acentric	Loc centric	Power acentric	Power centric	Reflection acentric	Reflection centric
1	11.5-50	1.3	1	0.6	0.4	0	0	113	86
1	6.5-11.5	1.41	1	0.6	0.4	0	0	649	196
1	4.53-6.5	1.48	1	0.6	0.4	0	0	1643	347
1	3.47-4.53	1.12	1	0.4	0.3	0	0	3111	484
1	2.82-3.47	1.39	1	0.3	0.2	0	0	5023	626
1	2.37-2.82	1.8	1	0.2	0.1	0	0	7414	789
1	2.05-2.37	2	1	0.2	0.1	0	0	10267	913
1	1.8-2.05	3.16	1	0.1	0	0	0	13533	1038
2	11.5-50	0.94	0.73	22.7	31.2	1.52	1.05	113	84
2	6.5-11.5	0.84	0.7	20	20.9	1.42	1.17	647	195
2	4.53-6.5	0.88	0.78	21.3	26.2	1.11	0.8	1643	347
2	3.47-4.53	0.92	0.84	24.4	29.1	0.7	0.59	3111	483
2	2.82-3.47	0.93	0.87	18.8	24.8	0.67	0.47	5023	625
2	2.37-2.82	0.93	0.88	13.5	18.3	0.64	0.42	7414	789
2	2.05-2.37	0.97	0.94	11.8	16.9	0.47	0.3	10266	911
2	1.8-2.05	0.98	0.98	10.2	14.6	0.39	0.26	7342	583

Phasing MAD set site

ID	Atom type symbol	B iso	Fract x	Fract y	Fract z	Occupancy
1	Se	22.16982	0.976	0.75	0.051	0
2	Se	29.37308	0.744	0.689	0.042	0
3	Se	35.1174	0.584	0.365	0.221	0
4	Se	28.56841	0.528	0.143	0.206	0
5	Se	26.33753	0.716	0.967	0.232	0
6	Se	28.6612	0.157	0.56	0.066	0
7	Se	18.68114	0.826	0.73	0.018	0
8	Se	35.90501	0.529	0.292	0.239	0
9	Se	46.51931	0.33	0.077	0.235	0
10	Se	32.19848	0.344	0.446	0.008	0
11	Se	42.87281	0.209	0.279	0.195	0
12	Se	69.46381	0.195	0.513	0.031	0
13	Se	64.89246	0.264	0.425	0.227	0
14	Se	97.44134	0.912	0.665	0.096	0
15	Se	34.92271	0.19	0.482	0.004	0
16	Se	30.99186	0.972	0.959	0.067	0
17	Se	120.53397	0.57	0.59	0.016	0
18	Se	24.63068	0.976	0.75	0.051	-0.225
19	Se	29.87798	0.744	0.689	0.042	-0.182
20	Se	38.5921	0.585	0.365	0.221	-0.19
21	Se	28.69478	0.527	0.143	0.206	-0.189
22	Se	27.53599	0.716	0.968	0.232	-0.155
23	Se	38.56681	0.157	0.561	0.066	-0.151
24	Se	19.893	0.826	0.729	0.018	-0.184
25	Se	75.3875	0.531	0.292	0.24	-0.145
26	Se	46.84411	0.329	0.078	0.235	-0.12
27	Se	35.31134	0.344	0.446	0.008	-0.091
28	Se	45.01043	0.208	0.278	0.195	-0.083
29	Se	85.78743	0.195	0.515	0.03	-0.107
30	Se	73.0556	0.265	0.423	0.227	-0.163
31	Se	93.01298	0.911	0.665	0.095	-0.06
32	Se	44.04457	0.19	0.48	0.004	-0.071
33	Se	30.66792	0.972	0.959	0.068	-0.054
34	Se	146.27252	0.568	0.591	0.016	-0.081

Phasing MAD shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
11.5-50	0.618	0.701	0.508	199	113	86
6.5-11.5	0.673	0.723	0.508	845	649	196
4.53-6.5	0.662	0.703	0.472	1990	1643	347
3.47-4.53	0.597	0.628	0.394	3595	3111	484
2.82-3.47	0.595	0.624	0.358	5649	5023	626
2.37-2.82	0.548	0.571	0.332	8203	7414	789
2.05-2.37	0.406	0.422	0.225	11180	10267	913
1.8-2.05	0.207	0.217	0.079	14571	13533	1038

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 46232

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
8.3-100	51.1	0.782	513
6.32-8.3	46.7	0.915	634
5.31-6.32	46.4	0.932	754
4.66-5.31	44.7	0.952	876
4.21-4.66	46.1	0.952	1002
3.86-4.21	47.2	0.944	1073
3.59-3.86	50.4	0.937	1154
3.37-3.59	48.2	0.933	1245
3.19-3.37	47.4	0.935	1319
3.03-3.19	50.3	0.921	1380
2.89-3.03	47.4	0.928	1454
2.77-2.89	47	0.932	1503
2.67-2.77	47.1	0.928	1569
2.57-2.67	48.4	0.931	1628
2.49-2.57	48.5	0.934	1664
2.41-2.49	51.1	0.931	1728
2.34-2.41	51.1	0.93	1800
2.28-2.34	51.9	0.935	1852
2.22-2.28	53.8	0.935	1873
2.16-2.22	57.5	0.938	1898
2.11-2.16	57.3	0.932	2011
2.06-2.11	61.8	0.929	2023
2.02-2.06	59.8	0.931	2058
1.98-2.02	61.9	0.926	2117
1.94-1.98	66.2	0.928	2141
1.9-1.94	66.7	0.928	2178
1.86-1.9	75.4	0.922	2246
1.83-1.86	76.6	0.901	2240
1.8-1.83	77.3	0.863	2299

-
Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
MLPHARE		phasing
DM	6	phasing
REFMAC		refinement
PDB_EXTRACT	3.005	data extraction
SBC-Collect		data collection
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing
SHELXD		phasing
SHELXE		model building
SOLVE		phasing
RESOLVE		phasing
ARP/wARP		model building
CCP4		phasing
O		model building
Coot		model building

Refinement

Method to determine structure:

MAD / Resolution: 1.8→43.48 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.949 / Occupancy max: 1 / Occupancy min: 0.15 / SU B: 4.017 / SU ML: 0.059 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.102
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.19545	2343	5.1 %	RANDOM
R_work	0.16692	-	-	-
obs	0.16839	43887	99.58 %	-
all	-	46230	-	-

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: 12.894 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.06 Å²	0 Å²	0 Å²
2-	-	0.45 Å²	0 Å²
3-	-	-	-0.51 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→43.48 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2948	0	45	355	3348

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.022	3276
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	2254
X-RAY DIFFRACTION	r_angle_refined_deg	1.407	1.992	4460
X-RAY DIFFRACTION	r_angle_other_deg	0.885	3	5473
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.158	5	419
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.896	23.865	163
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.038	15	559
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.502	15	34
X-RAY DIFFRACTION	r_chiral_restr	0.088	0.2	483
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	3759
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	671
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	0.801	1.5	2030
X-RAY DIFFRACTION	r_mcbond_other	0.213	1.5	798
X-RAY DIFFRACTION	r_mcangle_it	1.556	2	3285
X-RAY DIFFRACTION	r_scbond_it	2.735	3	1246
X-RAY DIFFRACTION	r_scangle_it	4.49	4.5	1175
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.8→1.847 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.27	170	-
R_work	0.241	3172	-
obs	-	-	99.46 %

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	1.3909	0.8013	-0.0216	2.5739	-0.7115	1.4537	-0.0457	0.0033	0.0802	0.0505	0.0176	-0.1093	-0.0421	0.0155	0.0281	0.0985	0.0084	0.0295	0.0051	0.0087	0.0591	30.9636	31.9253	30.156
2	3.0189	-1.3856	-1.2291	2.6822	0.9463	3.11	0.1729	0.194	0.1378	-0.4933	0.0075	-0.1446	-0.1257	0.0727	-0.1804	0.146	-0.0168	0.0522	0.0449	0.0061	0.0377	26.7518	18.4612	19.3854
3	3.2505	-1.7061	-0.7678	2.3091	0.3769	6.6494	0.0041	-0.2027	-0.1831	0.0853	0.1036	0.1799	0.0313	-0.1113	-0.1077	0.0994	0.0047	0.035	0.0184	0.0073	0.0904	26.3337	7.5489	31.0577
4	6.9845	-0.6505	1.0036	5.2796	-1.4435	5.2573	-0.1086	0.1435	0.4717	-0.002	-0.0018	0.0178	-0.3353	0.1137	0.1104	0.1	-0.0202	0.0065	0.0916	0.0308	0.0674	22.5785	26.8217	49.8709
5	3.2817	-0.4364	-0.445	1.721	-0.1468	1.3774	0.0468	-0.1331	0.0207	0.136	-0.0047	-0.0738	-0.0482	0.0449	-0.0421	0.0135	-0.0004	-0.0059	0.0855	-0.0067	0.0319	23.8124	19.0856	61.469
6	1.9387	1.2362	1.2619	3.4669	3.4746	6.5751	-0.0438	0.0054	0.0814	-0.0171	0.1128	-0.0345	-0.1121	0.0993	-0.069	0.0121	0.0051	0.0132	0.0713	0.0148	0.0508	11.9679	24.751	51.4018
7	1.9447	-0.1112	-2.1563	1.0939	-0.1725	6.7909	0.0902	0.1484	0.0261	-0.054	-0.0135	0.1185	-0.1319	-0.1564	-0.0766	0.0114	0.0057	0.0024	0.1075	-0.009	0.0584	1.4998	22.5144	50.5047
8	0.7644	1.2446	-2.5382	2.072	-4.2229	8.6254	-0.0899	0.1499	-0.0358	-0.0453	0.1195	-0.0292	0.1101	-0.3174	-0.0296	0.2324	-0.0973	-0.0005	0.2605	-0.0226	0.2403	-3.7953	12.7692	73.7082
9	2.6314	0.1744	0.4414	2.0815	0.0863	1.2727	-0.0249	-0.0848	-0.0769	0.0215	0.0667	-0.1181	-0.0173	0.0194	-0.0418	0.0124	0.0011	0.0088	0.0676	-0.0152	0.0477	23.0263	17.8056	59.8662
10	0.6377	0.1951	0.3921	3.0023	2.5423	3.9881	-0.0244	-0.0673	0.0323	0.1006	0.0058	-0.0002	-0.0976	-0.0928	0.0186	0.0249	0.0034	0.0104	0.0887	-0.0233	0.0526	7.4044	27.6071	64.8139
11	6.7581	-1.087	-2.6426	8.0784	-3.0889	13.2079	0.0357	0.4102	0.6597	-0.2038	-0.0323	-0.0376	-0.6283	-0.1638	-0.0033	0.0794	-0.0129	-0.0031	0.0502	0.027	0.1147	5.6035	34.2428	52.4508
12	15.6743	-15.904	-5.8191	37.2802	9.7678	10.8327	0.0035	0.5068	0.1544	-0.0273	-0.358	0.0016	0.1807	-0.2874	0.3545	0.1268	-0.0118	0.0381	0.1031	0.034	0.0438	22.7543	24.0817	44.1205
13	13.204	-6.7882	2.7976	13.0919	-3.7253	3.7459	-0.2763	-0.5915	0.3669	0.6637	0.2882	0.2643	-0.3323	-0.2944	-0.0119	0.1152	0.0033	0.0319	0.0513	-0.0204	0.0692	25.6688	37.8988	34.133
14	3.0768	0.2323	0.9994	2.1946	-0.108	2.4546	-0.0159	0.075	0.042	0.0437	-0.0631	-0.229	0.0523	0.0569	0.079	0.0928	0	0.0335	0.0122	0.0283	0.0872	32.1393	28.6976	28.604
15	7.4832	-1.3147	-2.2497	1.3052	0.39	1.7599	0.0746	-0.0192	0.0556	-0.0781	-0.0192	-0.1347	0.0272	-0.0326	-0.0555	0.0974	0.0003	0.0292	0.002	0.0023	0.0523	25.3199	16.8038	30.5958
16	4.7401	-0.7739	-3.6611	0.5479	1.1494	6.6006	0.0299	0.3571	-0.067	-0.1428	-0.1009	0.07	0.1469	-0.4972	0.071	0.099	-0.0161	-0.0034	0.0783	-0.026	0.0615	12.7673	13.5031	27.0511

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	-1 - 37
2	X-RAY DIFFRACTION	2	A	38 - 75
3	X-RAY DIFFRACTION	3	A	76 - 90
4	X-RAY DIFFRACTION	4	A	93 - 98
5	X-RAY DIFFRACTION	5	B	0 - 40
6	X-RAY DIFFRACTION	6	B	41 - 67
7	X-RAY DIFFRACTION	7	B	68 - 84
8	X-RAY DIFFRACTION	8	B	85 - 98
9	X-RAY DIFFRACTION	9	C	1 - 40
10	X-RAY DIFFRACTION	10	C	41 - 76
11	X-RAY DIFFRACTION	11	C	77 - 88
12	X-RAY DIFFRACTION	12	C	89 - 98
13	X-RAY DIFFRACTION	13	D	1 - 10
14	X-RAY DIFFRACTION	14	D	11 - 40
15	X-RAY DIFFRACTION	15	D	42 - 63
16	X-RAY DIFFRACTION	16	D	64 - 86

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein / Sugars , 2 types, 5 molecules ABCD

-
Non-polymers , 5 types, 364 molecules

-
Details

-
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

-Protein / Sugars , 2 types, 5 molecules ABCD

-Non-polymers , 5 types, 364 molecules

-Details

-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

-
Protein / Sugars , 2 types, 5 molecules ABCD

-
Non-polymers , 5 types, 364 molecules

-
Details

-
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