PDB-2x2j: Crystal structure of the Gracilariopsis lemaneiformis alpha- 1,4-...

ID or keywords:

Entry

Database: PDB / ID: 2x2j

Title

Crystal structure of the Gracilariopsis lemaneiformis alpha- 1,4-glucan lyase with deoxynojirimycin

Components

ALPHA-1,4-GLUCAN LYASE ISOZYME 1

Keywords

LYASE / STARCH BINDING DOMAIN / ANHYDROFRUCTOSE PATHWAY /

GLYCOSIDE HYDROLASE FAMILY 31

Function / homology

Function and homology information

exo-(1,4)-alpha-D-glucan lyase activity / hydrolase activity, hydrolyzing O-glycosyl compounds /

carbohydrate binding / carbohydrate metabolic process
Similarity search - Function

Biological species

GRACILARIOPSIS LEMANEIFORMIS (eukaryote)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.35 Å

Authors

Rozeboom, H.J. / Yu, S. / Madrid, S. / Kalk, K.H. / Dijkstra, B.W.

Citation

Journal: J.Biol.Chem. / Year: 2013
Title: Crystal Structure of Alpha-1,4-Glucan Lyase, a Unique Glycoside Hydrolase Family Member with a Novel Catalytic Mechanism.
Authors: Rozeboom, H.J. / Yu, S. / Madrid, S. / Kalk, K.H. / Zhang, R. / Dijkstra, B.W.

History

Deposition	Jan 13, 2010	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 19, 2011	Provider: repository / Type: Initial release
Revision 1.1	Aug 14, 2013	Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Version format compliance
Revision 1.2	Sep 25, 2013	Group: Database references
Revision 1.3	Jul 5, 2017	Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4	Jan 30, 2019	Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.5	Feb 6, 2019	Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.6	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Remark 700

SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BL" IN EACH CHAIN ON SHEET RECORDS BELOW ...

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	2x2j.cif.gz	1.6 MB	Display	PDBx/mmCIF format
PDB format	pdb2x2j.ent.gz	1.3 MB	Display	PDB format
PDBx/mmJSON format	2x2j.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x2/2x2j ftp://data.pdbj.org/pub/pdb/validation_reports/x2/2x2j	HTTPS FTP

-
Related structure data

Related structure data	2x2hSC 2x2iC 4amwC 4amxC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4amx-3 2x2i-4 2x2h-3 4amx-4 1qcn-d 3l4x-d 2x2i-2 2x2h-4 2x2h-1 1qco-d 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) 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

2x2hSC

2x2iC

4amwC

4amxC

C: citing same article (ref.)

S: Starting model for refinement

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#74 - Feb 2006 alpha-Amylase similarity (1) #198 - Jun 2016 Beta-galactosidase similarity (1) #203 - Nov 2016 Aminopeptidase 1 and Autophagy similarity (1) #39 - Mar 2003 lac Repressor similarity (1)

Deposited unit

A: ALPHA-1,4-GLUCAN LYASE ISOZYME 1

B: ALPHA-1,4-GLUCAN LYASE ISOZYME 1

C: ALPHA-1,4-GLUCAN LYASE ISOZYME 1

D: ALPHA-1,4-GLUCAN LYASE ISOZYME 1

hetero molecules

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

1

A: ALPHA-1,4-GLUCAN LYASE ISOZYME 1

hetero molecules

defined by author&software
117 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: ALPHA-1,4-GLUCAN LYASE ISOZYME 1

hetero molecules

defined by author&software
116 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: ALPHA-1,4-GLUCAN LYASE ISOZYME 1

hetero molecules

defined by author&software
117 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: ALPHA-1,4-GLUCAN LYASE ISOZYME 1

hetero molecules

defined by author&software
116 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	134.314, 91.707, 192.899
Angle α, β, γ (deg.)	90.00, 99.33, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: NOJ / End label comp-ID: NOJ / Refine code: 4 / Auth seq-ID: 14 - 1050 / Label seq-ID: 3

Dom-ID	Auth asym-ID	Label asym-ID
1	A	A - E
2	B	B - L
3	C	C - O
4	D	D - U

NCS oper:

ID	Code	Matrix	Vector
1	given	(-0.7329, -0.5877, 0.3428), (-0.5797, 0.2756, -0.7668), (0.3562, -0.7607, -0.5426)	13.17, 35.26, 48.11
2	given	(0.7317, -0.5902, -0.3411), (0.5788, 0.2734, 0.7683), (-0.3601, -0.7596, 0.5416)	-19.15, -117, 68.2

#1: Protein	ALPHA-1,4-GLUCAN LYASE ISOZYME 1 Mass: 116062.156 Da / Num. of mol.: 4 / Fragment: RESIDUES 62-1088 Source method: isolated from a genetically manipulated source Source: (gene. exp.) GRACILARIOPSIS LEMANEIFORMIS (eukaryote) Description: REPLICATING VECTOR WITH HARS SEQUENCE. COLLECTED AT TAPING BAY, TSINGTAO, CHINA Production host: PICHIA ANGUSTA (fungus) / Strain (production host): RB11 / References: UniProt: Q9STC1, EC: 4.2.2.13
#2: Chemical	ChemComp-NOJ / 1-DEOXYNOJIRIMYCIN / MORANOLINE / 1-Deoxynojirimycin Mass: 163.172 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₆H₁₃NO₄ / Comment: inhibitor*YM
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1577 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	FIRST 50 AMINO ACIDS ARE A SIGNAL PEPTIDE. THE NEXT 11 AMINO ACIDS ARE NOT PRESENT IN THE ENZYME.

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.5 Å³/Da / Density % sol: 51 % / Description: NONE
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 18-21% PEG 8000, 0.1 M SODIUM ACETATE, PH 5.0-5.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K

-
Data collection

Diffraction	Mean temperature: 110 K
Diffraction source	Source: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
Detector	Type: MAC Science DIP-2030 / Detector: IMAGE PLATE / Date: Mar 1, 2007 / Details: OSMIC MIRRORS
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 2.35→50 Å / Num. obs: 175340 / % possible obs: 91 % / Observed criterion σ(I): -3 / Redundancy: 4 % / B_iso Wilson estimate: 33.5 Å² / R_merge(I) obs: 0.21 / Net I/σ(I): 4.3
Reflection shell	Resolution: 2.35→2.43 Å / Redundancy: 2 % / R_merge(I) obs: 0.69 / Mean I/σ(I) obs: 1 / % possible all: 85.2

-
Processing

Software

Name	Version	Classification
REFMAC	5.5.0102	refinement
DENZO		data reduction
SCALEPACK		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2X2H

2x2h

Resolution: 2.35→33.19 Å / Cor.coef. F_o:F_c: 0.943 / Cor.coef. F_o:F_c free: 0.906 / SU B: 27.018 / SU ML: 0.276 / Cross valid method: THROUGHOUT / ESU R: 0.625 / ESU R Free: 0.326 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. U VALUES WITH TLS ADDED.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.29121	8712	5 %	RANDOM
R_work	0.23387	-	-	-
obs	0.23673	166607	90.98 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 46.07 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.57 Å²	0 Å²	-2.95 Å²
2-	-	-1.99 Å²	0 Å²
3-	-	-	-1.53 Å²

Refinement step

Cycle: LAST / Resolution: 2.35→33.19 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	32648	0	114	1577	34339

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.022	33627
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.301	1.929	45727
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.938	5.019	4104
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.389	24.634	1804
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.103	15	5140
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.333	15	188
X-RAY DIFFRACTION	r_chiral_restr	0.089	0.2	4696
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	26816
X-RAY DIFFRACTION	r_gen_planes_other
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	1.5	20308
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.004	2	32752
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	0.117	3	13319
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	0.148	4.5	12975
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

Ens-ID: 1 / Number: 8173 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Type	Rms dev position (Å)	Weight position
1	A	medium positional	0.26	0.5
2	B	medium positional	0.25	0.5
3	C	medium positional	0.26	0.5
4	D	medium positional	0.25	0.5
1	A	medium thermal	0.05	2
2	B	medium thermal	0.05	2
3	C	medium thermal	0.05	2
4	D	medium thermal	0.04	2

LS refinement shell

Resolution: 2.35→2.411 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.39	584	-
R_work	0.343	11083	-
obs	-	-	82.9 %

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	0.5357	-0.1388	0.6606	0.8925	-0.2947	0.9675	0.0455	-0.0443	0.0119	0.0807	-0.0555	0.1502	0.0279	-0.1624	0.0099	0.4562	-0.0023	0.113	0.5144	-0.0082	0.4302	38.461	3.39	99.334
2	0.4309	-0.1205	0.1008	0.6325	0.3272	1.3032	-0.0691	0.0094	0.0759	0.0991	0.0268	-0.0949	-0.1665	0.146	0.0424	0.4204	-0.0317	0.0614	0.4596	0.0098	0.4481	46.304	8.755	87.018
3	0.3467	0.169	0.1306	0.6232	0.2325	1.0379	-0.0241	0.0658	0.03	0.0506	-0.0246	0.1688	0.0346	-0.1358	0.0486	0.3941	-0.0407	0.0385	0.4857	0.0062	0.4688	25.89	-12.054	65.195
4	2.695	0.6184	0.1571	6.2338	0.4923	-0.2953	0.1183	-0.1832	0.0484	-0.199	-0.1835	0.9935	0.1567	-0.2232	0.0652	0.5045	-0.0811	0.0672	0.7811	0.0201	0.718	6.976	1.589	80.495
5	0.1836	-0.1394	0.458	1.7715	0.4957	1.4008	-0.1011	-0.0468	0.0405	0.0759	0.0041	0.2921	-0.071	-0.2258	0.097	0.3475	0.0092	0.1041	0.5778	-0.0158	0.5853	17.238	2.838	74.633
6	0.5464	-0.2831	-0.0747	0.933	0.2522	0.5623	-0.0625	0.0053	0.0559	-0.0302	0.003	0.0613	-0.0082	-0.0451	0.0594	0.4234	-0.0473	0.0299	0.4731	0.0069	0.3877	38.144	-4.539	67.398
7	0.9717	-0.2337	0.0519	1.026	-0.3091	1.1369	0.055	0.0384	-0.0783	-0.0309	-0.0073	-0.0178	0.1964	0.189	-0.0477	0.4109	-0.0028	0.083	0.4637	-0.0284	0.3882	51.367	-23.185	63.306
8	3.4722	-0.373	3.6197	1.2683	0.742	4.5146	0.1451	0.1202	-0.1658	-0.3089	-0.1825	0.0909	0.1909	0.0197	0.0373	0.6645	0.0857	0.0711	0.5485	-0.0581	0.4665	56.443	-37.702	54.663
9	-0.0913	-1.3779	0.1803	3.1476	-0.5141	-0.1881	0.0524	0.0292	0.0023	-0.1422	0.0647	0.0834	0.2408	0.1622	-0.1171	0.7662	0.0261	-0.0568	0.5682	-0.0258	0.4523	55.78	-36.07	62.632
10	0.6747	0.1134	0.7343	1.7314	0.2878	1.6193	0.0571	0.1678	-0.169	-0.5145	0.0374	-0.088	0.3142	0.2417	-0.0945	0.4969	-0.0285	0.0227	0.557	-0.0541	0.5748	18.19	-62.636	5.382
11	0.4048	0.662	0.0709	2.2562	0.8333	1.1535	0.0015	0.0665	-0.0754	-0.3187	0.063	0.2989	0.1567	-0.0811	-0.0645	0.3707	-0.0227	-0.0466	0.5579	-0.0051	0.5749	4.902	-56.335	10.588
12	0.7286	-0.0333	0.2817	1.3426	0.3313	1.0391	-0.0232	0.0167	0.0287	0.0468	0.0054	-0.067	-0.151	0.0853	0.0178	0.379	-0.0364	-0.011	0.4911	-0.0056	0.46	24.096	-33.458	31.401
13	6.1156	2.1162	6.3056	4.5802	1.529	10.5009	-0.0625	0.3265	0.2377	-0.0803	-0.0478	-0.3719	-0.3148	0.6391	0.1104	0.3692	-0.143	0.1812	0.6979	0.0269	0.5255	35.681	-30.341	6.2
14	1.3733	-0.1349	1.5036	0.8673	-0.1222	4.0562	-0.1419	0.1586	0.0182	-0.254	0.0726	0.0328	-0.3353	0.305	0.0693	0.444	-0.0906	0.0383	0.5312	0.0183	0.5327	25.338	-31.501	11.971
15	0.472	0.3951	0.178	1.2147	-0.0585	1.405	-0.0025	-0.023	0.0064	0.0548	-0.0697	0.1712	-0.0848	-0.0229	0.0722	0.2547	-0.0137	0.0475	0.5135	-0.0311	0.5204	11.589	-40.28	28.551
16	1.2351	0.0424	-0.1595	1.8189	-0.1012	1.3078	0.1291	-0.2148	-0.0989	0.4029	-0.1755	0.1911	0.0747	-0.0755	0.0465	0.5009	-0.1013	0.0481	0.5885	-0.0056	0.5113	11.36	-50.154	49.588
17	-0.0074	-0.1345	-0.1304	8.3662	0.4443	2.5149	-0.0094	-0.5211	0.0578	0.425	0.1531	0.2486	0.0444	-0.0018	-0.1437	0.8069	-0.1358	0.06	0.8258	-0.0164	0.5681	13.108	-50.691	67.144
18	1.0232	-1.5119	-0.5531	5.6258	-0.3374	0.6284	0.4181	-0.2324	-0.2891	0.2474	-0.3826	0.2527	0.0985	0.2015	-0.0355	0.8489	-0.1769	-0.1549	0.7078	0.0695	0.5347	15.516	-55.99	61.395
19	0.1608	-0.0236	0.3258	1.2062	-0.2078	1.3484	-0.056	0.0608	0.0113	-0.3243	0.0366	-0.1161	-0.012	0.1881	0.0194	0.2926	0.0092	0.1706	0.547	-0.013	0.4109	80.155	-50.402	-4.196
20	0.6038	-0.0956	0.3291	0.3957	-0.5833	1.2883	-0.0455	-0.0161	0.1018	-0.0601	0.025	0.082	-0.0979	-0.1006	0.0205	0.2637	0.0231	0.1316	0.4962	-0.0127	0.457	72.338	-45.092	8.198
21	0.1783	-0.1559	-0.0192	0.7205	-0.0473	0.8009	-0.01	-0.0682	0.0601	0.0612	0.0134	-0.1844	0.1318	0.0945	-0.0034	0.2534	0.0153	0.1084	0.5398	0.0127	0.4506	92.976	-65.861	29.831
22	2.2891	2.0815	0.3692	7.5046	2.061	2.0933	-0.1805	-0.0115	-0.1635	-0.3171	0.19	-0.561	-0.0538	0.6805	-0.0095	0.1249	0.0105	0.2979	0.8621	0.0157	0.6154	111.754	-52.133	14.425
23	0.5718	-0.3895	0.6736	1.8421	-1.0856	1.9555	-0.0875	0.0731	0.0608	0.0884	-0.059	-0.3556	-0.1045	0.2384	0.1464	0.2155	-0.0242	0.1331	0.5714	0.014	0.5463	101.483	-50.919	20.406
24	0.5405	0.2902	-0.0838	1.1698	-0.247	0.502	-0.015	0.0235	0.0363	0.1602	0.009	-0.114	0.0233	0.0119	0.0061	0.2118	0.0314	0.1289	0.5193	0.0009	0.3882	80.677	-58.367	27.717
25	0.732	0.0454	0.1531	1.0695	-0.2249	0.9281	0.0048	-0.0105	-0.0497	0.1357	-0.0121	-0.0153	0.0469	-0.1463	0.0073	0.3522	-0.0195	0.122	0.4744	0.0109	0.4051	67.653	-77.076	31.71
26	2.3809	0.7524	1.9599	0.2438	0.2693	3.6611	0.247	0.0234	-0.1836	0.3319	-0.2179	-0.1275	0.6456	-0.0967	-0.0291	0.6787	-0.1302	0.0431	0.5703	0.075	0.4567	62.532	-91.228	40.316
27	1.9788	-1.2724	-0.0044	2.7924	1.2313	2.9806	0.0975	0.0615	-0.1137	0.0153	0.067	0.0023	0.4863	-0.0458	-0.1645	0.4116	-0.0347	0.1135	0.4207	0.0193	0.3805	63.22	-90	32.452
28	0.3805	-0.317	0.5615	2.7746	-0.4014	0.8043	-0.0417	-0.1854	-0.1118	0.4891	0.0568	0.1858	0.1676	-0.2072	-0.0152	0.7179	0.0081	-0.0306	0.5897	0.0756	0.6055	100.596	-24.684	89.715
29	0.3302	-0.5429	0.142	2.0967	-0.635	1.2513	-0.0379	-0.08	-0.0993	0.3411	0.0349	-0.3266	0.1439	0.1519	0.003	0.6124	0.0297	-0.1589	0.531	0.0206	0.6167	113.864	-18.585	84.389
30	0.4013	-0.1039	0.0204	1.1303	-0.6058	1.0844	0.0437	-0.0217	-0.0427	-0.0067	0.0238	0.0821	-0.0066	-0.1041	-0.0675	0.4083	0.0173	-0.033	0.5092	-0.0115	0.5013	94.881	4.443	63.558
31	2.186	-0.6294	1.815	2.6281	-1.6081	8.9614	-0.2122	-0.2498	0.0222	0.5235	0.293	0.3881	-0.3418	-0.8464	-0.0808	0.7143	0.1377	0.0555	0.7339	-0.0125	0.5587	83.124	7.62	88.763
32	0.6717	-0.2744	0.7106	1.9512	0.1119	3.2379	-0.2072	-0.2501	0.0388	0.3845	0.1152	0.0109	-0.3748	-0.3219	0.092	0.6053	0.0652	-0.0229	0.5471	-0.0057	0.5482	93.535	6.384	83.017
33	0.5266	-0.453	0.1154	1.578	-0.2632	1.2373	0.0472	0.046	-0.0057	0.059	-0.0644	-0.2258	0.076	0.0365	0.0171	0.4232	0.0365	-0.0581	0.5053	0.0094	0.539	107.184	-2.343	66.653
34	1.8013	-0.109	0.0987	2.0977	-0.2717	1.2334	0.2759	0.2678	-0.1758	-0.5674	-0.2872	-0.2311	0.4038	0.1716	0.0113	0.721	0.1782	-0.0016	0.609	-0.0158	0.5192	107.886	-12.268	45.412
35	0.0214	-1.3751	-1.3437	4.5757	-2.1984	3.2242	0.2959	0.3195	-0.097	-1.4392	-0.2394	-0.0476	0.4926	-0.0971	-0.0565	1.0633	0.2357	0.0074	0.7923	-0.0662	0.6683	105.782	-12.833	27.846
36	1.2309	0.3406	0.025	2.3956	1.7873	3.1254	-0.2319	-0.1207	-0.0516	-0.451	-0.0797	-0.1451	0.0312	-0.1619	0.3115	0.79	0.1726	-0.0434	0.677	-0.0375	0.578	103.271	-18.114	33.581

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	14 - 124
2	X-RAY DIFFRACTION	2	A	125 - 323
3	X-RAY DIFFRACTION	3	A	324 - 468
4	X-RAY DIFFRACTION	4	A	469 - 503
5	X-RAY DIFFRACTION	5	A	504 - 585
6	X-RAY DIFFRACTION	6	A	586 - 842
7	X-RAY DIFFRACTION	7	A	843 - 973
8	X-RAY DIFFRACTION	8	A	974 - 1018
9	X-RAY DIFFRACTION	9	A	1019 - 1038
10	X-RAY DIFFRACTION	10	B	14 - 124
11	X-RAY DIFFRACTION	11	B	125 - 323
12	X-RAY DIFFRACTION	12	B	324 - 468
13	X-RAY DIFFRACTION	13	B	469 - 503
14	X-RAY DIFFRACTION	14	B	504 - 584
15	X-RAY DIFFRACTION	15	B	585 - 842
16	X-RAY DIFFRACTION	16	B	843 - 973
17	X-RAY DIFFRACTION	17	B	974 - 1018
18	X-RAY DIFFRACTION	18	B	1019 - 1038
19	X-RAY DIFFRACTION	19	C	14 - 124
20	X-RAY DIFFRACTION	20	C	125 - 323
21	X-RAY DIFFRACTION	21	C	324 - 468
22	X-RAY DIFFRACTION	22	C	469 - 503
23	X-RAY DIFFRACTION	23	C	504 - 585
24	X-RAY DIFFRACTION	24	C	586 - 842
25	X-RAY DIFFRACTION	25	C	843 - 972
26	X-RAY DIFFRACTION	26	C	973 - 1018
27	X-RAY DIFFRACTION	27	C	1019 - 1038
28	X-RAY DIFFRACTION	28	D	14 - 123
29	X-RAY DIFFRACTION	29	D	124 - 323
30	X-RAY DIFFRACTION	30	D	324 - 468
31	X-RAY DIFFRACTION	31	D	469 - 503
32	X-RAY DIFFRACTION	32	D	504 - 584
33	X-RAY DIFFRACTION	33	D	585 - 840
34	X-RAY DIFFRACTION	34	D	841 - 973
35	X-RAY DIFFRACTION	35	D	974 - 1018
36	X-RAY DIFFRACTION	36	D	1019 - 1038

-
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