PDB-2vz9: Crystal Structure of Mammalian Fatty Acid Synthase in complex wit...

ID or keywords:

Entry

Database: PDB / ID: 2vz9

Title

Crystal Structure of Mammalian Fatty Acid Synthase in complex with NADP

Components

FATTY ACID SYNTHASE

Keywords

TRANSFERASE / PHOSPHOPANTETHEINE / FATTY ACID SYNTHASE / MULTIENZYME / MEGASYNTHASE / FATTY ACID SYNTHESIS

Function / homology

Function and homology information

fatty-acid synthase system / enoyl-[acyl-carrier-protein] reductase (NADPH, Re-specific) / [acyl-carrier-protein] S-acetyltransferase / [acyl-carrier-protein] S-acetyltransferase activity / oleoyl-[acyl-carrier-protein] hydrolase / (3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity / fatty acyl-[ACP] hydrolase activity / enoyl-[acyl-carrier-protein] reductase (NADPH) activity / [acyl-carrier-protein] S-malonyltransferase / [acyl-carrier-protein] S-malonyltransferase activity ...
Similarity search - Function

Alpha-Beta Plaits - #3290 / Polyketide synthase dehydratase / : / Fatty acid synthase, pseudo-KR domain / Malonyl-Coenzyme A Acyl Carrier Protein, domain 2 / Malonyl-Coenzyme A Acyl Carrier Protein; domain 2 / Zinc-binding dehydrogenase / Methyltransferase type 12 / Methyltransferase domain / Thioesterase ...Alpha-Beta Plaits - #3290 / Polyketide synthase dehydratase / : / Fatty acid synthase, pseudo-KR domain / Malonyl-Coenzyme A Acyl Carrier Protein, domain 2 / Malonyl-Coenzyme A Acyl Carrier Protein; domain 2 / Zinc-binding dehydrogenase / Methyltransferase type 12 / Methyltransferase domain / Thioesterase / Thioesterase domain / Polyketide synthase dehydratase N-terminal domain / Polyketide synthase, dehydratase domain / PKS_DH / : / Polyketide synthase dehydratase domain / Polyketide synthase, dehydratase domain superfamily / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding / Thiol Ester Dehydrase; Chain A / : / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / Zinc-binding dehydrogenase / Acyl transferase/acyl hydrolase/lysophospholipase / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Polyketide synthase, enoylreductase domain / Enoylreductase / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / PKS_KR / Ketosynthase family 3 (KS3) domain profile. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / GroES-like superfamily / Thiolase-like / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Vaccinia Virus protein VP39 / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha/Beta hydrolase fold / NAD(P)-binding Rossmann-like Domain / Alpha-Beta Plaits / NAD(P)-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Roll / Alpha-Beta Complex / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology

Biological species

SUS SCROFA (pig)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.3 Å

Authors

Maier, T. / Leibundgut, M. / Ban, N.

Citation

Journal: Science / Year: 2008
Title: The Crystal Structure of a Mammalian Fatty Acid Synthase.
Authors: Maier, T. / Leibundgut, M. / Ban, N.

History

Deposition	Jul 31, 2008	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 9, 2008	Provider: repository / Type: Initial release
Revision 1.1	May 7, 2011	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Dec 13, 2023	Group: Data collection / Database references ...Data collection / Database references / 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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

Remark 650

HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

Remark 700

SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	2vz9.cif.gz	1.6 MB	Display	PDBx/mmCIF format
PDB format	pdb2vz9.ent.gz	1.3 MB	Display	PDB format
PDBx/mmJSON format	2vz9.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	2vz9_validation.pdf.gz	1.5 MB	Display	wwPDB validaton report
Full document	2vz9_full_validation.pdf.gz	1.8 MB	Display
Data in XML	2vz9_validation.xml.gz	166.7 KB	Display
Data in CIF	2vz9_validation.cif.gz	219.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vz/2vz9 ftp://data.pdbj.org/pub/pdb/validation_reports/vz/2vz9	HTTPS FTP

-
Related structure data

Related structure data	2vz8C 2cf2S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	2vz8-d 23017 2361 3zha-d 7cpx-d 6iy6-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#90 - Jun 2007 Fatty Acid Synthase similarity (19) #13 - Jan 2001 Alcohol Dehydrogenase similarity (4) #239 - Nov 2019 Phospholipase A2 similarity (1) #32 - Aug 2002 Chaperones similarity (1) #216 - Dec 2017 Biodegradable Plastic similarity (1)

Deposited unit

A: FATTY ACID SYNTHASE

B: FATTY ACID SYNTHASE

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	96.150, 244.890, 135.370
Angle α, β, γ (deg.)	90.00, 101.84, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details
1	1	1	CHAIN A AND (RESSEQ 1:116 OR RESSEQ 118:120 OR RESSEQ...
2	1	1	CHAIN B AND (RESSEQ 1:116 OR RESSEQ 118:120 OR RESSEQ...
1	1	2	CHAIN A AND (RESSEQ 474:479 OR RESSEQ 485:489))
2	1	2	CHAIN B AND (RESSEQ 474:479 OR RESSEQ 485:489))
1	1	3	CHAIN A AND (RESSEQ 490:499 OR RESSEQ 500:503 OR RESSEQ...
2	1	3	CHAIN B AND (RESSEQ 490:499 OR RESSEQ 500:503 OR RESSEQ...
1	1	4	CHAIN A AND RESSEQ 626:633)
2	1	4	CHAIN B AND RESSEQ 626:633)
1	1	5	CHAIN A AND RESSEQ 637:642)
2	1	5	CHAIN B AND RESSEQ 637:642)
1	1	6	CHAIN A AND RESSEQ 648:652)
2	1	6	CHAIN B AND RESSEQ 648:652)
1	1	7	CHAIN A AND RESSEQ 683:702)
2	1	7	CHAIN B AND RESSEQ 683:702)
1	1	8	CHAIN A AND (RESSEQ 706:722 OR RESSEQ 724:732 OR RESSEQ 734:750 OR RESSEQ 752:755))
2	1	8	CHAIN B AND (RESSEQ 706:722 OR RESSEQ 724:732 OR RESSEQ 734:750 OR RESSEQ 752:755))
1	1	9	CHAIN A AND RESSEQ 756:817)
2	1	9	CHAIN B AND RESSEQ 756:817)
1	1	10	CHAIN A AND RESSEQ 822:843)
2	1	10	CHAIN B AND RESSEQ 822:843)
1	1	11	CHAIN A AND RESSEQ 859:970)
2	1	11	CHAIN B AND RESSEQ 859:970)
1	1	12	CHAIN A AND (RESSEQ 985:1052 OR RESSEQ 1054:1104))
2	1	12	CHAIN B AND (RESSEQ 985:1052 OR RESSEQ 1054:1104))
1	1	13	CHAIN A AND RESSEQ 1105:1111)
2	1	13	CHAIN B AND RESSEQ 1105:1111)
1	1	14	CHAIN A AND RESSEQ 1113:1135)
2	1	14	CHAIN B AND RESSEQ 1113:1135)
1	1	15	CHAIN A AND (RESSEQ 1216:1275 OR RESSEQ 1277:1281 OR RESSEQ 1283:1289 OR RESSEQ 1294:1300))
2	1	15	CHAIN B AND (RESSEQ 1216:1275 OR RESSEQ 1277:1281 OR RESSEQ 1283:1289 OR RESSEQ 1294:1300))
1	1	16	CHAIN A AND RESSEQ 1312:1320)
2	1	16	CHAIN B AND RESSEQ 1312:1320)
1	1	17	CHAIN A AND RESSEQ 1327:1349)
2	1	17	CHAIN B AND RESSEQ 1327:1349)
1	1	18	CHAIN A AND RESSEQ 1376:1385)
2	1	18	CHAIN B AND RESSEQ 1376:1385)
1	1	19	CHAIN A AND RESSEQ 1387:1406)
2	1	19	CHAIN B AND RESSEQ 1387:1406)
1	1	20	CHAIN A AND RESSEQ 1414:1433)
2	1	20	CHAIN B AND RESSEQ 1414:1433)
1	1	21	CHAIN A AND RESSEQ 1438:1470)
2	1	21	CHAIN B AND RESSEQ 1438:1470)
1	1	22	CHAIN A AND RESSEQ 1471:1482)
2	1	22	CHAIN B AND RESSEQ 1471:1482)
1	1	23	CHAIN A AND RESSEQ 1492:1512)
2	1	23	CHAIN B AND RESSEQ 1492:1512)
1	1	24	CHAIN A AND RESSEQ 1513:1526)
2	1	24	CHAIN B AND RESSEQ 1513:1526)
1	1	25	CHAIN A AND (RESSEQ 1563:1594 OR RESSEQ 1696:1798 OR RESSEQ...
2	1	25	CHAIN B AND (RESSEQ 1563:1594 OR RESSEQ 1696:1798 OR RESSEQ...
1	1	26	CHAIN A AND (RESSEQ 1872:1974 OR RESSEQ 1991:2071 OR RESSEQ 2076:2110))
2	1	26	CHAIN B AND (RESSEQ 1872:1974 OR RESSEQ 1991:2071 OR RESSEQ 2076:2110))

NCS ensembles :

#1: Protein	FATTY ACID SYNTHASE Mass: 272532.188 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: LACTATING MAMMARY GLAND / Source: (natural) SUS SCROFA (pig) / Organ: MAMMARY GLAND / References: UniProt: A5YV76, fatty-acid synthase system
#2: Chemical	ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₂₈N₇O₁₇P₃
Sequence details	SEQUENCE CONTAINS A SINGLE X BASED ON TRANSLATION FROM NUCLEIC ACID SEQUENCE CONTAINING A K. THIS ...SEQUENCE CONTAINS A SINGLE X BASED ON TRANSLATION FROM NUCLEIC ACID SEQUENCE CONTAINING A K. THIS POSITION WAS ASSIGNED BASED ON FURTHER EST SEQUENCES.

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 8

-
Sample preparation

Crystal	Density Matthews: 3.49 Å³/Da / Density % sol: 64.45 % / Description: NONE
Crystal grow	pH: 7 / Details: pH 7.0

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9992
Detector	Type: MARRESEARCH / Detector: CCD / Date: Nov 11, 2006
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9992 Å / Relative weight: 1
Reflection	Resolution: 3.2→30 Å / Num. obs: 80129 / % possible obs: 90.4 % / Redundancy: 5.7 % / R_merge(I) obs: 0.16 / Net I/σ(I): 9.2
Reflection shell	Resolution: 3.3→3.5 Å / Redundancy: 3.1 % / R_merge(I) obs: 0.93 / Mean I/σ(I) obs: 1.1 / % possible all: 68.9

-
Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
XDS		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CF2

2cf2

Resolution: 3.3→30 Å / SU ML: 0.37 / Phase error: 26.38 / Stereochemistry target values: ML
Details: UNBIASED ELECTRON DENSITY MAPS FOR THE LINKERS (RESIDUES 852-857) IN THE REGION OF THE CENTRAL CONNECTION ARE NOT CONTIGUOUS FOR ONE OR TWO AMINO ACIDS SUCH THAT THE POSSIBILITY OF ...

	R_factor	Num. reflection	% reflection
R_free	0.2442	7420	5 %
R_work	0.193	-	-
obs	-	147640	84.09 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 78.38 Å² / k_sol: 0.29 e/Å³

Refinement step

Cycle: LAST / Resolution: 3.3→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	31757	0	192	0	31949

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	32647
X-RAY DIFFRACTION	f_angle_d	1.28	44406
X-RAY DIFFRACTION	f_dihedral_angle_d	19.474	11898
X-RAY DIFFRACTION	f_chiral_restr	0.079	5031
X-RAY DIFFRACTION	f_plane_restr	0.006	5776

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	A	3329	X-RAY DIFFRACTION	POSITIONAL
1	2	B	3329	X-RAY DIFFRACTION	POSITIONAL	0.034
2	1	A	65	X-RAY DIFFRACTION	POSITIONAL
2	2	B	65	X-RAY DIFFRACTION	POSITIONAL	0.043
3	1	A	785	X-RAY DIFFRACTION	POSITIONAL
3	2	B	785	X-RAY DIFFRACTION	POSITIONAL	0.037
4	1	A	73	X-RAY DIFFRACTION	POSITIONAL
4	2	B	73	X-RAY DIFFRACTION	POSITIONAL	0.037
5	1	A	37	X-RAY DIFFRACTION	POSITIONAL
5	2	B	37	X-RAY DIFFRACTION	POSITIONAL	0.047
6	1	A	35	X-RAY DIFFRACTION	POSITIONAL
6	2	B	35	X-RAY DIFFRACTION	POSITIONAL	0.035
7	1	A	168	X-RAY DIFFRACTION	POSITIONAL
7	2	B	168	X-RAY DIFFRACTION	POSITIONAL	0.034
8	1	A	373	X-RAY DIFFRACTION	POSITIONAL
8	2	B	373	X-RAY DIFFRACTION	POSITIONAL	0.032
9	1	A	476	X-RAY DIFFRACTION	POSITIONAL
9	2	B	476	X-RAY DIFFRACTION	POSITIONAL	0.034
10	1	A	178	X-RAY DIFFRACTION	POSITIONAL
10	2	B	178	X-RAY DIFFRACTION	POSITIONAL	0.028
11	1	A	884	X-RAY DIFFRACTION	POSITIONAL
11	2	B	884	X-RAY DIFFRACTION	POSITIONAL	0.038
12	1	A	942	X-RAY DIFFRACTION	POSITIONAL
12	2	B	942	X-RAY DIFFRACTION	POSITIONAL	0.041
13	1	A	64	X-RAY DIFFRACTION	POSITIONAL
13	2	B	64	X-RAY DIFFRACTION	POSITIONAL	0.029
14	1	A	171	X-RAY DIFFRACTION	POSITIONAL
14	2	B	171	X-RAY DIFFRACTION	POSITIONAL	0.114
15	1	A	589	X-RAY DIFFRACTION	POSITIONAL
15	2	B	589	X-RAY DIFFRACTION	POSITIONAL	0.181
16	1	A	61	X-RAY DIFFRACTION	POSITIONAL
16	2	B	61	X-RAY DIFFRACTION	POSITIONAL	0.255
17	1	A	162	X-RAY DIFFRACTION	POSITIONAL
17	2	B	162	X-RAY DIFFRACTION	POSITIONAL	0.131
18	1	A	79	X-RAY DIFFRACTION	POSITIONAL
18	2	B	79	X-RAY DIFFRACTION	POSITIONAL	0.162
19	1	A	165	X-RAY DIFFRACTION	POSITIONAL
19	2	B	165	X-RAY DIFFRACTION	POSITIONAL	0.155
20	1	A	167	X-RAY DIFFRACTION	POSITIONAL
20	2	B	167	X-RAY DIFFRACTION	POSITIONAL	0.143
21	1	A	245	X-RAY DIFFRACTION	POSITIONAL
21	2	B	245	X-RAY DIFFRACTION	POSITIONAL	0.16
22	1	A	82	X-RAY DIFFRACTION	POSITIONAL
22	2	B	82	X-RAY DIFFRACTION	POSITIONAL	0.357
23	1	A	167	X-RAY DIFFRACTION	POSITIONAL
23	2	B	167	X-RAY DIFFRACTION	POSITIONAL	0.145
24	1	A	125	X-RAY DIFFRACTION	POSITIONAL
24	2	B	125	X-RAY DIFFRACTION	POSITIONAL	0.221
25	1	A	1445	X-RAY DIFFRACTION	POSITIONAL
25	2	B	1445	X-RAY DIFFRACTION	POSITIONAL	0.041
26	1	A	1649	X-RAY DIFFRACTION	POSITIONAL
26	2	B	1649	X-RAY DIFFRACTION	POSITIONAL	0.038

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
3.3374-3.3752	0.3806	70	0.3572	1453	X-RAY DIFFRACTION	26
3.3752-3.4149	0.3672	107	0.3396	2257	X-RAY DIFFRACTION	40
3.4149-3.4565	0.3455	166	0.3413	3020	X-RAY DIFFRACTION	54
3.4565-3.5002	0.3608	191	0.3276	4249	X-RAY DIFFRACTION	76
3.5002-3.5462	0.3188	235	0.302	4217	X-RAY DIFFRACTION	76
3.5462-3.5947	0.3313	233	0.302	4212	X-RAY DIFFRACTION	77
3.5947-3.6459	0.3294	210	0.2897	4264	X-RAY DIFFRACTION	76
3.6459-3.7002	0.3346	228	0.2758	4454	X-RAY DIFFRACTION	79
3.7002-3.758	0.2828	232	0.2624	4310	X-RAY DIFFRACTION	78
3.758-3.8194	0.3113	248	0.2506	4581	X-RAY DIFFRACTION	82
3.8194-3.8852	0.2822	260	0.256	5112	X-RAY DIFFRACTION	93
3.8852-3.9557	0.2581	276	0.2509	5146	X-RAY DIFFRACTION	93
3.9557-4.0316	0.2552	283	0.2335	5198	X-RAY DIFFRACTION	93
4.0316-4.1137	0.2762	274	0.2309	5168	X-RAY DIFFRACTION	93
4.1137-4.2029	0.2583	263	0.225	5202	X-RAY DIFFRACTION	93
4.2029-4.3004	0.2831	284	0.2155	5166	X-RAY DIFFRACTION	93
4.3004-4.4076	0.2427	298	0.1917	5141	X-RAY DIFFRACTION	93
4.4076-4.5264	0.2438	298	0.1817	5170	X-RAY DIFFRACTION	93
4.5264-4.6591	0.218	288	0.1717	5178	X-RAY DIFFRACTION	93
4.6591-4.8089	0.2344	290	0.1643	5189	X-RAY DIFFRACTION	93
4.8089-4.98	0.218	257	0.1623	5144	X-RAY DIFFRACTION	93
4.98-5.1784	0.2345	309	0.1675	5128	X-RAY DIFFRACTION	93
5.1784-5.4128	0.2661	268	0.1708	5198	X-RAY DIFFRACTION	93
5.4128-5.6963	0.2406	243	0.1641	5275	X-RAY DIFFRACTION	94
5.6963-6.0505	0.2273	263	0.1645	5163	X-RAY DIFFRACTION	94
6.0505-6.5132	0.2304	277	0.1664	5207	X-RAY DIFFRACTION	93
6.5132-7.1606	0.2089	302	0.1519	5156	X-RAY DIFFRACTION	93
7.1606-8.1783	0.1879	275	0.1317	5202	X-RAY DIFFRACTION	94
8.1783-10.2351	0.1749	265	0.1098	5174	X-RAY DIFFRACTION	93
10.2351-29.97	0.2062	227	0.1842	4886	X-RAY DIFFRACTION	87

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	3.2878	0.5462	1.42	2.211	-0.293	2.3754	-0.4188	-0.0227	0.7764	-0.0214	-0.2199	0.1412	-0.18	-0.2854	0.0004	0.7668	0.0118	0.2057	0.4957	-0.0243	1.5055	34.7713	73.9885	50.214
2	0.2333	-0.0998	-0.0203	0.2802	-0.0175	-0.1809	-0.2069	0.1351	-0.3624	0.8673	-0.0376	-0.113	1.3727	-0.9443	-0.0012	1.2647	-0.0615	0.1757	0.8195	-0.0169	1.6318	17.3972	57.6968	57.8677
3	1.8354	2.0094	-1.6542	2.6162	1.8463	2.6965	-0.193	-0.9112	0.473	0.4236	-0.0213	0.4001	0.715	-0.8655	-0.0002	0.8806	-0.0766	0.3127	0.7545	-0.0383	1.4078	25.9985	62.9952	58.2595
4	1.5937	-0.4991	1.1256	1.4576	1.4877	1.1288	-0.281	-0.5119	-0.0271	-0.3336	0.0532	-0.59	-0.4155	-0.0074	-0.0001	0.8062	0.2002	0.125	0.8305	0.0898	1.4385	57.9582	62.2827	68.2223
5	0.6277	-2.4045	-0.2749	1.9222	-1.6015	1.7033	-0.0517	0.5136	0.7149	-0.1022	0.2205	0.0502	-0.3857	-0.4782	-0.0004	0.499	-0.0529	0.0443	0.5621	0.1097	0.7312	79.2714	40.3263	66.361
6	1.341	-0.2485	0.6961	0.9037	-0.6584	2.0755	-0.21	-0.9625	1.0003	-0.1731	0.4422	-0.2465	-0.1476	-0.3162	0.0006	0.842	-0.083	-0.013	0.8087	-0.3031	1.4274	100.8584	51.4876	78.7963
7	2.1301	-2.2145	0.4269	3.2198	-0.1778	-0.0827	0.1622	-0.1077	0.8788	-0.2638	0.0067	-0.1764	-0.1209	-0.1301	0.0003	0.7444	0.0017	0.1203	0.7122	0.1539	1.0314	78.166	53.8955	63.6483
8	4.1625	-0.6421	2.1031	3.911	-0.4202	5.665	0.1394	0.1078	-0.9272	-0.1474	-0.059	-0.6429	0.3471	0.0251	-0.0021	0.6802	0.1127	0.0705	0.5207	-0.2414	0.9092	52.1338	118.0756	50.4356
9	3.0696	1.1424	3.4895	4.4242	-0.2012	2.9958	0.3308	0.4104	-0.3465	-0.1763	0.0632	-0.6508	0.2032	0.5345	-0.0014	0.7735	0.1147	0.2004	0.717	-0.0725	0.538	66.2281	125.5033	52.7652
10	0.032	-0.6493	0.1078	0.5178	0.403	0.8054	-0.7956	-0.5331	-0.1412	0.7905	-0.3889	0.5875	1.03	-0.4876	-0.0008	2.4126	0.0472	0.1629	1.548	0.0886	1.6833	65.4027	112.0573	109.0744
11	0.7668	1.2043	0.1883	0.8811	0.4718	2.0706	0.0625	-1.0262	-1.0142	0.4539	-0.4419	-0.0522	1.0227	-0.0794	0.0006	2.484	0.112	-0.2447	1.7726	0.6204	1.6518	73.6291	95.9115	108.1573
12	1.8705	-0.012	-0.7474	0.4612	-0.6295	1.4541	0.049	0.0406	-1.1744	1.6777	-0.1093	-1.3601	0.4774	0.7196	0.0009	2.0361	0.5088	-0.6489	2.0067	0.2305	1.5638	98.6315	108.2773	95.7624
13	4.7849	-0.4066	2.9451	0.6465	-0.202	2.8566	-0.0951	-1.0616	-0.0532	0.3427	-0.1214	-0.0371	0.3395	-0.2366	0.0002	0.8265	-0.095	0.1393	1.0005	-0.1845	0.4171	44.5259	144.6223	80.7299
14	2.9689	0.0382	0.4126	1.8223	-0.6807	4.0322	-0.1371	-0.4746	-0.4558	0.237	0.0052	-0.3655	0.3834	0.6756	-0.0009	0.8789	0.0417	-0.1874	0.9209	0.1199	0.7278	83.7512	132.079	82.0134
15	1.1273	0.1519	-1.5285	1.4341	-1.443	1.1667	-0.1704	0.3378	-0.6111	0.7188	0.36	-0.9354	1.2605	1.0127	-0.0019	1.2458	0.1343	-0.0882	1.0503	0.2021	0.9466	77.9168	120.086	84.0901
16	4.0577	-0.7825	0.7057	1.5391	0.1327	2.1656	0.1662	1.2302	1.1966	-0.662	-0.6237	-0.2037	-0.3143	0.5174	0.0003	1.197	0.2027	0.1697	1.0101	0.689	1.7497	39.0175	80.9895	25.6071
17	0.0587	-0.0418	-0.4206	0.2758	0.3249	-0.0996	-0.2246	1.1414	-0.0714	-0.8522	-0.406	0.5364	1.0126	1.039	-0.0038	1.4947	0.1599	0.0387	2.1622	1.0794	1.9252	56.5628	71.2184	10.6567
18	0.7441	0.2509	-1.1169	1.7976	-0.2548	0.3192	-0.0016	1.434	0.4063	-0.9748	-0.3611	0.4902	-0.2264	0.9884	-0.0004	1.5435	0.3472	0.3102	1.8476	0.7307	1.7094	47.8876	75.9082	13.0321
19	0.4962	0.6567	-0.0022	-0.175	0.6646	-0.1889	-0.2078	1.314	-0.0999	-0.0005	-0.4543	1.0622	0.3701	-0.3073	-0.0012	1.8867	0.3987	-0.0278	1.6441	0.2112	1.7379	15.8476	80.2863	3.9779
20	1.4656	0.634	0.7582	1.1185	-0.3475	0.1041	0.032	0.6408	-0.0726	-0.6711	-0.1614	0.2359	-0.0251	-0.1387	0.0001	1.928	0.3589	-0.2348	1.794	-0.1207	1.2739	-4.192	59.2212	-4.8436
21	-0.5661	-0.0395	-0.5008	-0.3892	0.6315	-0.19	-1.1437	0.4606	1.0526	-0.7964	-0.5639	1.5425	-0.994	0.328	-0.0083	2.6213	0.2388	-0.6188	2.2476	-0.0369	1.663	-29.334	72.0452	-9.7053
22	0.771	0.0491	0.9538	0.2145	0.3046	1.8289	0.1472	0.2317	0.0668	-0.5152	-0.376	-0.0046	0.1182	-0.2071	-0.0001	1.7935	0.3537	-0.1299	1.6742	0.0341	1.4512	-3.8488	69.608	4.1242
23	5.471	-0.8879	1.878	4.2286	0.2786	2.7144	0.2886	0.1298	-1.1509	-0.2271	-0.2654	0.3297	0.5509	0.2285	-0.0001	0.658	-0.1781	-0.0136	0.64	-0.2687	0.9776	19.1847	122.2808	48.6516
24	3.1737	-1.5331	2.3942	3.1704	-0.256	2.1886	0.0714	-0.1605	-0.3992	-0.0122	0.0644	0.5592	-0.0029	-0.3739	-0.0001	0.7053	-0.1342	0.0239	0.8395	-0.0427	0.5878	6.9143	132.4228	51.7424
25	0.6758	-0.2328	0.4514	0.6306	0.2475	0.4797	-0.0939	0.4329	0.0606	-0.6486	0.0772	-0.397	0.5545	-0.6185	-0.0003	1.7529	-0.2805	-0.155	1.6026	-0.1111	1.0935	9.1889	152.0391	-3.8463
26	2.2237	0.7333	-0.2803	0.8562	-0.282	1.5497	-0.3157	1.186	-0.5436	-0.673	0.0676	-0.2775	0.2676	-0.7597	-0.0005	2.1877	-0.4	-0.4602	2.126	-0.2678	0.9957	-3.4418	139.9657	-10.3078
27	1.1278	0.6918	-1.1108	0.2358	-0.5079	1.3833	-0.4636	1.1938	-0.2621	-1.5764	0.155	1.6484	0.074	-1.0239	-0.0004	1.5987	-0.3956	-0.8771	2.6337	0.1209	1.2768	-25.8176	149.2897	8.5479
28	3.7815	-0.6338	2.0286	0.5681	-0.8449	1.9449	-0.2227	0.9083	0.4646	-0.4889	-0.1242	-0.004	-0.0775	-0.3372	0.0004	0.8803	0.0727	-0.0217	0.9419	0.0542	0.5708	33.6379	158.7576	38.1652
29	2.1907	-0.0014	-0.6496	2.2873	-0.9738	3.9778	-0.0243	0.8676	0.1528	-0.4062	-0.0026	0.421	0.126	-0.2816	-0.0006	0.609	-0.0226	-0.2653	0.9394	-0.0805	0.7051	-6.8786	157.4477	32.022
30	1.9158	0.0756	-0.6255	0.538	1.3112	1.9867	-0.4442	0.6141	-0.5148	0.0123	0.7275	0.3485	0.7217	-0.2524	-0.0008	0.8762	-0.1396	-0.2732	1.3124	-0.3115	0.4702	-3.6028	147.5093	23.2997

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND RESID 1:315)
2	X-RAY DIFFRACTION	2	CHAIN A AND RESID 316:325)
3	X-RAY DIFFRACTION	3	CHAIN A AND RESID 326:419)
4	X-RAY DIFFRACTION	4	CHAIN A AND RESID 420:488)
5	X-RAY DIFFRACTION	5	CHAIN A AND RESID 489:611)
6	X-RAY DIFFRACTION	6	CHAIN A AND RESID 612:672)
7	X-RAY DIFFRACTION	7	CHAIN A AND RESID 673:851)
8	X-RAY DIFFRACTION	8	CHAIN A AND RESID 858:981)
9	X-RAY DIFFRACTION	9	CHAIN A AND RESID 982:1105)
10	X-RAY DIFFRACTION	10	CHAIN A AND RESID 1106:1192)
11	X-RAY DIFFRACTION	11	CHAIN A AND RESID 1193:1418)
12	X-RAY DIFFRACTION	12	CHAIN A AND RESID 1419:1505)
13	X-RAY DIFFRACTION	13	CHAIN A AND RESID 1506:1856)
14	X-RAY DIFFRACTION	14	CHAIN A AND RESID 1857:2043)
15	X-RAY DIFFRACTION	15	CHAIN A AND RESID 2044:2113)
16	X-RAY DIFFRACTION	16	CHAIN B AND RESID 1:315)
17	X-RAY DIFFRACTION	17	CHAIN B AND RESID 316:325)
18	X-RAY DIFFRACTION	18	CHAIN B AND RESID 326:419)
19	X-RAY DIFFRACTION	19	CHAIN B AND RESID 420:488)
20	X-RAY DIFFRACTION	20	CHAIN B AND RESID 489:611)
21	X-RAY DIFFRACTION	21	CHAIN B AND RESID 612:672)
22	X-RAY DIFFRACTION	22	CHAIN B AND RESID 673:851)
23	X-RAY DIFFRACTION	23	CHAIN B AND RESID 858:981)
24	X-RAY DIFFRACTION	24	CHAIN B AND RESID 982:1105)
25	X-RAY DIFFRACTION	25	CHAIN B AND RESID 1106:1192)
26	X-RAY DIFFRACTION	26	CHAIN B AND RESID 1193:1418)
27	X-RAY DIFFRACTION	27	CHAIN B AND RESID 1419:1505)
28	X-RAY DIFFRACTION	28	CHAIN B AND RESID 1506:1856)
29	X-RAY DIFFRACTION	29	CHAIN B AND RESID 1857:2043)
30	X-RAY DIFFRACTION	30	CHAIN B AND RESID 2044:2113)

-
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