PDB-2vz8: Crystal Structure of Mammalian Fatty Acid Synthase

ID or keywords:

Entry

Database: PDB / ID: 2vz8

Title

Crystal Structure of Mammalian Fatty Acid Synthase

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 / enoyl-[acyl-carrier-protein] reductase (NADPH) activity / [acyl-carrier-protein] S-malonyltransferase / [acyl-carrier-protein] S-malonyltransferase activity / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase / (3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity / beta-ketoacyl-[acyl-carrier-protein] synthase I ...
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 / Polyketide synthase dehydratase N-terminal domain ...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 / Polyketide synthase dehydratase N-terminal domain / Thioesterase / Thioesterase domain / Polyketide synthase, dehydratase domain / PKS_DH / : / Polyketide synthase dehydratase domain / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, C-terminal extension / Thiol Ester Dehydrase; Chain A / Ketoacyl-synthetase C-terminal extension / Polyketide synthase, ketoreductase domain / KR domain / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Malonyl-CoA ACP transacylase, ACP-binding / : / Zinc-binding dehydrogenase / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Acyl transferase/acyl hydrolase/lysophospholipase / Polyketide synthase, enoylreductase domain / Enoylreductase / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / PKS_KR / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / GroES-like superfamily / Thiolase-like / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / 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: 3.219 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	2vz8.cif.gz	1.5 MB	Display	PDBx/mmCIF format
PDB format	pdb2vz8.ent.gz	1.3 MB	Display	PDB format
PDBx/mmJSON format	2vz8.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	2vz8_validation.pdf.gz	488.8 KB	Display	wwPDB validaton report
Full document	2vz8_full_validation.pdf.gz	700 KB	Display
Data in XML	2vz8_validation.xml.gz	154.9 KB	Display
Data in CIF	2vz8_validation.cif.gz	205.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vz/2vz8 ftp://data.pdbj.org/pub/pdb/validation_reports/vz/2vz8	HTTPS FTP

-
Related structure data

Related structure data	2vz9C 2cf2S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	2vz9-d 3t3s-d 23017 6igz-d 5816 10043 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

545 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)	96.320, 244.700, 135.250
Angle α, β, γ (deg.)	90.00, 101.65, 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 1054:1105))
2	1	12	CHAIN B AND (RESSEQ 985:1052 OR RESSEQ 1054:1105))
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
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: 16

-
Sample preparation

Crystal	Density Matthews: 3.2 Å³/Da / Density % sol: 57.03 % / Description: NONE
Crystal grow	pH: 7 / Details: pH 7.0

-
Data collection

Diffraction	Mean temperature: 10 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
Detector	Type: MARRESEARCH / Detector: CCD / Date: Dec 8, 2006
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 3.2→30 Å / Num. obs: 96975 / % possible obs: 98.5 % / Redundancy: 7 % / B_iso Wilson estimate: 94.87 Å² / R_merge(I) obs: 0.17 / Net I/σ(I): 9.9
Reflection shell	Resolution: 3.2→3.4 Å / Redundancy: 5.5 % / R_merge(I) obs: 0.99 / Mean I/σ(I) obs: 1.4 / % possible all: 93.2

-
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: 3.219→29.496 Å / SU ML: 0.48 / σ(F): 0.84 / Phase error: 28.62 / 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	0.2588	9286	5 %
R_work	0.2175	-	-
obs	0.2196	185581	94.79 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 71.89 Å² / k_sol: 0.288 e/Å³

Displacement parameters

B_iso mean: 143.83 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-10.6551 Å²	0 Å²	0.4366 Å²
2-	-	-7.3604 Å²	0 Å²
3-	-	-	18.0155 Å²

Refinement step

Cycle: LAST / Resolution: 3.219→29.496 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	30281	0	0	0	30281

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	30938
X-RAY DIFFRACTION	f_angle_d	1.231	42039
X-RAY DIFFRACTION	f_dihedral_angle_d	18.789	11220
X-RAY DIFFRACTION	f_chiral_restr	0.075	4761
X-RAY DIFFRACTION	f_plane_restr	0.006	5483

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	0.035
2	1	A	65	X-RAY DIFFRACTION	POSITIONAL
2	2	B	65	X-RAY DIFFRACTION	POSITIONAL	0.036
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	0.048
5	1	A	37	X-RAY DIFFRACTION	POSITIONAL
5	2	B	37	X-RAY DIFFRACTION	POSITIONAL	0.046
6	1	A	35	X-RAY DIFFRACTION	POSITIONAL
6	2	B	35	X-RAY DIFFRACTION	POSITIONAL	0.031
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	0.034
9	1	A	476	X-RAY DIFFRACTION	POSITIONAL
9	2	B	476	X-RAY DIFFRACTION	POSITIONAL	0.033
10	1	A	178	X-RAY DIFFRACTION	POSITIONAL
10	2	B	178	X-RAY DIFFRACTION	POSITIONAL	0.03
11	1	A	884	X-RAY DIFFRACTION	POSITIONAL
11	2	B	884	X-RAY DIFFRACTION	POSITIONAL	0.035
12	1	A	949	X-RAY DIFFRACTION	POSITIONAL
12	2	B	949	X-RAY DIFFRACTION	POSITIONAL	0.039
13	1	A	64	X-RAY DIFFRACTION	POSITIONAL
13	2	B	64	X-RAY DIFFRACTION	POSITIONAL	0.028
14	1	A	171	X-RAY DIFFRACTION	POSITIONAL
14	2	B	171	X-RAY DIFFRACTION	POSITIONAL	0.087
15	1	A	589	X-RAY DIFFRACTION	POSITIONAL
15	2	B	589	X-RAY DIFFRACTION	POSITIONAL	0.142
16	1	A	61	X-RAY DIFFRACTION	POSITIONAL
16	2	B	61	X-RAY DIFFRACTION	POSITIONAL	0.131
17	1	A	68	X-RAY DIFFRACTION	POSITIONAL
17	2	B	68	X-RAY DIFFRACTION	POSITIONAL	0.141
18	1	A	79	X-RAY DIFFRACTION	POSITIONAL
18	2	B	79	X-RAY DIFFRACTION	POSITIONAL	0.192
19	1	A	165	X-RAY DIFFRACTION	POSITIONAL
19	2	B	165	X-RAY DIFFRACTION	POSITIONAL	0.147
20	1	A	167	X-RAY DIFFRACTION	POSITIONAL
20	2	B	167	X-RAY DIFFRACTION	POSITIONAL	0.139
21	1	A	245	X-RAY DIFFRACTION	POSITIONAL
21	2	B	245	X-RAY DIFFRACTION	POSITIONAL	0.146
22	1	A	82	X-RAY DIFFRACTION	POSITIONAL
22	2	B	82	X-RAY DIFFRACTION	POSITIONAL	0.193
23	1	A	167	X-RAY DIFFRACTION	POSITIONAL
23	2	B	167	X-RAY DIFFRACTION	POSITIONAL	0.151
24	1	A	125	X-RAY DIFFRACTION	POSITIONAL
24	2	B	125	X-RAY DIFFRACTION	POSITIONAL	0.165
25	1	A	1446	X-RAY DIFFRACTION	POSITIONAL
25	2	B	1446	X-RAY DIFFRACTION	POSITIONAL	0.042
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 (%)
3.2188-3.2553	0.427	188	0.4013	3249	X-RAY DIFFRACTION	53
3.2553-3.2936	0.4075	193	0.3786	4339	X-RAY DIFFRACTION	69
3.2936-3.3337	0.3828	302	0.3762	5911	X-RAY DIFFRACTION	94
3.3337-3.3758	0.3906	323	0.3502	5942	X-RAY DIFFRACTION	97
3.3758-3.4202	0.3582	289	0.3565	6099	X-RAY DIFFRACTION	98
3.4202-3.467	0.3734	336	0.3358	6068	X-RAY DIFFRACTION	97
3.467-3.5164	0.376	302	0.3109	5978	X-RAY DIFFRACTION	98
3.5164-3.5688	0.2924	315	0.2982	6230	X-RAY DIFFRACTION	98
3.5688-3.6245	0.3465	330	0.312	6044	X-RAY DIFFRACTION	98
3.6245-3.6838	0.3599	314	0.3092	5979	X-RAY DIFFRACTION	97
3.6838-3.7472	0.3165	336	0.2863	5987	X-RAY DIFFRACTION	97
3.7472-3.8152	0.3273	291	0.2628	6125	X-RAY DIFFRACTION	98
3.8152-3.8884	0.2957	315	0.2572	6070	X-RAY DIFFRACTION	98
3.8884-3.9676	0.2719	308	0.2442	5965	X-RAY DIFFRACTION	96
3.9676-4.0537	0.2565	342	0.2294	6045	X-RAY DIFFRACTION	98
4.0537-4.1477	0.2688	306	0.2257	6091	X-RAY DIFFRACTION	98
4.1477-4.2511	0.2461	337	0.2079	6030	X-RAY DIFFRACTION	98
4.2511-4.3657	0.2583	340	0.2053	6081	X-RAY DIFFRACTION	98
4.3657-4.4938	0.2411	341	0.1854	5984	X-RAY DIFFRACTION	97
4.4938-4.6383	0.218	327	0.1796	6020	X-RAY DIFFRACTION	97
4.6383-4.8034	0.228	342	0.1789	6007	X-RAY DIFFRACTION	97
4.8034-4.9948	0.2261	299	0.1707	6037	X-RAY DIFFRACTION	97
4.9948-5.221	0.2401	354	0.1837	5946	X-RAY DIFFRACTION	97
5.221-5.4945	0.2553	307	0.1795	6056	X-RAY DIFFRACTION	97
5.4945-5.8363	0.2089	297	0.1796	6035	X-RAY DIFFRACTION	97
5.8363-6.2829	0.2372	300	0.1755	6009	X-RAY DIFFRACTION	97
6.2829-6.9078	0.2198	336	0.1686	6025	X-RAY DIFFRACTION	97
6.9078-7.8906	0.2014	312	0.1459	6015	X-RAY DIFFRACTION	97
7.8906-9.879	0.1542	334	0.1249	5946	X-RAY DIFFRACTION	97
9.879-29.4976	0.2027	270	0.1685	5982	X-RAY DIFFRACTION	96

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	3.605	0.4022	0.7633	2.0715	-0.0405	2.6706	-0.3173	-0.0626	0.8536	0.0622	-0.1435	0.1038	-0.1507	-0.2875	0.0005	0.8224	0.0045	0.0968	0.5831	-0.052	1.5876	34.9417	73.8683	50.658
2	0.252	-0.1087	-0.0736	0.1815	0.0255	0.0112	-0.2753	-0.3572	-0.7458	0.3156	-0.032	0.3924	2.2991	-1.3892	0.0029	1.2464	-0.3979	0.2663	1.2248	-0.3031	1.9169	17.7486	57.477	58.3008
3	3.2138	1.3975	-1.951	1.9183	1.8144	2.4502	-0.2183	-0.9039	0.5741	0.7491	0.1349	0.4247	0.4222	-0.9146	0.0005	0.8929	-0.0635	0.2104	0.8066	-0.1454	1.6768	26.1972	62.8296	58.7297
4	1.8075	-1.0609	1.8855	1.9249	1.0211	1.078	-0.397	-1.0411	-0.0218	-0.1617	-0.0535	-0.7757	-0.4102	-0.058	-0.0005	0.831	0.184	0.0806	0.8518	0.0898	1.7582	58.2035	62.1041	68.6618
5	2.1022	-2.2903	-0.7113	2.2238	-2.2457	2.2086	-0.4008	0.26	0.6173	-0.2872	0.4664	-0.0375	-0.2449	-0.3528	-0	0.6558	-0.1256	-0.0538	0.6305	0.0472	0.7263	79.4778	40.2059	66.6238
6	1.4428	-0.1135	0.3528	1.2729	-0.6122	2.6444	0.0284	-0.9477	0.9233	0.0641	0.098	0.0465	-0.2498	-0.2502	-0.001	0.754	-0.0948	-0.0692	1.0076	-0.3561	1.6575	101.1394	51.1973	79.2453
7	2.4365	-1.9849	0.7133	3.3095	-0.2913	0.5152	0.0229	-0.1511	0.9927	-0.1437	0.0264	-0.3571	-0.115	-0.013	-0.0002	0.7648	-0.0265	0.1312	0.7483	0.0619	1.1516	78.3979	53.7899	63.9912
8	4.0407	-0.3396	2.7074	4.1263	0.0529	4.152	0.1762	0.1374	-1.3385	-0.175	-0.0147	0.0256	0.3663	-0.0629	-0.0006	0.851	0.1233	0.0511	0.6549	-0.1735	1.4707	52.5849	117.759	50.4163
9	2.7515	0.1531	2.4723	5.8374	0.8971	2.5451	0.4533	0.3978	-1.0161	0.163	0.1119	-0.6659	0.1804	0.5152	-0.0008	0.8961	0.06	0.1375	0.8295	-0.1212	0.888	66.7238	125.1249	52.5095
10	0.7868	0.5564	-0.4874	0.1788	0.2132	0.2035	-1.0277	-0.2636	0.1614	0.4692	-0.6417	-0.3053	0.4065	0.3141	0.0006	2.4086	0.0995	-0.22	1.5087	0.341	1.8326	73.0328	115.0164	96.2184
11	0.544	0.3389	-1.3754	2.4215	0.0606	1.163	-0.1541	-0.493	-0.7814	0.3763	-0.344	-0.4746	0.9537	0.4061	0.0002	3.0209	0.1285	-0.282	2.0068	0.7187	1.9971	77.1351	96.6776	104.2604
12	0.6629	0.8083	-0.4783	0.0623	-0.3303	1.1986	-0.1949	0.0568	-1.196	1.368	0.5315	-2.3416	0.8639	0.0623	-0.0006	2.5523	0.6026	-0.7865	2.3083	0.2097	2.7123	99.4821	108.3268	96.3904
13	5.7704	-0.427	3.4362	0.028	-0.1636	3.4306	-0.0401	-1.2069	-0.3554	0.3157	-0.1843	-0.065	0.3966	-0.201	-0	1.0764	-0.098	0.1305	1.2394	-0.1078	0.4184	45.0256	144.4135	80.3704
14	3.4657	0.4778	0.6305	2.1483	-0.0578	4.911	0.0417	-0.5526	-1.1431	0.5422	0.0022	-0.5261	0.5383	0.7938	-0.0002	1.1531	0.0289	-0.2077	1.1098	0.1583	0.9532	82.9134	133.9791	82.1113
15	0.9322	0.6314	-0.8377	0.6082	-1.2408	0.4464	0.1157	0.7222	-1.6213	0.6956	0.5039	-0.6066	1.4166	1.7732	-0.002	1.8975	0.149	-0.2534	1.5106	0.3332	1.5706	78.8655	120.0871	84.6607
16	3.1893	-0.3378	0.2274	1.4918	0.6651	1.997	-0.1129	1.1833	1.1209	-0.5807	-0.395	-0.0186	-0.35	0.3497	0.0003	1.2828	0.1223	0.0114	1.1116	0.6784	1.8772	39.0944	80.9938	26.0112
17	0.0671	0.0276	-0.2095	0.0554	0.2358	-0.1843	-0.3099	0.7869	0.0342	-0.7998	-0.3177	0.0243	0.9666	1.1413	0.0021	1.556	0.0439	0.0547	2.8649	1.3062	2.2663	56.4221	71.2958	10.9304
18	1.4369	-0.6635	-1.4606	1.4572	-0.7948	0.677	0.0154	1.2859	0.8241	-1.0228	-0.2905	0.1987	-0.0914	1.2821	0.001	1.4841	0.2018	0.2436	1.9326	0.5891	1.9359	47.9499	75.9874	13.3508
19	0.2355	0.3311	0.4941	0.0617	0.3639	0.1629	-0.7855	1.5346	-0.1484	0.2436	-0.4444	0.0794	-0.3273	-0.6061	-0.0002	1.9502	0.2488	-0.0891	1.8611	0.292	2.1315	15.9109	80.3845	4.307
20	0.9292	-0.0948	0.4694	0.6274	-0.6686	0.8222	0.25	1.0082	-0.017	-0.563	-0.5671	0.4224	-0.1043	-0.2448	-0.0006	2.0039	0.2832	-0.3029	2.2893	-0.2634	1.5361	-4.1902	59.3617	-4.5893
21	-0.3527	-0.3341	-0.0928	-0.2292	0.5019	-0.309	0.2585	0.7879	-0.3371	-1.2177	-0.0507	0.8318	-1.377	0.2296	-0.0016	3.2114	0.3588	-0.3789	2.7566	-0.0801	2.0259	-29.1495	72.2681	-9.3985
22	0.8734	-0.3318	0.7781	0.331	0.348	2.4742	-0.0909	0.5315	0.2351	-0.4153	-0.1623	0.0817	0.2829	-0.4869	-0.0003	1.7375	0.2222	-0.0994	2.0968	0.0753	1.7549	-3.8096	69.7184	4.4762
23	5.9404	-2.1537	1.4514	5.185	0.3579	3.7343	0.1983	0.0705	-1.7797	-0.22	-0.2503	0.6824	0.4966	0.0171	-0.0001	0.6952	-0.172	-0.1496	0.7502	-0.262	1.5838	19.6446	121.9545	48.7298
24	3.579	-1.3505	2.2721	4.0994	0.3406	3.2322	0.2124	0.0364	-1.0434	-0.1101	-0.129	0.7359	-0.1235	-0.4718	0.0005	0.8413	-0.1168	-0.0411	0.9822	-0.052	0.92	7.3123	132.0411	51.5879
25	0.9962	0.7678	-0.3179	0.2662	-0.0693	0.1101	-0.9299	0.3104	0.2046	-0.2515	0.7181	-0.6937	0.315	-1.117	0.0008	1.9187	-0.3459	-0.282	2.024	-0.3514	1.2274	4.3902	150.8536	5.1874
26	2.398	1.4213	-0.65	1.025	-0.6088	1.3524	-0.6115	1.0989	-0.8887	-0.9081	0.296	0.0737	0.2718	-0.7733	-0.0012	2.4893	-0.6914	-0.2573	3.0342	-0.4902	1.1156	-7.1162	139.0661	-7.5187
27	0.8754	0.3683	-0.8205	0.4337	-0.3613	0.6684	-0.3657	1.4086	-0.1098	-1.8591	0.019	1.9594	-0.1069	-0.8862	0.0018	2.2368	-0.5134	-0.6991	3.1145	0.1779	1.544	-25.7282	149.534	8.0593
28	5.4036	-0.7186	2.4332	-0.2935	-0.8079	2.158	-0.2474	1.2017	0.6146	-0.5629	-0.161	0.2546	0.0481	-0.3987	0.0007	1.117	0.0725	-0.0709	1.2115	0.0488	0.7381	34.0498	158.3508	37.8483
29	2.6154	-0.7726	-0.963	2.4466	-1.2978	5.3109	-0.014	1.168	0.0303	-0.7214	0.1617	0.5693	0.2174	-0.7142	-0.0014	0.8617	-0.0537	-0.2756	1.2717	-0.0752	0.6168	-6.5837	157.0899	31.7675
30	2.4619	-1.459	-0.609	3.8353	1.0756	1.7482	-0.7212	0.8157	-1.3642	-0.6199	1.5786	2.3369	0.8154	-0.3136	0.1076	1.386	-0.2454	-0.2818	2.0411	-0.312	0.652	-3.2418	147.8367	22.3872

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