PDB-9enj: L-amino acid oxidase 4 (HcLAAO4) from the fungus Hebeloma cylindr...

ID or keywords:

Entry

Database: PDB / ID: 9enj

Title

L-amino acid oxidase 4 (HcLAAO4) from the fungus Hebeloma cylindrosporum in complex with L-glutamate

Components

L-amino acid oxidase 4

Keywords

OXIDOREDUCTASE / L-AMINO ACID OXIDASE / FAD / FLAVOPROTEIN

Function / homology

Function and homology information

L-amino-acid oxidase activity / amino acid catabolic process
Similarity search - Function

Biological species

Hebeloma cylindrosporum (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

FOURIER SYNTHESIS / Resolution: 2.1 Å

Authors

Gilzer, D. / Koopmeiners, S. / Fischer von Mollard, G. / Niemann, H.H.

Funding support

1items

Citation

Journal: to be published
Title: Crystal structure and enzyme engineering of the broad substrate spectrum L-amino acid oxidase 4 from the fungus Hebeloma cylindrosporum
Authors: Koopmeiners, S. / Gilzer, D. / Widmann, C. / Berelsmann, N. / Spross, J. / Niemann, H.H. / Fischer von Mollard, G.

History

Deposition	Mar 13, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 14, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9enj.cif.gz	1.5 MB	Display	PDBx/mmCIF format
PDB format	pdb9enj.ent.gz	1 MB	Display	PDB format
PDBx/mmJSON format	9enj.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/en/9enj ftp://data.pdbj.org/pub/pdb/validation_reports/en/9enj	HTTPS FTP

-
Related structure data

Related structure data	9enhC 9eniC 9enkC 9ennC 9enl PDB Unreleased entry 9enm PDB Unreleased entry C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Experimental dataset #1	Data reference: 10.15151/ESRF-DC-1562905483 / Data set type: diffraction image data
Experimental dataset #2	Data reference: 10.15785/SBGRID/1091 / Data set type: diffraction image data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#231 - Mar 2019 Measles Virus Proteins similarity (2) #235 - Jul 2019 AMPA Receptor similarity (1) #191 - Nov 2015 Glutamate-gated Chloride Receptors similarity (1)

Deposited unit

A: L-amino acid oxidase 4

B: L-amino acid oxidase 4

C: L-amino acid oxidase 4

D: L-amino acid oxidase 4

hetero molecules

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

1

A: L-amino acid oxidase 4

B: L-amino acid oxidase 4

hetero molecules

defined by author
Evidence: gel filtration
130 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: L-amino acid oxidase 4

D: L-amino acid oxidase 4

hetero molecules

defined by author
Evidence: gel filtration
129 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	84.760, 130.790, 107.300
Angle α, β, γ (deg.)	90.000, 95.655, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
d_1	ens_1	(chain "A" and (resid 64 through 83 or resid 85...
d_2	ens_1	(chain "B" and (resid 64 through 83 or resid 85...
d_3	ens_1	(chain "C" and (resid 64 through 83 or resid 85...
d_4	ens_1	(chain "D" and (resid 64 through 83 or resid 85...

NCS domain segments:

Ens-ID: ens_1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
d_1	1	GLY	GLY	LEU	LEU	A	A	64 - 83	11 - 30
d_1	2	SER	SER	PHE	PHE	A	A	85 - 90	32 - 37
d_1	3	ILE	ILE	TYR	TYR	A	A	92 - 135	39 - 82
d_1	4	PRO	PRO	GLY	GLY	A	A	137 - 144	84 - 91
d_1	5	LEU	LEU	VAL	VAL	A	A	146 - 205	93 - 152
d_1	6	ASP	ASP	ASP	ASP	A	A	207 - 229	154 - 176
d_1	7	MET	MET	ASP	ASP	A	A	231 - 272	178 - 219
d_1	8	SER	SER	LYS	LYS	A	A	274 - 323	221 - 270
d_1	9	ALA	ALA	ALA	ALA	A	A	327 - 332	274 - 279
d_1	10	VAL	VAL	GLY	GLY	A	A	334 - 355	281 - 302
d_1	11	LYS	LYS	LYS	LYS	A	A	357	304
d_1	12	LYS	LYS	GLY	GLY	A	A	359 - 418	306 - 365
d_1	13	LYS	LYS	TYR	TYR	A	A	420 - 477	367 - 424
d_1	14	GLU	GLU	VAL	VAL	A	A	479 - 505	426 - 452
d_1	15	VAL	VAL	ASN	ASN	A	A	507 - 513	454 - 460
d_1	16	ASN	ASN	GLU	GLU	A	A	515 - 598	462 - 545
d_1	18	GLU	GLU	GLU	GLU	A	F	702
d_2	1	GLY	GLY	LEU	LEU	B	B	64 - 83	11 - 30
d_2	2	SER	SER	PHE	PHE	B	B	85 - 90	32 - 37
d_2	3	ILE	ILE	TYR	TYR	B	B	92 - 135	39 - 82
d_2	4	PRO	PRO	GLY	GLY	B	B	137 - 144	84 - 91
d_2	5	LEU	LEU	VAL	VAL	B	B	146 - 205	93 - 152
d_2	6	ASP	ASP	ASP	ASP	B	B	207 - 229	154 - 176
d_2	7	MET	MET	ASP	ASP	B	B	231 - 272	178 - 219
d_2	8	SER	SER	ALA	ALA	B	B	274 - 332	221 - 279
d_2	9	VAL	VAL	GLY	GLY	B	B	334 - 355	281 - 302
d_2	10	LYS	LYS	LYS	LYS	B	B	357	304
d_2	11	LYS	LYS	GLY	GLY	B	B	359 - 418	306 - 365
d_2	12	LYS	LYS	TYR	TYR	B	B	420 - 477	367 - 424
d_2	13	GLU	GLU	VAL	VAL	B	B	479 - 505	426 - 452
d_2	14	VAL	VAL	ASN	ASN	B	B	507 - 513	454 - 460
d_2	15	ASN	ASN	GLU	GLU	B	B	515 - 598	462 - 545
d_2	17	GLU	GLU	GLU	GLU	B	BA	702
d_3	1	GLY	GLY	LEU	LEU	C	C	64 - 83	11 - 30
d_3	2	SER	SER	PHE	PHE	C	C	85 - 90	32 - 37
d_3	3	ILE	ILE	TYR	TYR	C	C	92 - 135	39 - 82
d_3	4	PRO	PRO	GLY	GLY	C	C	137 - 144	84 - 91
d_3	5	LEU	LEU	VAL	VAL	C	C	146 - 205	93 - 152
d_3	6	ASP	ASP	ASP	ASP	C	C	207 - 229	154 - 176
d_3	7	MET	MET	ASP	ASP	C	C	231 - 272	178 - 219
d_3	8	SER	SER	LYS	LYS	C	C	274 - 323	221 - 270
d_3	9	ALA	ALA	ALA	ALA	C	C	327 - 332	274 - 279
d_3	10	VAL	VAL	GLY	GLY	C	C	334 - 355	281 - 302
d_3	11	LYS	LYS	LYS	LYS	C	C	357	304
d_3	12	LYS	LYS	GLY	GLY	C	C	359 - 418	306 - 365
d_3	13	LYS	LYS	TYR	TYR	C	C	420 - 477	367 - 424
d_3	14	GLU	GLU	VAL	VAL	C	C	479 - 505	426 - 452
d_3	15	VAL	VAL	ASN	ASN	C	C	507 - 513	454 - 460
d_3	16	ASN	ASN	GLU	GLU	C	C	515 - 598	462 - 545
d_3	18	GLU	GLU	GLU	GLU	C	ZA	702
d_4	1	GLY	GLY	LEU	LEU	D	D	64 - 83	11 - 30
d_4	2	SER	SER	PHE	PHE	D	D	85 - 90	32 - 37
d_4	3	ILE	ILE	TYR	TYR	D	D	92 - 135	39 - 82
d_4	4	PRO	PRO	GLY	GLY	D	D	137 - 144	84 - 91
d_4	5	LEU	LEU	VAL	VAL	D	D	146 - 205	93 - 152
d_4	6	ASP	ASP	ASP	ASP	D	D	207 - 229	154 - 176
d_4	7	MET	MET	ASP	ASP	D	D	231 - 272	178 - 219
d_4	8	SER	SER	VAL	VAL	D	D	274 - 295	221 - 242
d_4	9	GLU	GLU	LYS	LYS	D	D	299 - 323	246 - 270
d_4	10	ALA	ALA	ALA	ALA	D	D	327 - 332	274 - 279
d_4	11	VAL	VAL	GLY	GLY	D	D	334 - 355	281 - 302
d_4	12	LYS	LYS	LYS	LYS	D	D	357	304
d_4	13	LYS	LYS	GLY	GLY	D	D	359 - 418	306 - 365
d_4	14	LYS	LYS	TYR	TYR	D	D	420 - 477	367 - 424
d_4	15	GLU	GLU	VAL	VAL	D	D	479 - 505	426 - 452
d_4	16	VAL	VAL	ASN	ASN	D	D	507 - 513	454 - 460
d_4	17	ASN	ASN	GLU	GLU	D	D	515 - 598	462 - 545
d_4	19	GLU	GLU	GLU	GLU	D	TB	702

NCS oper:

ID	Code	Matrix	Vector
1	given	(-0.999965962803, 0.00616966739911, -0.00547799596943), (-0.00656102321108, -0.997194954959, 0.0745598737833), (-0.00500262032144, 0.0745932772329, 0.997201492569)	40.5406839457, -9.9765481187, 0.515472560193
2	given	(0.411971839991, -0.91118889393, 0.00374200927926), (0.911195203638, 0.411960613163, -0.00342842086372), (0.0015823785776, 0.00482211375872, 0.999987121566)	-1.21136398818, -21.2821354073, 52.0807538848
3	given	(-0.407430942076, 0.910344619076, -0.0726133731397), (-0.913220303021, -0.406600464448, 0.0265469482466), (-0.00535775975449, 0.0771280547554, 0.997006799164)	24.7670843214, 11.2447862862, 52.6103143969

-
Protein , 1 types, 4 molecules ABCD

#1: Protein	L-amino acid oxidase 4 Mass: 62197.676 Da / Num. of mol.: 4 / Mutation: K474A, K475A Source method: isolated from a genetically manipulated source Details: residues 54 - 615 obtained by limited proteolysis; surface entropy reduction mutations K474A and K475A Source: (gene. exp.) Hebeloma cylindrosporum (fungus) / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): Arctic Express / References: UniProt: S4S6Z0, L-amino-acid oxidase

#1: Protein

L-amino acid oxidase 4

Mass: 62197.676 Da / Num. of mol.: 4 / Mutation: K474A, K475A
Source method: isolated from a genetically manipulated source
Details: residues 54 - 615 obtained by limited proteolysis; surface entropy reduction mutations K474A and K475A
Source: (gene. exp.)

Hebeloma cylindrosporum (fungus) / Plasmid: pET28b / Production host:

Escherichia coli (E. coli) / Strain (production host): Arctic Express / References: UniProt: S4S6Z0, L-amino-acid oxidase

-
Non-polymers , 6 types, 1036 molecules

#2: Chemical	ChemComp-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE Mass: 787.566 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₇H₃₅N₉O₁₅P₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-GLU / GLUTAMIC ACID Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₅H₉NO₄ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	... ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 51 / Source method: obtained synthetically / Formula: SO₄
#5: Chemical	ChemComp-PGR / R-1,2-PROPANEDIOL Mass: 76.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₃H₈O₂
#6: Chemical	ChemComp-PGO / S-1,2-PROPANEDIOL Mass: 76.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C₃H₈O₂
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 951 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has ligand of interest	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.38 Å³/Da / Density % sol: 48.3 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: protein: 10 mg/ml; reservoir solution: 2.05 M (NH4)2SO4, 0.1 M sodium citrate, pH 7.0; drop with 1000 nl protein + 500 nl reservoir

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
Detector	Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 22, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9677 Å / Relative weight: 1
Reflection	Resolution: 2.1→50 Å / Num. obs: 134327 / % possible obs: 99.2 % / Redundancy: 7.1 % / B_iso Wilson estimate: 39.62 Å² / CC_1/2: 0.997 / R_rim(I) all: 0.106 / Net I/σ(I): 12.45
Reflection shell	Resolution: 2.1→2.15 Å / Redundancy: 7.36 % / Mean I/σ(I) obs: 1.27 / Num. unique obs: 9924 / CC_1/2: 0.5 / R_rim(I) all: 1.901 / % possible all: 99.9

-
Processing

Software

Name	Version	Classification
PHENIX	1.21_5207	refinement
XDS	VERSION Jun 30, 2023 BUILT=20230630	data reduction
XSCALE	VERSION Jun 30, 2023 BUILT=20230630	data scaling
PHENIX		phasing

Refinement

Method to determine structure:

FOURIER SYNTHESIS / Resolution: 2.1→40.62 Å / SU ML: 0.2684 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.2027
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.195	6714	5 %
R_work	0.174	127583	-
obs	0.1751	134297	99.16 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 43.78 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→40.62 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16787	0	637	951	18375

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0022	18017
X-RAY DIFFRACTION	f_angle_d	0.5204	24562
X-RAY DIFFRACTION	f_chiral_restr	0.0404	2578
X-RAY DIFFRACTION	f_plane_restr	0.0039	3108
X-RAY DIFFRACTION	f_dihedral_angle_d	11.4203	6443

Refine LS restraints NCS

Ens-ID	Dom-ID	Asym-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)
ens_1	d_2	A	A	X-RAY DIFFRACTION	Torsion NCS	0.340606058429
ens_1	d_3	A	A	X-RAY DIFFRACTION	Torsion NCS	0.371529091288
ens_1	d_4	A	A	X-RAY DIFFRACTION	Torsion NCS	0.46611948406

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 (%)
2.1-2.12	0.4335	222	0.4011	4231	X-RAY DIFFRACTION	99.84
2.12-2.15	0.3129	226	0.3166	4300	X-RAY DIFFRACTION	99.89
2.15-2.18	0.2926	225	0.2679	4275	X-RAY DIFFRACTION	99.82
2.18-2.2	0.2695	225	0.2527	4276	X-RAY DIFFRACTION	99.89
2.2-2.23	0.29	226	0.2481	4275	X-RAY DIFFRACTION	99.89
2.23-2.26	0.2876	221	0.2593	4205	X-RAY DIFFRACTION	99.82
2.26-2.29	0.3097	227	0.2842	4312	X-RAY DIFFRACTION	99.78
2.29-2.33	0.2875	224	0.2802	4256	X-RAY DIFFRACTION	99.91
2.33-2.37	0.2438	226	0.2507	4293	X-RAY DIFFRACTION	99.82
2.37-2.4	0.2411	223	0.2172	4237	X-RAY DIFFRACTION	99.82
2.4-2.45	0.2444	223	0.1955	4240	X-RAY DIFFRACTION	99.8
2.45-2.49	0.2175	229	0.1807	4344	X-RAY DIFFRACTION	99.78
2.49-2.54	0.2281	222	0.1804	4212	X-RAY DIFFRACTION	99.8
2.54-2.59	0.2081	224	0.1709	4263	X-RAY DIFFRACTION	99.45
2.59-2.65	0.2194	225	0.1721	4279	X-RAY DIFFRACTION	99.01
2.65-2.71	0.1896	221	0.1815	4188	X-RAY DIFFRACTION	98.75
2.71-2.77	0.2246	224	0.1876	4276	X-RAY DIFFRACTION	99.12
2.77-2.85	0.2231	221	0.1774	4200	X-RAY DIFFRACTION	98.53
2.85-2.93	0.1742	221	0.1616	4212	X-RAY DIFFRACTION	97.99
2.93-3.03	0.1907	219	0.1632	4155	X-RAY DIFFRACTION	96.66
3.03-3.14	0.1855	211	0.1702	4003	X-RAY DIFFRACTION	93.67
3.14-3.26	0.1745	214	0.1616	4077	X-RAY DIFFRACTION	94.7
3.26-3.41	0.185	224	0.1652	4253	X-RAY DIFFRACTION	99.87
3.41-3.59	0.1699	226	0.1524	4296	X-RAY DIFFRACTION	99.93
3.59-3.82	0.1542	227	0.152	4304	X-RAY DIFFRACTION	99.98
3.82-4.11	0.1498	226	0.1362	4300	X-RAY DIFFRACTION	99.89
4.11-4.52	0.1513	226	0.133	4287	X-RAY DIFFRACTION	99.93
4.52-5.18	0.1557	227	0.137	4313	X-RAY DIFFRACTION	99.98
5.18-6.52	0.1994	229	0.1718	4352	X-RAY DIFFRACTION	100
6.52-40.62	0.2076	230	0.192	4369	X-RAY DIFFRACTION	99.57

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	0.528862866218	-0.108272464058	-0.362457712442	0.094324736289	-0.00696001095341	0.542962525149	-0.103863378913	-0.0726518781321	0.214942722634	0.38403430691	0.0441795610849	0.274621246937	-0.342620914448	-0.283720662737	0.000192285671974	0.574647290234	0.0795062019434	-0.0281631440331	0.395688198682	0.0236203638325	0.4597971599	-2.38494705826	21.5601575185	100.649420108
2	0.710777653732	-0.224588248923	0.00949938884332	1.15015322291	-0.214479325	0.781764786336	-0.047236454673	0.0417631666057	0.0508230858157	0.148383131007	-0.0080531564413	-0.0848692630827	-0.118470131015	0.0746790929738	3.62018449258E-6	0.418692717932	0.00389384455063	-0.0177567183218	0.376349876688	0.00665185419764	0.338854217023	13.9162885759	9.48083282047	93.8115229644
3	0.687367927606	-0.433210065705	0.150948398177	1.18048308424	-0.235431551582	0.884142406885	-0.00560311642533	0.0983759445311	-0.200171517052	-0.0618023279415	0.00528559950669	0.218701745003	0.171270777103	-0.0296913627462	-9.29607013377E-5	0.379270296049	-0.0128511118147	-0.0045821300567	0.325720314331	-0.0595937321276	0.392059919556	1.45294735657	-21.0737879465	83.8053454466
4	0.898873563298	-0.0760899610628	-0.358334091067	1.3172290134	-0.102922846506	0.539553679568	-0.037652401592	0.0988895770607	-0.34596721538	0.211806310604	0.0742370445418	0.0486180886666	0.223568734625	0.144273981376	-0.000228519966604	0.493667049073	0.0650083086283	0.0262069023676	0.396450236142	-0.0182537820138	0.428830607943	15.072766901	-30.372335911	98.0514582086
5	0.685437168879	-0.452022983433	0.0866847145425	1.32609666848	-0.082718443593	0.7039706873	-0.0157216574421	-0.0091376202499	-0.0985490922341	0.0643566684906	0.048637555376	0.139930040139	0.100250493838	-0.00787968470347	-2.12509293937E-5	0.432723224531	0.0222377191256	0.026044463858	0.403538853312	-0.0121123841183	0.402902216448	7.22926887547	-18.4984823075	94.0081074117
6	0.760367171793	0.145333038704	-0.00516110491908	0.592203095386	0.0747575089745	0.415765608729	0.0448018571999	0.0103112105794	-0.0485432084686	-0.0259874408891	-0.0340409963893	-0.110782481879	0.017366747781	0.117277384045	-8.90405232723E-6	0.392658624104	0.018301152262	0.00252682099875	0.42484968812	0.0102915872642	0.391626200575	39.6413589576	-5.56826717016	32.3883828743
7	0.198060566087	-0.137664743655	0.135548816107	0.102764441305	-0.0834054912474	0.276291942919	0.0871791427879	-0.0908261612823	-0.104507737322	0.0428290560085	-0.0922410373023	-0.0912185235209	0.111217696321	0.0404176053845	-5.73160029324E-5	0.409859181557	0.00964961778144	-0.0127840407778	0.46065481689	-0.00370652638891	0.429093733047	38.2442935618	-6.52744800472	31.3084174402
8	0.208246876433	0.0219528357774	0.0950221345998	0.261614130422	0.325120243322	0.425408855184	-0.0165309197911	-0.216539916959	0.492079635867	0.1932710751	-0.0844130982588	-0.383286196841	-0.236622411122	0.0940537918885	-0.00176910095327	0.419213601319	-0.0576060999248	-0.0154216674069	0.433686329423	-0.0255682646676	0.51251525857	38.6738363181	19.0020739084	48.3471011813
9	0.930893240476	0.155934024632	-0.0357709391445	0.965507448692	0.0714747203701	0.541119699002	0.0514050626839	-0.115853058286	-0.0113819349545	0.0173923950614	-0.030864417937	-0.0380482292396	-0.00462539804092	0.0645158762776	-2.18842492132E-6	0.371898962383	-0.00589551977394	-0.016451699277	0.418825693109	0.00271448281685	0.375145191042	34.3367060612	-0.750104090078	41.6039311468
10	0.542230337614	0.124863816318	-0.15571965877	0.546467762626	-0.120204823007	0.729419985188	0.048736192427	0.0308408455919	0.058037024402	-0.0308816482854	-0.0582380306303	0.0682189258171	-0.0349229598463	-0.0903571760236	-8.92171146831E-5	0.355124378191	0.0147737551012	-0.0311830274457	0.394620431628	-0.0134118060768	0.362184962334	0.757620354918	-2.22074553604	32.1484408917
11	0.105795295683	0.0224716832702	-0.133361423926	0.0048662929122	-0.0321175551968	0.220652761494	0.0624301550835	0.0688748354488	0.32079523764	-0.00227734316746	0.030626265877	0.0943872985889	-0.0734957000423	-0.166885386441	-0.00010277956866	0.419063254838	-0.0110723606474	0.00190659281403	0.427270481233	0.0114557103571	0.424442353857	1.90886588131	-1.54362621429	31.0947084557
12	0.301970134175	0.140863757447	-0.010973286404	0.475213553389	-0.316345462048	0.459691896414	0.00379473301096	-0.20879647245	-0.242248256708	0.231184603278	-0.0675914417246	0.168819786456	0.232723540964	-0.0936227972561	-5.06663703712E-5	0.489350784804	-0.0559486643964	-0.00748299274406	0.419891953554	0.0082755385658	0.428097423544	1.78675220198	-25.6853895434	49.8213501206
13	0.519193057116	0.215096119932	-0.142430212767	0.815020397718	0.0319038680801	0.481369021142	0.0319018055439	-0.0583582399228	0.00231497972325	0.0180485442858	-0.0228927731529	-0.0074056854664	-0.00408218362738	-0.0255513905951	-2.58016321843E-6	0.392507429229	-0.00392557849697	-0.0224134090726	0.401875120256	-0.00280786201748	0.358366608119	6.02894954311	-6.4006128007	41.8596430477
14	0.800221966474	-0.159696763586	0.033766534855	1.01399041306	-0.067883594238	0.856288092769	-0.0570448177098	0.134372534023	0.10186698617	-0.0518245469176	-0.0248337107745	-0.118662886767	-0.214286794699	0.156100695783	-0.000310667705857	0.411952885061	-0.0380901890522	-0.00644005630508	0.420072590348	0.0582372517962	0.369580564579	19.8403868215	12.6356093345	84.727007552
15	0.125498646109	0.073509382567	-0.0448403706012	0.121091270545	0.114142283253	0.264104531076	-0.0707061710176	0.128300574944	-0.135310980465	-0.00383860324613	0.0520950306135	-0.266503611548	-0.0255539130277	0.344362704432	-3.40263277413E-5	0.436547760637	-0.030994654939	-0.0102927285047	0.491271336113	0.0260963265713	0.398066115759	20.6112153821	10.9938194313	83.4441439212

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'C' and (resid 309 through 348 )	C	I	309 - 348	245 - 282
2	2	chain 'C' and (resid 349 through 600 )	C	I	349 - 600	283 - 534
3	3	chain 'D' and (resid 64 through 291 )	D	L	64 - 291	1 - 228
4	4	chain 'D' and (resid 292 through 348 )	D	L	292 - 348	229 - 283
5	5	chain 'D' and (resid 349 through 598 )	D	L	349 - 598	284 - 533
6	6	chain 'A' and (resid 64 through 272 )	A	A	64 - 272	1 - 209
7	7	chain 'A' and (resid 273 through 308 )	A	A	273 - 308	210 - 242
8	8	chain 'A' and (resid 309 through 348 )	A	A	309 - 348	243 - 280
9	9	chain 'A' and (resid 349 through 600 )	A	A	349 - 600	281 - 532
10	10	chain 'B' and (resid 64 through 272 )	B	D	64 - 272	1 - 209
11	11	chain 'B' and (resid 273 through 308 )	B	D	273 - 308	210 - 242
12	12	chain 'B' and (resid 309 through 348 )	B	D	309 - 348	243 - 279
13	13	chain 'B' and (resid 349 through 600 )	B	D	349 - 600	280 - 531
14	14	chain 'C' and (resid 62 through 272 )	C	I	62 - 272	1 - 211
15	15	chain 'C' and (resid 273 through 308 )	C	I	273 - 308	212 - 244

-
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://pdbjlc1.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 , 1 types, 4 molecules ABCD

-
Non-polymers , 6 types, 1036 molecules

-
Details

-
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

-Protein , 1 types, 4 molecules ABCD

-Non-polymers , 6 types, 1036 molecules

-Details

-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

-
Protein , 1 types, 4 molecules ABCD

-
Non-polymers , 6 types, 1036 molecules

-
Details

-
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