PDB-9wpn: Crystal structure of the nitrilase superfamily protein CJ1056C fr...

ID or keywords:

Entry

Database: PDB / ID: 9wpn

Title

Crystal structure of the nitrilase superfamily protein CJ1056C from Campylobacter jejuni in space group P212121

Components

Carbon-nitrogen hydrolase family protein

Keywords

HYDROLASE / CJ1056C / Campylobacter jejuni / nitrilase / amidase

Function / homology

N-carbamoylputrescine amidase activity / putrescine biosynthetic process from arginine / : / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase family protein

Function and homology information

Biological species

Campylobacter jejuni (Campylobacter)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.9 Å

Authors

Ahn, S.Y. / Yoon, S.I.

Funding support

Korea, Republic Of, 1items

Citation

Journal: Biochem.Biophys.Res.Commun. / Year: 2025
Title: Structural analysis of the unique nitrilase superfamily protein CJ1056C from Campylobacter jejuni.
Authors: Ahn, S.Y. / Yoon, S.I.

History

Deposition	Sep 9, 2025	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Oct 8, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9wpn.cif.gz	695.3 KB	Display	PDBx/mmCIF format
PDB format	pdb9wpn.ent.gz	512.1 KB	Display	PDB format
PDBx/mmJSON format	9wpn.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	9wpn_validation.pdf.gz	469.8 KB	Display	wwPDB validaton report
Full document	9wpn_full_validation.pdf.gz	482.6 KB	Display
Data in XML	9wpn_validation.xml.gz	57.4 KB	Display
Data in CIF	9wpn_validation.cif.gz	72.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wp/9wpn ftp://data.pdbj.org/pub/pdb/validation_reports/wp/9wpn	HTTPS FTP

-
Related structure data

Related structure data	9wpoC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Carbon-nitrogen hydrolase family protein

B: Carbon-nitrogen hydrolase family protein

C: Carbon-nitrogen hydrolase family protein

D: Carbon-nitrogen hydrolase family protein

E: Carbon-nitrogen hydrolase family protein

F: Carbon-nitrogen hydrolase family protein

186 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Carbon-nitrogen hydrolase family protein

B: Carbon-nitrogen hydrolase family protein

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

2

C: Carbon-nitrogen hydrolase family protein

D: Carbon-nitrogen hydrolase family protein

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

3

E: Carbon-nitrogen hydrolase family protein

F: Carbon-nitrogen hydrolase family protein

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

Unit cell

Length a, b, c (Å)	80.829, 133.433, 152.811
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1
3	1
4	1
5	1
6	1

NCS domain segments:

Ens-ID: 1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	SER	SER	PRO	PRO	(chain 'A' and ((resid 2 through 3 and (name N...	A	A	2 - 10	8 - 16
1	2	LEU	LEU	THR	THR	(chain 'A' and ((resid 2 through 3 and (name N...	A	A	19 - 46	25 - 52
1	3	LEU	LEU	GLU	GLU	(chain 'A' and ((resid 2 through 3 and (name N...	A	A	48 - 61	54 - 67
1	4	LYS	LYS	LYS	LYS	(chain 'A' and ((resid 2 through 3 and (name N...	A	A	64	70
1	5	SER	SER	GLU	GLU	(chain 'A' and ((resid 2 through 3 and (name N...	A	A	66 - 118	72 - 124
1	6	PHE	PHE	CYS	CYS	(chain 'A' and ((resid 2 through 3 and (name N...	A	A	121 - 173	127 - 179
1	7	GLU	GLU	ILE	ILE	(chain 'A' and ((resid 2 through 3 and (name N...	A	A	176 - 237	182 - 243
1	8	PRO	PRO	PRO	PRO	(chain 'A' and ((resid 2 through 3 and (name N...	A	A	239	245
1	9	LYS	LYS	ILE	ILE	(chain 'A' and ((resid 2 through 3 and (name N...	A	A	241 - 255	247 - 261
1	10	PHE	PHE	PHE	PHE	(chain 'A' and ((resid 2 through 3 and (name N...	A	A	258	264
2	1	SER	SER	PRO	PRO	(chain 'B' and ((resid 2 through 3 and (name N...	B	B	2 - 10	8 - 16
2	2	LEU	LEU	THR	THR	(chain 'B' and ((resid 2 through 3 and (name N...	B	B	19 - 46	25 - 52
2	3	LEU	LEU	GLU	GLU	(chain 'B' and ((resid 2 through 3 and (name N...	B	B	48 - 61	54 - 67
2	4	LYS	LYS	LYS	LYS	(chain 'B' and ((resid 2 through 3 and (name N...	B	B	64	70
2	5	SER	SER	GLU	GLU	(chain 'B' and ((resid 2 through 3 and (name N...	B	B	66 - 118	72 - 124
2	6	PHE	PHE	CYS	CYS	(chain 'B' and ((resid 2 through 3 and (name N...	B	B	121 - 173	127 - 179
2	7	GLU	GLU	ILE	ILE	(chain 'B' and ((resid 2 through 3 and (name N...	B	B	176 - 237	182 - 243
2	8	PRO	PRO	PRO	PRO	(chain 'B' and ((resid 2 through 3 and (name N...	B	B	239	245
2	9	LYS	LYS	ILE	ILE	(chain 'B' and ((resid 2 through 3 and (name N...	B	B	241 - 255	247 - 261
2	10	PHE	PHE	PHE	PHE	(chain 'B' and ((resid 2 through 3 and (name N...	B	B	258	264
3	1	SER	SER	PRO	PRO	(chain 'C' and ((resid 2 through 3 and (name N...	C	C	2 - 10	8 - 16
3	2	LEU	LEU	THR	THR	(chain 'C' and ((resid 2 through 3 and (name N...	C	C	19 - 46	25 - 52
3	3	LEU	LEU	GLU	GLU	(chain 'C' and ((resid 2 through 3 and (name N...	C	C	48 - 61	54 - 67
3	4	LYS	LYS	LYS	LYS	(chain 'C' and ((resid 2 through 3 and (name N...	C	C	64	70
3	5	SER	SER	GLU	GLU	(chain 'C' and ((resid 2 through 3 and (name N...	C	C	66 - 118	72 - 124
3	6	PHE	PHE	CYS	CYS	(chain 'C' and ((resid 2 through 3 and (name N...	C	C	121 - 173	127 - 179
3	7	GLU	GLU	ILE	ILE	(chain 'C' and ((resid 2 through 3 and (name N...	C	C	176 - 237	182 - 243
3	8	PRO	PRO	PRO	PRO	(chain 'C' and ((resid 2 through 3 and (name N...	C	C	239	245
3	9	LYS	LYS	ILE	ILE	(chain 'C' and ((resid 2 through 3 and (name N...	C	C	241 - 255	247 - 261
3	10	PHE	PHE	PHE	PHE	(chain 'C' and ((resid 2 through 3 and (name N...	C	C	258	264
4	1	SER	SER	PRO	PRO	(chain 'D' and ((resid 2 through 3 and (name N...	D	D	2 - 10	8 - 16
4	2	LEU	LEU	THR	THR	(chain 'D' and ((resid 2 through 3 and (name N...	D	D	19 - 46	25 - 52
4	3	LEU	LEU	GLU	GLU	(chain 'D' and ((resid 2 through 3 and (name N...	D	D	48 - 61	54 - 67
4	4	LYS	LYS	LYS	LYS	(chain 'D' and ((resid 2 through 3 and (name N...	D	D	64	70
4	5	SER	SER	GLU	GLU	(chain 'D' and ((resid 2 through 3 and (name N...	D	D	66 - 118	72 - 124
4	6	PHE	PHE	CYS	CYS	(chain 'D' and ((resid 2 through 3 and (name N...	D	D	121 - 173	127 - 179
4	7	GLU	GLU	ILE	ILE	(chain 'D' and ((resid 2 through 3 and (name N...	D	D	176 - 237	182 - 243
4	8	PRO	PRO	PRO	PRO	(chain 'D' and ((resid 2 through 3 and (name N...	D	D	239	245
4	9	LYS	LYS	ILE	ILE	(chain 'D' and ((resid 2 through 3 and (name N...	D	D	241 - 255	247 - 261
4	10	PHE	PHE	PHE	PHE	(chain 'D' and ((resid 2 through 3 and (name N...	D	D	258	264
5	1	SER	SER	PRO	PRO	(chain 'E' and ((resid 2 through 3 and (name N...	E	E	2 - 10	8 - 16
5	2	LEU	LEU	THR	THR	(chain 'E' and ((resid 2 through 3 and (name N...	E	E	19 - 46	25 - 52
5	3	LEU	LEU	GLU	GLU	(chain 'E' and ((resid 2 through 3 and (name N...	E	E	48 - 61	54 - 67
5	4	LYS	LYS	LYS	LYS	(chain 'E' and ((resid 2 through 3 and (name N...	E	E	64	70
5	5	SER	SER	GLU	GLU	(chain 'E' and ((resid 2 through 3 and (name N...	E	E	66 - 118	72 - 124
5	6	PHE	PHE	CYS	CYS	(chain 'E' and ((resid 2 through 3 and (name N...	E	E	121 - 173	127 - 179
5	7	GLU	GLU	ILE	ILE	(chain 'E' and ((resid 2 through 3 and (name N...	E	E	176 - 237	182 - 243
5	8	PRO	PRO	PRO	PRO	(chain 'E' and ((resid 2 through 3 and (name N...	E	E	239	245
5	9	LYS	LYS	ILE	ILE	(chain 'E' and ((resid 2 through 3 and (name N...	E	E	241 - 255	247 - 261
5	10	PHE	PHE	PHE	PHE	(chain 'E' and ((resid 2 through 3 and (name N...	E	E	258	264
6	1	SER	SER	PRO	PRO	(chain 'F' and ((resid 2 through 3 and (name N...	F	F	2 - 10	8 - 16
6	2	LEU	LEU	THR	THR	(chain 'F' and ((resid 2 through 3 and (name N...	F	F	19 - 46	25 - 52
6	3	LEU	LEU	GLU	GLU	(chain 'F' and ((resid 2 through 3 and (name N...	F	F	48 - 61	54 - 67
6	4	LYS	LYS	LYS	LYS	(chain 'F' and ((resid 2 through 3 and (name N...	F	F	64	70
6	5	SER	SER	GLU	GLU	(chain 'F' and ((resid 2 through 3 and (name N...	F	F	66 - 118	72 - 124
6	6	PHE	PHE	CYS	CYS	(chain 'F' and ((resid 2 through 3 and (name N...	F	F	121 - 173	127 - 179
6	7	GLU	GLU	ILE	ILE	(chain 'F' and ((resid 2 through 3 and (name N...	F	F	176 - 237	182 - 243
6	8	PRO	PRO	PRO	PRO	(chain 'F' and ((resid 2 through 3 and (name N...	F	F	239	245
6	9	LYS	LYS	ILE	ILE	(chain 'F' and ((resid 2 through 3 and (name N...	F	F	241 - 255	247 - 261
6	10	PHE	PHE	PHE	PHE	(chain 'F' and ((resid 2 through 3 and (name N...	F	F	258	264

#1: Protein	Carbon-nitrogen hydrolase family protein Mass: 30993.930 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: BGG17_02735 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A5T0F3Q1
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.22 Å³/Da / Density % sol: 44.49 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: PEG 8000, NaCl, imidazole

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 Å
Detector	Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Nov 20, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97933 Å / Relative weight: 1
Reflection	Resolution: 2.9→30 Å / Num. obs: 37653 / % possible obs: 100 % / Redundancy: 6.5 % / B_iso Wilson estimate: 54.62 Å² / CC_1/2: 0.992 / Net I/σ(I): 6.3
Reflection shell	Resolution: 2.9→2.95 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 1837 / CC_1/2: 0.521 / % possible all: 99.9

-
Processing

Software

Name	Version	Classification
PHENIX	1.15.2_3472	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 2.9→29.91 Å / SU ML: 0.4015 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.4697
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2333	1878	5.03 %
R_work	0.1985	35430	-
obs	0.2002	37308	99.97 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 49.9 Å²

Refinement step

Cycle: LAST / Resolution: 2.9→29.91 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12185	0	0	25	12210

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0033	12467
X-RAY DIFFRACTION	f_angle_d	0.6771	16880
X-RAY DIFFRACTION	f_chiral_restr	0.0463	1891
X-RAY DIFFRACTION	f_plane_restr	0.0048	2121
X-RAY DIFFRACTION	f_dihedral_angle_d	25.907	4470

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 (%)
2.9-2.98	0.3443	143	0.3051	2672	X-RAY DIFFRACTION	99.96
2.98-3.07	0.3183	136	0.2768	2680	X-RAY DIFFRACTION	99.96
3.07-3.16	0.3258	147	0.2672	2693	X-RAY DIFFRACTION	100
3.16-3.28	0.3111	143	0.2626	2682	X-RAY DIFFRACTION	99.96
3.28-3.41	0.2865	150	0.2389	2685	X-RAY DIFFRACTION	99.96
3.41-3.56	0.2514	151	0.2137	2686	X-RAY DIFFRACTION	100
3.56-3.75	0.264	152	0.2053	2704	X-RAY DIFFRACTION	100
3.75-3.99	0.217	151	0.1856	2704	X-RAY DIFFRACTION	100
3.99-4.29	0.2033	156	0.1566	2719	X-RAY DIFFRACTION	100
4.29-4.72	0.1757	135	0.144	2741	X-RAY DIFFRACTION	100
4.72-5.4	0.2124	141	0.1633	2761	X-RAY DIFFRACTION	100
5.4-6.79	0.2353	128	0.2015	2799	X-RAY DIFFRACTION	100
6.79-29.91	0.1837	145	0.1922	2904	X-RAY DIFFRACTION	99.71

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	2.0407261786	2.3428403561	0.305324046121	7.56575473482	-0.00808570819183	2.16989102157	-0.113358565044	0.317833975356	0.185712933436	-0.536473180454	0.110264838452	-0.0233062664528	-0.0981582278296	0.146094484333	0.0025608342107	0.206041538824	0.0401488062086	0.030254438826	0.327349883202	0.0478849364341	0.271912219733	14.900934911	-18.4682820292	-13.0683282939
2	1.63768903288	0.518153133318	0.185544246924	2.69413073319	-0.682607005715	4.53323966893	-0.0687640148285	0.218257365257	-0.206212640104	-0.179853632472	-0.0817726731268	-0.466087834262	0.314619606132	0.532656157937	0.140317614801	0.228702506259	0.0924768198818	0.0687162139441	0.345433659961	0.0255422486101	0.332213565929	20.1727209397	-28.8300378466	-1.63387263048
3	1.24191002417	0.709740488644	-0.513208790175	3.43144581284	-0.826054394152	5.5028449065	-0.0299940457388	0.0419516811771	-0.00273753018768	0.196892784243	0.11578262574	0.317957753883	-0.34960028594	-0.480204602635	-0.0859351496665	0.211474382362	0.104749965697	0.0476074550902	0.341643770639	0.0161177288454	0.318102051409	9.46733025127	-22.8572184986	7.83837102683
4	2.68517851475	2.20067170597	0.305804790574	3.68245256197	0.0230298740129	3.12004893943	0.00334023965241	-0.143425509368	-0.0455611114277	0.393075233864	-0.0110376904309	0.218944478761	0.00742498021226	-0.043012975487	0.0257347398823	0.292373677567	0.0784767095363	0.0213505351374	0.280502933803	0.0656911036396	0.297124908567	-0.205016192209	-43.1907260956	39.7159419725
5	1.47837397255	0.0231103592651	-0.468718597649	4.81687791488	2.38863439407	5.12889416514	0.0938380997864	-0.262404747499	-0.240434754876	-0.0141675727855	-0.0794399156871	-0.012090993814	-0.245021210937	-0.0174514093485	-0.0378159043828	0.194101974361	0.00804449533526	0.0162579667927	0.276438121624	0.0919000039177	0.306057217757	11.291412768	-38.3772903847	27.6055556512
6	1.95100920002	1.15075973959	-1.51505846841	2.24809607118	-0.135360591389	4.3441039358	-0.0128750832318	0.228031372613	0.0883732461637	-0.231327105267	0.00868068861671	0.218602266933	-0.118888334709	-0.570986137867	0.0159485954928	0.258889361535	0.0957136074259	-0.0426932216903	0.359436279236	0.0370180080832	0.313788110687	0.619389100949	-37.0418779104	19.2628363792
7	7.03464409321	0.412784499355	-1.43816871197	1.2360673065	-0.629776804037	2.16933765712	0.145435898923	-0.561988760538	-0.292982392894	0.437011810552	-0.162177371311	-0.265268615804	0.0691034544985	0.149109658329	0.0234505285672	0.549153167853	-0.0428930477616	-0.136418198792	0.253062403239	-0.00290296610593	0.295883441653	-3.38650418762	0.58608666422	-14.5882092439
8	2.89682323881	-0.324181990261	-0.0862258766294	1.34599412576	-0.548930757435	4.69108796659	-0.0395351469333	-0.201082974902	0.168219508974	0.220618429834	-0.00623127225431	-0.139779219581	-0.220178882373	-0.39173127078	0.0511342816424	0.396801760377	-0.0352064115625	-0.0668069376516	0.25008825997	-0.0218630509375	0.266769695689	-12.9194112311	9.58903487866	-23.5434984548
9	2.87296704102	-0.731202742517	0.634053968091	1.03670360382	-0.591267020613	3.7418357393	0.174280971147	0.058828988269	-0.132775419815	-0.312792367744	-0.0128840255201	-0.00285579319132	0.546046320415	-0.0936320881128	-0.139447964438	0.463304930977	-0.0557572413468	-0.0665451393563	0.233133980764	-0.0390444818146	0.265669142365	-9.61432223743	0.228632581905	-35.1954234718
10	6.73656874769	-1.65373441498	-0.459814856334	4.27104746746	-1.66276004071	2.02411347508	0.437725617166	1.92219919201	-0.987668999531	-0.70301254541	-0.426770312143	0.52341819923	1.756697654	-1.9564195566	0.0513819758095	0.679423741653	-0.180816496116	-0.39423583197	0.948883711825	0.0047426152272	0.850812017534	-39.2514382003	-7.06528029124	-60.3433533628
11	5.82735735735	-0.0837535173886	-1.6208852756	3.2171933641	-2.28534733773	4.96618345753	0.187680395662	1.36043171361	0.121245666528	-0.588210218783	0.173422792683	0.29964945812	-0.0570437848593	-0.995337333852	-0.386901489669	0.723811618759	0.0733738938533	-0.12335487347	0.595907504557	0.0660418713213	0.355028045908	-31.9800713318	4.50228865745	-67.9997592662
12	5.76038197014	-1.88198696752	1.19300549796	1.72895234796	1.19855919245	2.83546265227	0.504231891268	0.719957287067	0.526645898794	-0.275735381161	0.00975613501139	0.508069298327	-0.364868267152	-0.840959501596	-0.542183462463	0.766257192058	0.0257942398553	-0.126615734116	0.550136142945	0.214615329445	0.491457055293	-33.8849681659	12.4645429626	-63.1921020213
13	5.41984058327	-1.53011444786	-2.04351110796	2.5379723778	-0.879678866592	7.19421111647	0.543907519561	0.489115030861	0.289860032876	-0.593356226003	-0.0570565645526	0.237158881008	-0.395323890672	-0.130960863803	-0.424010276198	0.511727617548	-0.00459994509117	-0.0350850823297	0.232943618683	0.0372271472464	0.272420140887	-25.5196093488	11.6038743228	-52.7617908638
14	3.97125636312	-0.313382598806	-0.536954639639	3.9732986927	-1.15758701554	4.14418527006	0.122256195142	0.28849964427	-0.368351286135	-0.304798422023	0.0735070361907	0.0705299476955	0.751724715817	0.131484966718	-0.187011950993	0.386286127376	0.00724474346627	-0.122929170689	0.247744455949	0.0355565515163	0.32476079416	-24.4616154695	-2.56107865776	-50.3933442241
15	4.99322255324	1.3134092972	1.45995787353	4.97188117595	3.1760389622	2.39047529863	-0.100355919709	-0.685568247868	0.0577393129496	-0.247577271022	0.0833636920938	0.43755890534	-0.159409799376	-0.325443106448	-0.131361857155	0.446776895741	-0.0269464029498	-0.0118639927093	0.418917200786	0.157357761798	0.351231471242	-33.9113250516	1.83777785509	-37.5055295994
16	1.25268310061	0.551451356456	-1.24715866936	3.7756756922	-2.70701996031	4.79342055717	-0.503925985451	0.31521965364	0.957525850366	0.0580264207899	-0.242803714245	-0.074300504925	-0.477753758532	1.21584135785	0.752667179264	0.414132993247	-0.149217564529	-0.104899524093	0.498266641802	0.215288669847	0.708150562595	16.5507713277	-17.1829506095	-41.7777043632
17	6.41870889271	1.20517795822	1.82446826172	3.67557411507	1.96605672884	3.17502593671	0.296041909177	-0.256690014411	0.323614619766	0.486727393751	-0.243879736604	0.320632649693	-0.0212237866102	0.0801059443487	-0.0519654353046	0.286747665738	0.0103483400836	-0.0145443261098	0.303225726495	-0.0712934363736	0.215281310762	6.42357583064	-26.1820837092	-36.6547357922
18	4.43828345891	2.54358429894	0.727397349912	8.45979866889	-1.99606983637	5.39244829117	-0.022477475211	-0.343516548184	0.71922984682	0.76856672631	-0.550110712642	0.0330401637838	-0.684714356725	0.00260037581525	0.551300720234	0.409163604659	-0.0327612402817	-0.0846042684583	0.432808109473	-0.0742672291642	0.500463216639	8.75824385856	-16.6051426155	-29.5106092862
19	4.57368871073	-1.07091512686	1.65436626539	4.07659601886	1.2135914968	5.81683347595	-0.27352471337	-0.141845983459	0.959064166414	0.132870859274	-0.238072514523	0.432152733858	-0.741381418397	-0.795577036584	0.499659516585	0.393933677332	0.138377807182	-0.0526044746275	0.393195323709	-0.152087862623	0.627327676954	0.399459023821	-16.7094405861	-35.7101010984
20	3.42235966509	-0.0384602517862	2.13218451577	4.17208990679	-1.84983231518	6.56503694774	-0.118733581716	-0.238181347926	0.621752579042	0.319389904604	-0.0592175372315	0.347590973906	-0.181091885788	-0.869461750613	0.194124142814	0.282915303235	0.0470600975666	0.0300345858687	0.432763123451	-0.101641822487	0.398615240277	-6.15604787731	-23.5544416139	-46.0187099824
21	3.76668927264	1.40284136389	2.323549087	0.778418058747	-0.360196729303	9.2075762601	0.425939200707	0.261156573033	0.59543212156	-0.298189743323	-0.612983441463	-0.199408532913	0.919203473762	0.150744408019	0.152817167913	0.367029229421	0.0931749872817	0.110522778319	0.313321264225	-0.00648025462565	0.420428975629	1.03216921718	-26.7448134613	-55.4536966172
22	4.36397411687	-0.664270514253	3.27302070497	4.67263222446	-4.09245713188	2.31947472289	0.106877881526	0.210651029565	0.366099168531	-0.421422850057	-0.434761527869	-0.410152253612	0.872825911665	0.384562950106	0.452047072409	0.334420033259	0.0650217205479	0.00933137978622	0.326547193003	0.00727808154847	0.322182498383	7.96182161481	-28.9320695423	-50.452916681
23	7.56133242878	-0.273717103441	7.0135868711	4.03648954419	-1.44409439344	7.87134035139	-0.379320543916	0.337611379731	0.816164298022	-0.0761740629457	-0.294429549526	0.0374646139114	-0.558869223027	0.592972230659	0.636904122532	0.342265633053	-0.0502591534884	0.116411340175	0.474290583874	0.160750990998	0.5435752354	3.37701031878	-18.8234799477	-61.0547098474
24	2.9752787727	1.1302340143	-0.0839986238874	2.07653202669	1.20921358246	2.25336835754	-0.358969446161	1.09449009692	-0.0622575129423	-0.702266508371	0.594787835593	-0.0839935095562	0.11631970416	0.460362767678	-0.225647241105	0.566124862572	0.00532763918749	-0.147798769917	0.971829033299	0.0324915195214	0.446033625868	-10.8248027586	-42.663964972	-84.049166797
25	3.09152877295	1.93190775354	1.42869599098	1.79810949066	1.38619898975	2.54254996631	-0.246248118796	0.758390604876	0.450572345201	-0.504365263865	0.287655579369	0.508779734642	-0.373034905405	-0.0832740473904	-0.0846450217082	0.529243568493	0.118926737485	-0.139057584342	0.586987478885	0.1790841826	0.631569779401	-19.224692038	-35.3919020434	-82.120114275
26	3.64106497187	0.939065675604	2.15322051856	3.21068285124	-0.206405417277	3.67002474164	0.183562526751	0.976177474705	0.0627160240544	-0.348811189606	-0.0519241807105	0.189675476296	0.0421634161548	0.623320827177	-0.140827494262	0.364642656547	0.123710750487	-0.0371687965638	0.524356399858	0.0779223556074	0.394601666137	-7.09894123129	-36.5320837383	-69.6859432776
27	4.31797321763	1.15150243377	-0.975684314227	3.93644405694	1.6586127576	8.22750469953	0.527545519273	-0.141993920591	-0.0383257555867	0.137909844229	-0.599677250959	0.95176315109	0.607551073574	0.106689114802	0.0126465092477	0.336882899879	0.108881806979	-0.141695559038	0.4643531414	0.120362654186	0.481952112962	-12.4638448003	-41.006619479	-56.5991657117

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 74 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 75 through 174 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 175 through 260 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 1 through 106 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 107 through 174 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 175 through 258 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 1 through 74 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 75 through 177 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 178 through 258 )
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 1 through 28 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 29 through 86 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 87 through 106 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 107 through 161 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 162 through 232 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 233 through 258 )
16	X-RAY DIFFRACTION	16	chain 'E' and (resid 1 through 29 )
17	X-RAY DIFFRACTION	17	chain 'E' and (resid 30 through 52 )
18	X-RAY DIFFRACTION	18	chain 'E' and (resid 53 through 74 )
19	X-RAY DIFFRACTION	19	chain 'E' and (resid 75 through 106 )
20	X-RAY DIFFRACTION	20	chain 'E' and (resid 107 through 161 )
21	X-RAY DIFFRACTION	21	chain 'E' and (resid 162 through 192 )
22	X-RAY DIFFRACTION	22	chain 'E' and (resid 193 through 223 )
23	X-RAY DIFFRACTION	23	chain 'E' and (resid 224 through 258 )
24	X-RAY DIFFRACTION	24	chain 'F' and (resid 2 through 52 )
25	X-RAY DIFFRACTION	25	chain 'F' and (resid 53 through 139 )
26	X-RAY DIFFRACTION	26	chain 'F' and (resid 140 through 232 )
27	X-RAY DIFFRACTION	27	chain 'F' and (resid 233 through 260 )

-
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