[English] 日本語

Yorodumi

- PDB-7bxb: Crystal structure of Ca_00311 -

+
Open data

-
Basic information

Entry

Database: PDB / ID: 7bxb

Title

Crystal structure of Ca_00311

Components

GDSL-like Lipase/Acylhydrolase

Keywords

HYDROLASE

Function / homology

SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / SGNH hydrolase superfamily / carboxylic ester hydrolase activity / PHOSPHATE ION / GDSL-like Lipase/Acylhydrolase

Function and homology information

Biological species

Collinsella aerofaciens (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.72 Å

Authors

Fan, C.P.

Funding support

China, 1items

Citation

Journal: To Be Published
Title: crystal structure of Ca_00311
Authors: Fan, C.P.

History

Deposition	Apr 18, 2020	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Apr 21, 2021	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewer	Molecule: MolmilJmol/JSmol

-
Downloads & links

-
Download

PDBx/mmCIF format	7bxb.cif.gz	650.1 KB	Display	PDBx/mmCIF format
PDB format	pdb7bxb.ent.gz	443.3 KB	Display	PDB format
PDBx/mmJSON format	7bxb.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7bxb_validation.pdf.gz	459.9 KB	Display	wwPDB validaton report
Full document	7bxb_full_validation.pdf.gz	464.6 KB	Display
Data in XML	7bxb_validation.xml.gz	62.2 KB	Display
Data in CIF	7bxb_validation.cif.gz	92.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bx/7bxb ftp://data.pdbj.org/pub/pdb/validation_reports/bx/7bxb	HTTPS FTP

-
Related structure data

Related structure data	4xt1S S: Starting model for refinement
Similar structure data	7bxc-2 7bxc-1 7bxc-3 4tx1-1 3dci-1 5k45-2 3t89-d 3pga-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

-
Assembly

Deposited unit

A: GDSL-like Lipase/Acylhydrolase

B: GDSL-like Lipase/Acylhydrolase

C: GDSL-like Lipase/Acylhydrolase

D: GDSL-like Lipase/Acylhydrolase

E: GDSL-like Lipase/Acylhydrolase

F: GDSL-like Lipase/Acylhydrolase

hetero molecules

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

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	112.929, 112.929, 305.943
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	92
Space group name H-M	P4₁2₁2
Space group name Hall	P4abw2nw
Symmetry operation	#1: x,y,z #2: -y+1/2,x+1/2,z+1/4 #3: y+1/2,-x+1/2,z+3/4 #4: x+1/2,-y+1/2,-z+3/4 #5: -x+1/2,y+1/2,-z+1/4 #6: -x,-y,z+1/2 #7: y,x,-z #8: -y,-x,-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	ALA	ALA	LEU	LEU	(chain 'A' and (resid 0 through 43 or resid 45...	A	A	0 - 42	1 - 43
1	2	GLY	GLY	PHE	PHE	(chain 'A' and (resid 0 through 43 or resid 45...	A	A	45 - 154	46 - 155
1	3	HIS	HIS	VAL	VAL	(chain 'A' and (resid 0 through 43 or resid 45...	A	A	157 - 172	158 - 173
1	4	PHE	PHE	MET	MET	(chain 'A' and (resid 0 through 43 or resid 45...	A	A	176 - 198	177 - 199
1	5	SER	SER	LEU	LEU	(chain 'A' and (resid 0 through 43 or resid 45...	A	A	201 - 217	202 - 218
2	6	ALA	ALA	LEU	LEU	(chain 'B' and (resid 0 through 43 or resid 45...	B	B	0 - 42	1 - 43
2	7	GLY	GLY	PHE	PHE	(chain 'B' and (resid 0 through 43 or resid 45...	B	B	45 - 154	46 - 155
2	8	HIS	HIS	VAL	VAL	(chain 'B' and (resid 0 through 43 or resid 45...	B	B	157 - 172	158 - 173
2	9	PHE	PHE	MET	MET	(chain 'B' and (resid 0 through 43 or resid 45...	B	B	176 - 198	177 - 199
2	10	SER	SER	LEU	LEU	(chain 'B' and (resid 0 through 43 or resid 45...	B	B	201 - 217	202 - 218
3	11	ALA	ALA	LEU	LEU	(chain 'C' and (resid 0 through 43 or resid 45...	C	C	0 - 42	1 - 43
3	12	GLY	GLY	PHE	PHE	(chain 'C' and (resid 0 through 43 or resid 45...	C	C	45 - 154	46 - 155
3	13	HIS	HIS	VAL	VAL	(chain 'C' and (resid 0 through 43 or resid 45...	C	C	157 - 172	158 - 173
3	14	PHE	PHE	MET	MET	(chain 'C' and (resid 0 through 43 or resid 45...	C	C	176 - 198	177 - 199
3	15	SER	SER	LEU	LEU	(chain 'C' and (resid 0 through 43 or resid 45...	C	C	201 - 217	202 - 218
4	16	ALA	ALA	LEU	LEU	(chain 'D' and (resid 0 through 43 or resid 45...	D	D	0 - 42	1 - 43
4	17	GLY	GLY	PHE	PHE	(chain 'D' and (resid 0 through 43 or resid 45...	D	D	45 - 154	46 - 155
4	18	HIS	HIS	VAL	VAL	(chain 'D' and (resid 0 through 43 or resid 45...	D	D	157 - 172	158 - 173
4	19	PHE	PHE	MET	MET	(chain 'D' and (resid 0 through 43 or resid 45...	D	D	176 - 198	177 - 199
4	20	SER	SER	LEU	LEU	(chain 'D' and (resid 0 through 43 or resid 45...	D	D	201 - 217	202 - 218
5	21	ALA	ALA	LEU	LEU	(chain 'E' and (resid 0 through 43 or resid 45...	E	E	0 - 42	1 - 43
5	22	GLY	GLY	PHE	PHE	(chain 'E' and (resid 0 through 43 or resid 45...	E	E	45 - 154	46 - 155
5	23	HIS	HIS	VAL	VAL	(chain 'E' and (resid 0 through 43 or resid 45...	E	E	157 - 172	158 - 173
5	24	PHE	PHE	MET	MET	(chain 'E' and (resid 0 through 43 or resid 45...	E	E	176 - 198	177 - 199
5	25	SER	SER	LEU	LEU	(chain 'E' and (resid 0 through 43 or resid 45...	E	E	201 - 217	202 - 218
6	26	ALA	ALA	LEU	LEU	(chain 'F' and (resid 0 through 43 or resid 45...	F	F	0 - 42	1 - 43
6	27	GLY	GLY	PHE	PHE	(chain 'F' and (resid 0 through 43 or resid 45...	F	F	45 - 154	46 - 155
6	28	HIS	HIS	VAL	VAL	(chain 'F' and (resid 0 through 43 or resid 45...	F	F	157 - 172	158 - 173
6	29	PHE	PHE	MET	MET	(chain 'F' and (resid 0 through 43 or resid 45...	F	F	176 - 198	177 - 199
6	30	SER	SER	LEU	LEU	(chain 'F' and (resid 0 through 43 or resid 45...	F	F	201 - 217	202 - 218

-
Components

#1: Protein	GDSL-like Lipase/Acylhydrolase / Ca_00311 Mass: 24330.625 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Collinsella aerofaciens (bacteria) / Gene: NCTC11838_00845 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A381K2L8
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: PO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1422 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.34 Å³/Da / Density % sol: 63.23 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M pH7.50, 0.8 sodium phosphate monobasic, 0.8M potassium phosphate monobasic

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 1, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9793 Å / Relative weight: 1
Reflection	Resolution: 1.72→48.57 Å / Num. obs: 211217 / % possible obs: 100 % / Redundancy: 23.5 % / B_iso Wilson estimate: 19.21 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.138 / R_pim(I) all: 0.029 / R_rim(I) all: 0.142 / R_sym value: 0.138 / Net I/σ(I): 20.3
Reflection shell	Resolution: 1.72→1.74 Å / R_merge(I) obs: 1.383 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 10262 / CC_1/2: 0.565 / R_pim(I) all: 0.421 / R_rim(I) all: 1.449 / R_sym value: 1.383

-
Processing

Software

Name	Version	Classification
PHENIX	1.15.2_3472	refinement
XDS		data reduction
Aimless		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4XT1

4xt1

Resolution: 1.72→48.57 Å / SU ML: 0.1744 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.2012

	R_factor	Num. reflection	% reflection
R_free	0.1938	1999	5 %
R_work	0.1608	-	-
obs	0.1611	210916	99.85 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso mean: 23.22 Å²

Refinement step

Cycle: LAST / Resolution: 1.72→48.57 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10153	0	75	1422	11650

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0142	10447
X-RAY DIFFRACTION	f_angle_d	1.2853	14192
X-RAY DIFFRACTION	f_chiral_restr	0.086	1530
X-RAY DIFFRACTION	f_plane_restr	0.0087	1873
X-RAY DIFFRACTION	f_dihedral_angle_d	4.0874	6173

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 (%)
1.71-1.76	0.3301	139	0.2735	14619	X-RAY DIFFRACTION	99.14
1.76-1.81	0.226	142	0.2236	14748	X-RAY DIFFRACTION	99.97
1.81-1.86	0.2432	141	0.1985	14788	X-RAY DIFFRACTION	99.99
1.86-1.92	0.211	142	0.1888	14780	X-RAY DIFFRACTION	99.96
1.92-1.99	0.1909	141	0.1798	14779	X-RAY DIFFRACTION	99.95
1.99-2.07	0.1808	142	0.1629	14821	X-RAY DIFFRACTION	99.92
2.07-2.16	0.2102	142	0.1622	14804	X-RAY DIFFRACTION	99.92
2.16-2.27	0.1881	142	0.1578	14841	X-RAY DIFFRACTION	99.82
2.27-2.42	0.2031	141	0.16	14868	X-RAY DIFFRACTION	99.79
2.42-2.6	0.1898	143	0.1608	14891	X-RAY DIFFRACTION	99.8
2.6-2.87	0.1908	144	0.1643	14960	X-RAY DIFFRACTION	99.88
2.87-3.28	0.2114	143	0.16	15061	X-RAY DIFFRACTION	99.89
3.28-4.13	0.1934	146	0.1359	15179	X-RAY DIFFRACTION	99.89
4.13-48.57	0.1499	151	0.1442	15778	X-RAY DIFFRACTION	99.94

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	2.16980168648	1.04192486008	0.298730861253	4.45722573698	0.312050789261	1.85951197226	-0.0164766092285	-0.00657703509324	0.0704799260749	0.0517712403153	0.0876919852997	-0.0716743190792	-0.0194548865036	0.215760351432	-0.0638052822612	0.151865219868	0.0362657440464	-0.00797096015021	0.188292499865	-0.0234499139942	0.0992678949655	-42.9514732803	-0.193308011274	-11.1565663553
2	5.09666821687	-0.0750105582607	0.000437232258904	4.24462472496	0.605911945245	6.67669894829	-0.024157080924	-0.230977163153	0.263620401	-0.0921820675155	0.0366627603343	-0.420650465054	0.0279562551641	0.781642613631	0.0146997435335	0.131593683991	0.0466319189765	-0.024351220188	0.319311023232	-0.0312121159038	0.208714914084	-34.0714186647	2.63185496807	-9.50261280339
3	2.01076103456	1.32567406018	-0.327516455079	5.37877715299	-1.99196746377	6.44099540187	0.0129789317782	-0.148984551534	-0.143880876845	0.299202297487	0.0383832139133	-0.174071690966	0.323570403527	0.455393620987	-0.0567962351524	0.180791230231	0.0791546684823	-0.0212340973429	0.203899683731	-0.0217760095942	0.149928915701	-43.7809724102	-9.30546187093	-5.10570554518
4	0.573814523652	0.0380732928278	-0.129812746219	1.93730081659	-0.179969514653	0.68706472391	-0.00650680906255	-0.0208270011677	0.0132695211712	0.0215208346102	0.00798255513736	-0.0266622455286	0.0166970603065	0.0211091095725	-0.00347220602158	0.140146176172	0.00146061083024	-0.0109887201633	0.155326704111	-0.00858495039224	0.138107998877	-51.5412776196	1.64541220946	-20.6104961568
5	0.869014894322	-1.57116356102	-0.233085824679	8.92371132338	1.27451029529	1.06879663883	-0.0165925668748	-0.00547949239666	-0.163181060136	0.21029369983	-0.0368251147321	0.377089101628	0.129554256437	-0.0496535672683	0.0523401895324	0.147859786245	0.00907347094292	0.00404925951588	0.17380506099	0.00321922133176	0.168830069912	-61.3078568906	-6.44705260506	-17.136627059
6	0.971358874358	1.09286205865	-0.385777207925	2.14872415766	-0.59649664274	1.00051459256	-0.00085002177336	-0.130308013638	0.0853006405892	0.122362782638	-0.0208915499635	-0.0729350867363	-0.158800671363	0.0945319573556	0.0154451070066	0.169270516103	0.00878833205144	-0.00970757302498	0.189894030947	-0.0350522487922	0.158265340875	-50.3782259204	13.411325904	-10.9129247607
7	4.67322033229	3.61387443021	-0.803071940731	2.81752143108	-0.517229638209	2.69417099937	0.0857626253515	-0.207299429934	0.293996031003	0.209898697652	0.0253144063447	0.41363621219	-0.154645192961	-0.279319273981	-0.114583517701	0.150402630442	0.0650040151759	0.011122316932	0.214342368546	-0.0103355651331	0.183590620506	-61.9429129097	9.78078154477	-9.29139995899
8	2.59132884313	1.18411928747	-1.24860049413	2.24140514586	-1.08464665111	1.49614261451	-0.0189920405007	-0.142807217085	0.0947495182925	0.268870042394	0.0527230079811	-0.0203115074293	-0.138582323076	0.0297231195501	-0.0161413008827	0.18367241616	0.0327768861742	-0.0212150274141	0.197938759075	-0.0241370058922	0.158312054904	-49.2696727614	7.97808635921	-4.58614031543
9	6.8116519161	5.01069674303	-1.28966126313	3.73338882265	-1.29233069442	2.57104128433	0.111512435398	-0.465205714049	-0.137718305652	0.291615158926	-0.166299301493	-0.143790536321	0.151935635354	0.0903834514257	0.0600698450815	0.206453099688	0.0684825616123	-0.00114287324641	0.218262283279	-0.0020682089202	0.140167185082	-48.926880036	-4.4211068497	0.441537762762
10	1.81026129568	-0.0320623925037	0.0246971867024	2.03904705903	0.303721600882	3.60896595317	0.00331699990611	-0.15960900467	-0.164932594156	0.244449188892	-0.060327966845	0.287578371716	0.130722730582	-0.204172951727	0.0425364105833	0.107535135515	0.0126871408976	0.0315356689267	0.145287699468	-0.00681154385101	0.233864954666	-83.5913819273	1.27665500208	-31.9895599278
11	4.63471319148	-0.468862051264	2.1626469924	2.33688403168	1.24424584853	3.95853729343	-0.0154225599681	0.154383210617	-0.240151416869	0.00377469185528	-0.18195227101	0.431918394171	0.00580120006643	-0.308018115808	0.210532790171	0.132516249805	-0.0173731592452	0.00393638090859	0.143221660014	-0.0240496385221	0.247408728484	-88.2268769375	2.28600324349	-42.9410927871
12	0.366777708861	0.180351434526	0.267982744018	0.954467789489	0.603876251307	1.82535534595	-0.016154767058	-0.0285825852484	0.00128810920218	-0.0253121978508	0.017360287111	0.0129428443964	-0.00648317232834	-0.0148298278171	-0.00593923433385	0.120939758298	0.00701621059344	-0.000892571412562	0.144712049165	0.00300843137944	0.16067790496	-69.5829064608	6.45712174323	-36.1381029598
13	0.904775966522	0.528113612865	0.752647646672	4.26184381614	4.09619595091	5.08961785013	-0.0899775869764	0.101824691639	0.0351058013132	-0.386313133919	0.0136582942351	0.101877141182	-0.286678701317	-0.0182743268401	0.0916242107532	0.161779996263	-0.0012315258708	-0.00466565972281	0.154046249211	0.0239157105475	0.170573287286	-70.0082089001	11.9058071298	-48.0932714046
14	1.08222297693	-0.28287238507	0.407531604044	0.660636834523	-0.122190889338	3.41680337711	-0.0895885503379	-0.195483565715	0.0420127815786	0.063531154844	0.040107160131	0.111383576583	-0.16919603559	-0.325422366435	0.072878794505	0.136907848595	0.0331011646754	0.00706134399173	0.129529570632	-0.00676154796433	0.170007632435	-76.9374720525	14.980925055	-25.8656608661
15	1.8186025747	-0.253679242754	0.387529160086	2.83611245222	-0.50234353783	8.1119025289	-0.0245942315487	0.0234207792874	0.264923694606	0.00304542433506	-0.00907281228412	0.0262604307056	-0.507532958992	0.0489219475765	0.0217287107976	0.138966934124	0.00461446971928	-0.00187673620754	0.126965220947	0.00153086535675	0.231804976333	-74.3798061032	22.9801974838	-34.9404058359
16	0.781764931273	-0.105721494614	0.494651902698	1.65664883971	-1.48201070669	3.79011093158	-0.0896843403461	-0.0790933584165	0.0364722101318	0.0680418067477	0.0388348534015	0.16027099261	-0.145992661938	-0.163182208792	0.0283929614438	0.167273018714	0.0287367138519	0.00457438898241	0.176667174938	-0.00714034961354	0.223973696979	-84.0713690899	14.4511117219	-30.6761076959
17	2.68884994086	-0.156551529341	0.296083560507	2.6907688179	-2.14556354113	6.23424721037	0.065978599585	0.135162256509	0.0356232468994	-0.0827374277332	0.0515670087831	0.410515467341	-0.0789825785105	-0.378590169234	-0.169525778265	0.120681089376	0.0340051410972	-0.0321899191918	0.164483122866	-0.0267221790335	0.292641789681	-90.4025801996	10.771119275	-41.4263695513
18	3.01422187791	-0.807807756073	0.304951742768	3.63889700104	-0.296384422828	2.38439200632	0.0496537493664	-0.0654717335864	0.0152857377507	0.00874128247745	0.0147413413184	-0.269946747998	-0.0885170325242	0.320866064157	-0.0490712830646	0.158266917645	-0.0570318255581	0.0372105684937	0.210737090079	-0.028573107807	0.142843345573	-36.1499009903	7.37418692987	-58.1395439099
19	9.37435517138	-2.59378390533	0.159914682737	6.26592557691	1.93858613542	6.5797066387	-0.0247662464011	0.093172759317	0.104925067741	0.0129729147783	0.11611103369	-1.11583319819	-0.287080852886	0.512008411224	-0.0163638249894	0.173437313586	-0.0969573746397	0.0131903869047	0.26529704641	-0.0159211246183	0.308123427521	-26.8300862993	8.03693829161	-56.6411733043
20	1.52735219144	-0.489118398691	0.52440852335	5.13066878296	-2.28935936997	3.97829820005	0.096027486301	0.158025851052	0.379565599112	-0.404802218554	-0.00364078857313	-0.404244708299	-0.42726528071	0.513713773108	-0.0955008727793	0.241851339129	-0.0840501701143	0.0593705846329	0.198909952506	0.00355770715629	0.211534638519	-38.3688208916	15.6035101814	-64.6899860328
21	0.71933087633	-0.249661802179	0.149344702332	1.06979417958	-0.0513077838036	0.759893310197	0.00238357370347	0.0529893519379	0.0300229042934	-0.0956446711234	-0.00895704766674	-0.0053761159599	-0.0374960289104	0.0638565465539	0.00614312792377	0.139567742695	-0.0196606818237	0.010971730718	0.171866569678	-0.00278817497393	0.138714773967	-46.6024665746	0.673432710519	-55.3573654152
22	6.83370743625	-3.40824394023	3.99597702479	3.33948806679	-2.34809466677	4.32421498781	0.0251858527607	0.0727763733547	-0.358014529515	-0.242566651125	0.110183440152	0.118596211743	0.172370122915	0.0128640032932	-0.132844729272	0.191355483244	-0.0396285738351	0.00938618565038	0.168880546447	-0.0302671491336	0.157242591101	-48.469993436	-8.61246773832	-65.2051049399
23	4.92846437638	-1.55540502408	1.77873978294	1.95245648235	-0.768535131968	2.26844498528	0.0762492253144	0.195247790211	-0.00704509820864	-0.28622628142	-0.0206998286568	-0.142482336639	0.105090804121	0.246877115794	-0.0411152992206	0.197088710412	-0.0228783912694	0.036893206359	0.197534267247	-0.0203360865669	0.166951930799	-36.6664978396	-2.03237787858	-65.8715822146
24	7.89461158123	-4.44601699728	2.95094706312	4.94389379128	-1.94179415539	3.93338190774	0.107317075989	0.516313066701	0.439575984766	-0.467052878533	-0.18054448052	-0.354371393214	-0.164901330207	0.239912300305	0.0968018612846	0.297736869296	-0.0640000077878	0.0727939407602	0.229860174336	0.0338269922293	0.15176890301	-39.2143293214	9.76302423954	-71.2316001031
25	4.82818284583	-1.69474729971	0.0172509529458	3.19424581819	0.0708694099979	2.20875044776	-0.0240476270535	0.294939858267	0.173247585901	-0.222340705493	0.00547096474652	0.126254695779	-0.12444999809	-0.0978869343738	0.00866520391546	0.177181474812	-0.0534398119839	-0.0153040593397	0.149908552918	0.00207347944647	0.177433028835	-45.3718183904	25.1763666562	-49.0867557344
26	6.82752385827	-0.611981373996	1.10108751627	7.34248034702	0.0591106473242	5.19764212737	0.0445666551978	0.334940054938	0.0978144092448	-0.429254600448	-0.144124035895	-0.173789597799	-0.270816008495	-0.0925816088811	0.0503719390125	0.221852760251	-0.0499313195383	-0.0151320822178	0.157967952662	0.0411242428288	0.124421450741	-48.3361918448	28.5964457963	-55.6909108174
27	2.58520773757	-0.0957467076338	-0.667011211371	2.63276353189	-0.661466452214	1.96516216241	-0.0607366090452	0.233055697585	0.0160881086645	-0.357735137857	0.0354471637208	-0.11782131487	-0.126979931894	0.0429011548412	0.0577430049743	0.242868675514	-0.0457565145693	0.022324847807	0.187784372802	0.00368593184351	0.206076047007	-34.3419997297	25.4816932872	-51.9059102256
28	1.3684377439	-0.535541372867	-0.614899733711	0.732222179367	0.416845561129	1.02347398953	-0.0293546314056	0.0560787104298	0.0122367659424	0.00885627240922	0.0380371381819	-0.0243529517327	-0.0331152777108	0.0330022455467	-0.00647027247746	0.132549980322	-0.0144102708378	-0.00928602043764	0.127247827088	0.00379040848381	0.159306639565	-47.5004723429	15.9160596152	-39.7806891862
29	4.09648124791	-4.23325790673	-4.17741199085	4.4172830541	4.23442136315	4.33468280425	-0.169100337901	-0.377925184904	0.145638896973	0.222811825779	0.309677809274	-0.227322739252	0.181392457796	0.333611269297	-0.174628281659	0.142497746871	-0.0165249326366	-0.0175402669542	0.199072775256	-0.00285316434316	0.184817044463	-40.6627208968	16.521493847	-30.1539584235
30	4.26437335152	0.759132280971	-2.40567276797	7.01872361208	0.672901947566	8.73174785269	-0.176832964103	-0.103655478848	-0.445625322816	-0.308027018882	0.136440313454	-1.27350245077	0.352575353122	0.840963434387	0.0349521559364	0.189130690837	0.021644988484	0.032823695578	0.218633016593	-0.0173229509006	0.342495019255	-27.9337077778	8.53199130496	-41.3927233565
31	3.37380188813	-0.748675558751	-0.0418667168944	1.00565600738	-0.233204899447	0.251234522842	-0.0397844846162	0.126854500184	0.3449010892	-0.00746562949189	0.0280688742721	0.0641830107267	-0.106004942933	-0.0054846305798	-0.000544953472508	0.188643252901	-0.0178640832812	-0.0235008833123	0.132017111359	-0.0182857610138	0.209004285995	-52.2900922767	29.9330644748	-36.2698092483
32	2.9546586508	-3.82228341925	0.792671601719	5.3921417154	-0.0188058970228	2.83165488053	-0.280762225265	-0.347003392861	0.258609746688	0.306335458382	0.145118193581	-0.119135988662	-0.386241200348	0.0669596031721	0.146434472737	0.240129083346	-0.0354986177292	-0.0200827583913	0.174093247742	-0.0297936825975	0.173434147554	-43.7795205201	27.5539868365	-27.5210670667
33	7.87554944162	-6.15223070885	2.76237318519	6.16114760694	-2.61901377697	3.25576889598	0.0315509475949	-0.0820369746777	0.398715254579	-0.0860085645513	-0.0108906107883	-0.331727207894	-0.165844801123	0.306176020363	-0.011526176104	0.183641343965	-0.0646485151987	-0.0180072447487	0.20449798172	-0.0315234139029	0.215817998189	-35.5688139147	29.4752954383	-34.9296311195
34	7.30574859425	-0.998724956614	-0.0757769427629	0.205169754991	-0.276725528614	1.09517468032	-0.0573576375365	-0.222905757796	0.413292242038	-0.0344110513184	0.0741827622211	0.1511234758	-0.196543495576	-0.0955165647656	-0.0130213584389	0.236734204196	-0.00713886461098	-0.0314072909521	0.169425976515	0.00189961398121	0.276540850855	-51.0274432076	35.3623895033	-43.0364547006
35	3.50872056791	-2.23294999175	3.90862843274	2.98389696035	-2.16187783333	4.4602994056	-0.13730144893	0.350563595008	0.0117666388771	-0.0122729657617	-0.00724186201013	-0.111348420593	-0.222892100449	0.257681170614	0.20720004392	0.194781662385	-0.0915218709676	0.0119193511133	0.156395843085	0.00191014256483	0.194253998122	-33.6110823016	31.5816885376	-45.4356357085
36	1.96024176071	-0.329578135813	-0.669155926815	1.72152496774	0.0570188562463	3.80226573999	-0.0253252409629	0.224208651617	0.129835249864	-0.157311187033	-0.044337545667	0.145743887417	-0.0795358715583	-0.148200295337	0.0489581494859	0.131835586478	-0.0351071348971	-0.0219353423069	0.152936216816	0.00161484694358	0.185432197474	-77.5987290112	-10.2571025117	-51.9690787861
37	6.42020827267	2.51618424142	-2.14367852771	5.08629637126	-0.0329240640435	5.88979744604	-0.053827801816	0.15134594634	0.167080141422	0.0489248386296	0.0499536391958	0.5163791536	0.0672868422218	-0.398571302574	0.0374705344847	0.129876664068	0.0136996512414	-0.0129986991854	0.129707117166	0.0117822088332	0.221924538435	-85.3150987395	-13.6490147025	-43.2690510966
38	1.26565910574	-0.346137248873	-0.867977080987	0.930749693592	0.367350397834	1.54466100539	-0.00827592926391	0.0241334794005	0.00638446350448	0.0599434075348	0.00583015127279	0.00966341285194	0.0104068789202	-0.0186713916214	-0.00598861979075	0.1277661382	-0.0089590663546	-0.0115074354389	0.119995628051	0.00165460657828	0.133776306795	-65.1049610626	-10.1883773523	-42.9114538195
39	4.92562911849	-2.91650702427	-3.75869296397	3.34266459766	3.01414088637	4.72266009889	-0.224977416169	-0.193756591228	-0.0974544387898	0.313160647068	0.0852846437134	0.159412106036	0.232816413175	-0.0200046473702	0.190039598211	0.168996969369	-0.00434628401017	0.00556206762559	0.143091912877	0.0125958793755	0.153029090925	-67.5871173102	-16.1764328344	-31.4691284839
40	1.11504505229	0.208522317584	-1.14217463107	0.420185704347	-0.241726060883	3.52193310932	-0.0528615353619	0.124121373163	-0.0635908740451	-0.07241931419	0.02748047487	0.0340624136407	0.153601110762	-0.0895520143325	0.0512165171605	0.164348511906	-0.0122986366285	-0.0141632427638	0.139640866538	-0.0166283165348	0.170253925068	-64.7973096949	-20.2218378113	-54.4427948965
41	4.26760362516	1.11096787932	-3.64140813717	3.3291870516	-1.40633592955	3.19955697333	-0.176588128347	-0.0656228265545	-0.387721452775	-0.122135535074	-0.0092589432587	-0.105279947432	0.521850912871	0.250285417672	0.225641205429	0.16276878271	0.00807741630652	-0.0305183905547	0.123292672936	0.00490377484301	0.220799444318	-62.4907290182	-27.3074410393	-44.7573902608
42	2.0284119983	-0.877064565768	-1.0599527105	1.85157420589	-1.11014038595	2.26225665753	-0.0518818863243	0.00549141434522	-0.216448968947	0.0585968313536	0.0103367858906	0.198986315077	0.381891695358	-0.408468628954	0.0441154303627	0.176616323162	-0.0261308924856	0.025933445395	0.136160924186	0.00723628578234	0.227650743111	-73.6800713025	-26.8863369329	-41.9047003697
43	2.6945744083	0.956558886016	-2.39313814485	0.986499456212	-1.30092403017	4.43001885865	-0.0529632476045	0.115321709927	-0.0879390308322	-0.0705786518036	0.0521626421029	0.149649468197	0.161040696449	-0.181871181428	0.0153414586931	0.176399009065	-0.0336987418407	-0.0173675035685	0.143616556762	-0.0177380369028	0.218496565364	-78.7967478158	-21.3462004136	-50.5487239962
44	2.46145467574	0.714141191469	0.209276557525	3.20460530414	0.423600216556	2.22011136165	-0.0802789970813	-0.219519953263	-0.181668428046	0.330207085619	0.0993263394894	0.0996459139379	0.230432801146	-0.077365566481	-0.0314179290609	0.160202248904	0.0688793186492	0.00646940080764	0.145993891081	0.0162036366298	0.123642067523	-42.9292334169	-21.1275169073	-19.6887782568
45	4.7413904515	0.133803708945	2.11644119647	3.31366550427	0.818654125077	3.45698350564	-0.11589246724	-0.31264406611	-0.100746152479	0.595278369236	0.182052495216	-0.181533521715	0.141239576975	0.115640718514	-0.051303784733	0.208473813929	0.0607131733926	-0.0305878230668	0.211601588803	-0.0205064870157	0.115032839564	-32.9809335311	-16.1632942692	-14.6775544913
46	1.01912065986	0.217957803713	-0.044997747233	1.24514664361	0.98046457498	1.65716262844	-0.0289940766515	-0.0131234055998	0.0190513712801	-0.0352812058179	0.0387304468168	-0.0281444351418	-0.0322763319397	0.0498594719589	-0.00437754732521	0.103523176978	0.00941104031204	-0.00752519814073	0.111323913257	0.00243831759698	0.128772615038	-43.7047673726	-11.1789459235	-31.4738516472
47	0.584706263906	0.423855450907	0.727539498582	4.33698319721	3.35567109996	4.56675072481	0.0289088879294	0.0248323607224	0.0518292274153	0.0579930175176	0.21769610537	-0.331878907786	-0.145744550322	0.312101224992	-0.331327316883	0.133982414151	-0.0138390210019	0.00861246432699	0.21623356742	-0.0239881515137	0.194717621349	-32.5248320849	-4.29954096958	-32.5368973776
48	3.21444048445	1.89210483806	1.5680093657	2.44337266597	0.825148618648	0.854499696947	0.0834095067574	-0.129692458847	-0.23671696551	0.0364982000088	0.0231360769413	-0.0816630471935	0.105209618895	0.0331991099439	-0.132958243819	0.165307185364	0.0402922023007	0.00943346874576	0.174241916773	-0.0156675699775	0.18254412453	-41.6174276425	-25.7723735488	-35.4779533156
49	8.08318709098	3.82475445995	1.34401719295	4.71084786534	0.730250831516	2.14861997053	-0.20325461184	0.28800802701	-0.26274831042	-0.375962495617	0.19128787674	-0.306250896176	0.0741893042967	0.290650615391	-0.0168953919143	0.16074212341	0.0469006828746	0.041648574631	0.207877168118	-0.0305758997535	0.166436319407	-32.9130644113	-20.551617524	-41.1944695671
50	4.68019080076	6.0763052424	-1.0095866553	8.41502167023	-0.792872451992	2.08022957531	0.0462466226627	0.128882664531	-0.0918406366236	0.159545085786	-0.0154583591709	-0.28546109946	0.0918949204202	0.44713112892	-0.0302729725245	0.125451477067	0.0544079972085	-0.00695527537306	0.289071018345	-0.0237700600309	0.19913761711	-26.862988198	-19.3601946163	-31.0806937199
51	4.2083105864	3.53604914748	1.97543038326	3.05533957856	1.47696435368	1.63681608859	0.093310623148	0.149880429062	-0.440676816344	0.143101551974	0.0752544831884	-0.0692352636117	0.262199926275	0.176117802891	-0.206554890601	0.185535743306	0.0517775743988	0.00694272662678	0.156267330969	0.00139494286096	0.200447666796	-40.8992374174	-30.7236105597	-28.3735269681
52	8.82491818638	7.31244890726	2.26854774503	9.35454591875	1.65108379909	1.65981903375	0.0549695293821	-0.275046778407	-0.366872533055	0.418480957312	0.087948672095	-0.615954386001	0.209205416184	0.378572446866	-0.110371265762	0.176283981054	0.111456135588	-0.0294537798798	0.28886666757	-0.0468331953562	0.199096044063	-27.5515548428	-20.8414900134	-19.9889647026

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 0 through 21 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 22 through 33 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 34 through 51 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 52 through 105 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 106 through 132 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 133 through 155 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 156 through 176 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 177 through 198 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 199 through 219 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 0 through 33 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 34 through 51 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 52 through 105 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 106 through 132 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 133 through 155 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 156 through 176 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 177 through 198 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 199 through 219 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 0 through 21 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 22 through 33 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 34 through 51 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 52 through 155 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 156 through 176 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 177 through 198 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 199 through 219 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 0 through 22 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 23 through 33 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 34 through 51 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 52 through 105 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 106 through 122 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 123 through 132 )
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 133 through 155 )
32	X-RAY DIFFRACTION	32	chain 'D' and (resid 156 through 176 )
33	X-RAY DIFFRACTION	33	chain 'D' and (resid 177 through 185 )
34	X-RAY DIFFRACTION	34	chain 'D' and (resid 186 through 198 )
35	X-RAY DIFFRACTION	35	chain 'D' and (resid 199 through 219 )
36	X-RAY DIFFRACTION	36	chain 'E' and (resid 0 through 33 )
37	X-RAY DIFFRACTION	37	chain 'E' and (resid 34 through 51 )
38	X-RAY DIFFRACTION	38	chain 'E' and (resid 52 through 105 )
39	X-RAY DIFFRACTION	39	chain 'E' and (resid 106 through 132 )
40	X-RAY DIFFRACTION	40	chain 'E' and (resid 133 through 155 )
41	X-RAY DIFFRACTION	41	chain 'E' and (resid 156 through 176 )
42	X-RAY DIFFRACTION	42	chain 'E' and (resid 177 through 185 )
43	X-RAY DIFFRACTION	43	chain 'E' and (resid 186 through 219 )
44	X-RAY DIFFRACTION	44	chain 'F' and (resid 0 through 33 )
45	X-RAY DIFFRACTION	45	chain 'F' and (resid 34 through 51 )
46	X-RAY DIFFRACTION	46	chain 'F' and (resid 52 through 105 )
47	X-RAY DIFFRACTION	47	chain 'F' and (resid 106 through 132 )
48	X-RAY DIFFRACTION	48	chain 'F' and (resid 133 through 155 )
49	X-RAY DIFFRACTION	49	chain 'F' and (resid 156 through 176 )
50	X-RAY DIFFRACTION	50	chain 'F' and (resid 177 through 185 )
51	X-RAY DIFFRACTION	51	chain 'F' and (resid 186 through 198 )
52	X-RAY DIFFRACTION	52	chain 'F' and (resid 199 through 219 )

+
About Yorodumi

-
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://pdbjlvh1.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