[English] 日本語

Yorodumi

- PDB-7c72: Structure of a mycobacterium tuberculosis puromycin-hydrolyzing p... -

+
Open data

-
Basic information

Entry

Database: PDB / ID: 7c72

Title

Structure of a mycobacterium tuberculosis puromycin-hydrolyzing peptidase

Components

Prolyl oligopeptidase

Keywords

HYDROLASE / Prolyl oligopeptidase / tuberculosis / acyl aminopeptidase

Function / homology

D-MALATE

Function and homology information

Biological species

Mycobacterium tuberculosis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.00004456732 Å

Authors

Ruiz-Carrillo, D. / Zhao, Y.H. / Feng, Q. / Zhou, X. / Zhang, Y. / Jiang, J. / Lukman, M.

Funding support

China, 1items

Citation

Journal: Proteins / Year: 2021
Title: Mycobacterium tuberculosis puromycin hydrolase displays a prolyl oligopeptidase fold and an acyl aminopeptidase activity.
Authors: Zhao, Y. / Feng, Q. / Zhou, X. / Zhang, Y. / Lukman, M. / Jiang, J. / Ruiz-Carrillo, D.

History

Deposition	May 22, 2020	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Mar 24, 2021	Provider: repository / Type: Initial release
Revision 1.1	May 19, 2021	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2	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	7c72.cif.gz	634.3 KB	Display	PDBx/mmCIF format
PDB format	pdb7c72.ent.gz	444 KB	Display	PDB format
PDBx/mmJSON format	7c72.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7c72_validation.pdf.gz	484.2 KB	Display	wwPDB validaton report
Full document	7c72_full_validation.pdf.gz	527.1 KB	Display
Data in XML	7c72_validation.xml.gz	50.1 KB	Display
Data in CIF	7c72_validation.cif.gz	67.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c7/7c72 ftp://data.pdbj.org/pub/pdb/validation_reports/c7/7c72	HTTPS FTP

-
Related structure data

Related structure data	3azoS S: Starting model for refinement
Similar structure data	3azp-2 3azo-1 3azp-1 3sqc-3 2q4h-d 3azq-2 1j0b-7 3azq-1 3azo-2 2c9h-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#154 - Oct 2012 Citric Acid Cycle similarity (1) #21 - Sep 2001 Antibodies similarity (1)

-
Assembly

Deposited unit

A: Prolyl oligopeptidase

B: Prolyl oligopeptidase

hetero molecules

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

A: Prolyl oligopeptidase

hetero molecules

defined by author&software
Evidence: gel filtration
75.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

B: Prolyl oligopeptidase

defined by author&software
75.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	183.950, 183.950, 146.310
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	173
Space group name H-M	P6₃
Space group name Hall	P6c
Symmetry operation	#1: x,y,z #2: x-y,x,z+1/2 #3: y,-x+y,z+1/2 #4: -y,x-y,z #5: -x+y,-x,z #6: -x,-y,z+1/2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	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 5 through 26 or resid 28...	A	A	5 - 26	25 - 46
1	2	LEU	LEU	LEU	LEU	(chain 'A' and (resid 5 through 26 or resid 28...	A	A	28 - 56	48 - 76
1	3	GLY	GLY	ASP	ASP	(chain 'A' and (resid 5 through 26 or resid 28...	A	A	58 - 70	78 - 90
1	4	THR	THR	THR	THR	(chain 'A' and (resid 5 through 26 or resid 28...	A	A	73	93
1	5	VAL	VAL	ILE	ILE	(chain 'A' and (resid 5 through 26 or resid 28...	A	A	75 - 86	95 - 106
1	6	THR	THR	THR	THR	(chain 'A' and (resid 5 through 26 or resid 28...	A	A	88	108
1	7	GLY	GLY	PRO	PRO	(chain 'A' and (resid 5 through 26 or resid 28...	A	A	91 - 112	111 - 132
1	8	PRO	PRO	PRO	PRO	(chain 'A' and (resid 5 through 26 or resid 28...	A	A	114 - 119	134 - 139
1	9	PRO	PRO	PRO	PRO	(chain 'A' and (resid 5 through 26 or resid 28...	A	A	121 - 136	141 - 156
1	10	THR	THR	GLU	GLU	(chain 'A' and (resid 5 through 26 or resid 28...	A	A	139 - 146	159 - 166
1	11	ARG	ARG	VAL	VAL	(chain 'A' and (resid 5 through 26 or resid 28...	A	A	177 - 199	197 - 219
1	12	GLY	GLY	ASP	ASP	(chain 'A' and (resid 5 through 26 or resid 28...	A	A	201 - 241	221 - 261
1	13	THR	THR	PRO	PRO	(chain 'A' and (resid 5 through 26 or resid 28...	A	A	244 - 247	264 - 267
1	14	THR	THR	LEU	LEU	(chain 'A' and (resid 5 through 26 or resid 28...	A	A	249 - 254	269 - 274
1	15	GLU	GLU	GLU	GLU	(chain 'A' and (resid 5 through 26 or resid 28...	A	A	256 - 266	276 - 286
1	16	SER	SER	PRO	PRO	(chain 'A' and (resid 5 through 26 or resid 28...	A	A	268 - 291	288 - 311
1	17	ALA	ALA	THR	THR	(chain 'A' and (resid 5 through 26 or resid 28...	A	A	293 - 383	313 - 403
1	18	VAL	VAL	ARG	ARG	(chain 'A' and (resid 5 through 26 or resid 28...	A	A	386 - 390	406 - 410
1	19	GLU	GLU	LEU	LEU	(chain 'A' and (resid 5 through 26 or resid 28...	A	A	392 - 393	412 - 413
1	20	PRO	PRO	PRO	PRO	(chain 'A' and (resid 5 through 26 or resid 28...	A	A	397 - 413	417 - 433
1	21	GLY	GLY	PRO	PRO	(chain 'A' and (resid 5 through 26 or resid 28...	A	A	415 - 433	435 - 453
1	22	GLY	GLY	ARG	ARG	(chain 'A' and (resid 5 through 26 or resid 28...	A	A	435 - 490	455 - 510
1	23	GLN	GLN	LEU	LEU	(chain 'A' and (resid 5 through 26 or resid 28...	A	A	492 - 568	512 - 588
1	24	GLY	GLY	GLU	GLU	(chain 'A' and (resid 5 through 26 or resid 28...	A	A	570 - 579	590 - 599
1	25	ALA	ALA	SER	SER	(chain 'A' and (resid 5 through 26 or resid 28...	A	A	581 - 614	601 - 634
1	26	PHE	PHE	LEU	LEU	(chain 'A' and (resid 5 through 26 or resid 28...	A	A	617 - 621	637 - 641
1	27	LYS	LYS	PHE	PHE	(chain 'A' and (resid 5 through 26 or resid 28...	A	A	624 - 640	644 - 660
1	28	LYS	LYS	THR	THR	(chain 'A' and (resid 5 through 26 or resid 28...	A	A	642 - 660	662 - 680
1	29	GLY	GLY	ILE	ILE	(chain 'A' and (resid 5 through 26 or resid 28...	A	A	662 - 671	682 - 691
1	30	LEU	LEU	VAL	VAL	(chain 'A' and (resid 5 through 26 or resid 28...	A	A	673 - 675	693 - 695
2	1	ALA	ALA	LEU	LEU	(chain 'B' and (resid 5 through 26 or resid 28...	B	B	5 - 26	25 - 46
2	2	LEU	LEU	LEU	LEU	(chain 'B' and (resid 5 through 26 or resid 28...	B	B	28 - 56	48 - 76
2	3	GLY	GLY	ASP	ASP	(chain 'B' and (resid 5 through 26 or resid 28...	B	B	58 - 70	78 - 90
2	4	THR	THR	THR	THR	(chain 'B' and (resid 5 through 26 or resid 28...	B	B	73	93
2	5	VAL	VAL	ILE	ILE	(chain 'B' and (resid 5 through 26 or resid 28...	B	B	75 - 86	95 - 106
2	6	THR	THR	THR	THR	(chain 'B' and (resid 5 through 26 or resid 28...	B	B	88	108
2	7	GLY	GLY	PRO	PRO	(chain 'B' and (resid 5 through 26 or resid 28...	B	B	91 - 112	111 - 132
2	8	PRO	PRO	PRO	PRO	(chain 'B' and (resid 5 through 26 or resid 28...	B	B	114 - 119	134 - 139
2	9	PRO	PRO	PRO	PRO	(chain 'B' and (resid 5 through 26 or resid 28...	B	B	121 - 136	141 - 156
2	10	THR	THR	GLU	GLU	(chain 'B' and (resid 5 through 26 or resid 28...	B	B	139 - 146	159 - 166
2	11	ARG	ARG	VAL	VAL	(chain 'B' and (resid 5 through 26 or resid 28...	B	B	177 - 199	197 - 219
2	12	GLY	GLY	ASP	ASP	(chain 'B' and (resid 5 through 26 or resid 28...	B	B	201 - 241	221 - 261
2	13	THR	THR	PRO	PRO	(chain 'B' and (resid 5 through 26 or resid 28...	B	B	244 - 247	264 - 267
2	14	THR	THR	LEU	LEU	(chain 'B' and (resid 5 through 26 or resid 28...	B	B	249 - 254	269 - 274
2	15	GLU	GLU	GLU	GLU	(chain 'B' and (resid 5 through 26 or resid 28...	B	B	256 - 266	276 - 286
2	16	SER	SER	PRO	PRO	(chain 'B' and (resid 5 through 26 or resid 28...	B	B	268 - 291	288 - 311
2	17	ALA	ALA	THR	THR	(chain 'B' and (resid 5 through 26 or resid 28...	B	B	293 - 383	313 - 403
2	18	VAL	VAL	ARG	ARG	(chain 'B' and (resid 5 through 26 or resid 28...	B	B	386 - 390	406 - 410
2	19	GLU	GLU	LEU	LEU	(chain 'B' and (resid 5 through 26 or resid 28...	B	B	392 - 393	412 - 413
2	20	PRO	PRO	PRO	PRO	(chain 'B' and (resid 5 through 26 or resid 28...	B	B	397 - 413	417 - 433
2	21	GLY	GLY	PRO	PRO	(chain 'B' and (resid 5 through 26 or resid 28...	B	B	415 - 433	435 - 453
2	22	GLY	GLY	ARG	ARG	(chain 'B' and (resid 5 through 26 or resid 28...	B	B	435 - 490	455 - 510
2	23	GLN	GLN	LEU	LEU	(chain 'B' and (resid 5 through 26 or resid 28...	B	B	492 - 568	512 - 588
2	24	GLY	GLY	GLU	GLU	(chain 'B' and (resid 5 through 26 or resid 28...	B	B	570 - 579	590 - 599
2	25	ALA	ALA	SER	SER	(chain 'B' and (resid 5 through 26 or resid 28...	B	B	581 - 614	601 - 634
2	26	PHE	PHE	LEU	LEU	(chain 'B' and (resid 5 through 26 or resid 28...	B	B	617 - 621	637 - 641
2	27	LYS	LYS	PHE	PHE	(chain 'B' and (resid 5 through 26 or resid 28...	B	B	624 - 640	644 - 660
2	28	LYS	LYS	THR	THR	(chain 'B' and (resid 5 through 26 or resid 28...	B	B	642 - 660	662 - 680
2	29	GLY	GLY	ILE	ILE	(chain 'B' and (resid 5 through 26 or resid 28...	B	B	662 - 671	682 - 691
2	30	LEU	LEU	VAL	VAL	(chain 'B' and (resid 5 through 26 or resid 28...	B	B	673 - 675	693 - 695

-
Components

#1: Protein	Prolyl oligopeptidase Mass: 75498.156 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: CNE19725.1 / Plasmid: pet28a+ / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₆O₅
Has ligand of interest	N

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 4.87 Å³/Da / Density % sol: 74.73 % Description: diamond shaped crystals with a hexagonal symmetry
Crystal grow	Temperature: 287.15 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1 M BIS-TRIS propane pH 7, 2.4 M DL-Malic acid pH 7.0 20 % (v/v) glycerol

-
Data collection

Diffraction	Mean temperature: 120 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
Detector	Type: DECTRIS PILATUS3 X CdTe 1M / Detector: PIXEL / Date: Dec 12, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97853 Å / Relative weight: 1
Reflection	Resolution: 3→46.4897392546 Å / Num. obs: 56249 / % possible obs: 99.9 % / Redundancy: 19.5 % / B_iso Wilson estimate: 111.913128818 Å² / CC_1/2: 0.996 / CC star: 0.999 / R_merge(I) obs: 0.2407 / R_pim(I) all: 0.0564 / R_rim(I) all: 0.2473 / Net I/σ(I): 7.97
Reflection shell	Resolution: 3→3.107 Å / Redundancy: 19.5 % / R_merge(I) obs: 3.358 / Mean I/σ(I) obs: 0.86 / Num. unique obs: 5581 / CC_1/2: 0.297 / CC star: 0.676 / R_pim(I) all: 0.7807 / R_rim(I) all: 3.448 / % possible all: 100

-
Processing

Software

Name	Version	Classification
PHENIX	1.12_2829	refinement
XDS		data reduction
XSCALE		data scaling
BALBES		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3AZO

3azo

Resolution: 3.00004456732→46.4897392546 Å / SU ML: 0.436494325758 / Cross valid method: FREE R-VALUE / σ(F): 1.35974463903 / Phase error: 24.7533958124

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.218114150504	2004	3.56361696452 %	0.05
R_work	0.17714709451	-	-	-
obs	0.178582720641	56235	99.9306962363 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 134.932464909 Å²

Refinement step

Cycle: LAST / Resolution: 3.00004456732→46.4897392546 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10055	0	21	0	10076

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.00792193339951	10367
X-RAY DIFFRACTION	f_angle_d	1.22176225122	14180
X-RAY DIFFRACTION	f_chiral_restr	0.0644565888372	1508
X-RAY DIFFRACTION	f_plane_restr	0.00848852292959	1889
X-RAY DIFFRACTION	f_dihedral_angle_d	10.2415411243	6057

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 (%)
3.00004456732-3.0751	0.356182828844	136	0.340078730319	3831	X-RAY DIFFRACTION	100
3.0751-3.1582	0.378865826398	148	0.312169508644	3885	X-RAY DIFFRACTION	100
3.1582-3.2511	0.323637296381	140	0.291205039903	3850	X-RAY DIFFRACTION	100
3.2511-3.356	0.279386459242	144	0.249519115608	3886	X-RAY DIFFRACTION	100
3.356-3.4759	0.259871556981	144	0.229102650749	3834	X-RAY DIFFRACTION	99.9497487437
3.4759-3.615	0.259110492632	136	0.212819015219	3887	X-RAY DIFFRACTION	99.9751491054
3.615-3.7795	0.224404312605	141	0.204468749194	3836	X-RAY DIFFRACTION	99.9246231156
3.7795-3.9786	0.234940307588	144	0.181380513354	3886	X-RAY DIFFRACTION	99.97519226
3.9786-4.2278	0.202279974339	140	0.174714432997	3858	X-RAY DIFFRACTION	99.9250187453
4.2278-4.5539	0.199890473003	149	0.15471066669	3885	X-RAY DIFFRACTION	99.9504459861
4.5539-5.0117	0.191571679062	144	0.149463910943	3871	X-RAY DIFFRACTION	99.9502116007
5.0117-5.7358	0.1928599812	147	0.157249246162	3892	X-RAY DIFFRACTION	100
5.7358-7.2221	0.253118492862	147	0.192333539685	3876	X-RAY DIFFRACTION	99.8263027295
7.2221-46.4897392546	0.180848655045	144	0.142401990261	3954	X-RAY DIFFRACTION	99.5626822157

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	3.88029834902	3.07369827128	0.484887524931	7.02863465769	3.03086381712	1.51244054423	-0.270582392844	-0.354551334214	0.999947354407	0.0756862132009	-0.147472180763	1.11818276555	-0.577561860099	-0.276875556943	0.623107054343	1.03265719257	0.140638753713	-0.300461434023	0.848158156203	0.0960367841224	1.29842434872	-25.0535966124	-65.1576257089	1.18721676066
2	8.95935121623	-1.95867897959	0.847838219469	7.94861336773	-0.954073922905	8.57075943053	0.197299611303	0.101364761453	0.623754405245	-0.169657510165	-0.251544821748	1.28558916104	0.286308952009	-1.34436012545	0.158342137083	0.752769521049	-0.0157162722111	-0.0822309320051	0.632551633029	-0.134255807888	0.821021974486	-32.3199970353	-84.0893404557	-1.29707268048
3	3.47858243598	-3.26840730967	2.30558142049	4.37605561216	-3.65670261292	3.50176630672	0.29704529628	-2.12571715768	1.60327560663	0.155566250222	0.0268456738756	-0.264201676878	0.89455650373	-2.46205740631	-0.174681792104	1.0970939024	-0.0138552596976	0.148833112682	1.03922582186	-0.11894458992	1.20804995641	-36.1756786028	-92.3853117154	4.29750281532
4	4.85156318577	-4.14510519572	2.82743108041	7.47310364478	-7.50921572255	8.0822391218	0.245361547049	0.118775850969	-0.387792313913	0.304107627263	-0.110789599506	0.298325230651	1.40548358192	-0.610045218144	-0.14299539986	0.781766442874	-0.0896728853957	0.0107481311856	0.668156004815	-0.0936486478427	0.931617526757	-23.6854585397	-96.5332304428	0.35380312087
5	7.45928542426	-2.19271673391	2.54011969623	7.4576172202	-1.88848624642	3.26054331208	-0.308123478214	-1.37099086106	0.45282594619	1.05942363785	-0.128487970458	0.65303208383	0.611366929458	-0.527197191	0.482641749956	0.816580717364	-0.0303057386426	-0.0596488953021	0.490615744569	-0.0248285133925	0.7703621907	-20.6308499838	-98.2331730312	6.40363223101
6	8.24514348672	1.04127073337	-1.35200349347	4.70046021239	0.581288415784	2.40596301036	-0.0674442754044	-0.163589430661	-0.534924799993	0.177080378202	-0.32709605542	0.160092510956	0.412201785484	-0.359987644142	0.403052995572	0.730905628845	0.0228440119304	-0.0714221222103	0.51432678409	-0.0487234476263	0.655713862603	-15.6700870863	-99.0421348379	-7.22606181615
7	4.706676965	-3.91593729314	4.30675861126	8.69795682045	-4.42074328894	5.34711874278	-0.311334650654	1.33259811795	-0.116022868683	-0.782958568074	-0.174745225923	-0.347621231799	0.647539897451	1.28095732248	0.392825433912	0.843067799819	0.0668036056823	0.0367662162997	0.721648240475	0.0944037001721	0.855448493528	-8.70078790567	-90.5890408323	-17.3712766649
8	4.71264853354	5.43260763709	4.54739174402	6.74968604223	6.05367206366	5.93674544644	0.269244569363	0.628796446099	-0.204918788696	0.273050165687	0.0465157988239	-1.45956479807	0.452598857612	-0.357269815689	-0.396733032279	1.11964821516	0.205273114153	-0.10729739828	0.998221444864	-0.0178308344496	0.790901751993	-5.83394357086	-89.8380604825	-20.2350162363
9	4.81655673544	-0.635310621035	-2.08680522339	3.61213254434	-1.24515062322	9.31999994446	-0.279334592746	0.177109194327	0.508997378471	0.484745899412	-0.0828091263956	-0.939034908947	0.139489652339	1.47586427305	0.261166932547	0.840047222492	0.133368496595	-0.163298840717	0.868755946875	0.0355607712093	1.17630691474	-7.89705374346	-81.9103279488	-15.016581057
10	8.10771943603	2.96944599577	-1.74495100119	6.49588710787	3.44090258021	7.56324120699	-0.177793057437	1.19707171062	1.32151319672	-0.690196634066	-0.144714481765	0.378994326138	-0.893671064178	0.481279334643	0.579821041149	0.850710030912	0.125797648134	-0.290404243595	1.01706711978	0.264509021939	1.11110131973	-14.6492232164	-77.0058171571	-22.9784592814
11	7.4739613841	-2.92783196601	-5.15020155975	3.45709593365	1.44527838574	3.59140004573	0.128119163297	0.331810347671	0.679761213699	-0.51886144802	-0.286588917052	0.327490649081	-0.115608510878	-0.742436792574	0.142150895031	0.763765044928	0.0838130869038	-0.305913465057	0.799771959612	0.14858223057	0.95455573224	-23.5975401073	-70.2252837336	-15.3300628641
12	7.87150773467	-2.03078987876	1.45994926984	8.26931661419	0.129769150167	7.49503663604	0.595786527867	0.635923287008	0.517966391217	-0.452929289045	-0.405613766374	1.01088069458	-0.558084789633	-0.0584291891366	0.188925083621	1.15006286637	0.0111385489211	-0.416326022617	0.97684332326	0.089822951353	1.4747336471	-17.5625658511	-55.5769285701	-4.20637000237
13	9.32142078716	-8.58803041976	4.30701570759	8.09957433415	-3.19496375851	9.36783261112	-0.530498305001	3.02428268824	2.59830727049	-1.18539919789	-3.11866100018	-2.23745105153	-0.161705720693	2.51546417379	2.5521961661	1.48962377193	-0.074677393413	0.0534171489368	1.43311558088	0.535678563909	1.79756229389	9.3707935576	-65.8483948639	-4.22591732182
14	2.01452638451	-2.89958897629	-2.29924757301	4.71962689316	4.80122785693	5.94006990332	0.0766187819454	0.0331591558985	1.16882925848	-1.47403570491	0.110234989059	-0.124820190941	-0.893271603193	-0.441336826927	-0.161736632579	0.9883772671	-0.0231662556311	-0.355617532805	0.849577515246	0.0446852704633	1.53456731037	-6.3355024919	-54.0966806242	2.05882747664
15	1.99105771785	-1.47552777885	-2.76971152394	5.88051386364	1.5374891437	3.31935444843	-0.255957055231	0.471084604768	0.640932950198	-0.43678816978	0.064112178961	0.103832489913	-0.371000052453	0.128652792484	0.170659671943	0.725827977345	-0.0299353965638	-0.420144555761	0.613284204946	-0.00293725059297	1.13775213563	-2.4166579465	-66.0723080681	4.94471274153
16	9.23870423042	1.56148517444	-6.90756757557	6.39589478323	2.47559904079	8.40862683022	-0.4971348349	-0.852360327596	-0.698245766043	0.131684118375	-0.0840396814987	-0.618227398408	1.34469311915	0.114903153649	0.517542023057	0.951278094643	0.177821513006	-0.304101324493	0.743765368899	0.0733585575943	0.765376210591	-2.24026386736	-86.5396291133	10.6826309223
17	5.41890257674	-5.6847629453	-1.12410710078	5.95896295515	1.03242473704	5.057870152	-1.04682152002	-1.45859602048	0.761304124445	1.24492671196	0.519573226733	-1.65441274537	0.196572615556	1.78881211445	0.0919980193009	1.26136940275	0.254551670244	-0.405151382914	1.0926431028	-0.0690051669773	1.23077816195	7.39774646132	-82.5809199179	15.5759548217
18	4.98532213441	1.99253808745	0.935054638962	5.93062803241	1.63328945828	7.12390033432	0.025058198657	-0.362310461337	-0.00988570335913	0.53796656227	-0.0947012657672	0.37369177752	0.291787590572	-0.21122392258	-0.0149770468703	0.926325399551	0.122415691265	-0.24660438483	0.652272485614	-0.139379337112	1.00371812857	-7.97761153752	-72.2448415136	21.302719218
19	3.50183418994	-3.77737100638	-1.44499203755	5.5144657163	-0.558597923495	3.81567110348	-0.176352345501	-1.30823286976	2.1717168557	-0.889446979925	-0.569484427576	0.967512476995	-1.14829778317	-0.578289633446	0.481070322759	1.11435831333	0.180543454592	-0.305796023868	0.876415885964	-0.27846962727	1.70716527056	-15.7483953289	-58.1923392133	15.3551161881
20	2.53441098622	-2.45124222663	-0.875450547977	9.89177289763	-2.10997261437	1.46851098828	1.99537122227	0.682945586735	-0.897968352924	-0.972181717801	-0.786487284924	2.56770686502	0.37530117512	-1.18932376519	-1.32841152996	1.08288212408	0.0887780097127	-0.44388315248	1.33329516229	-0.395435728336	1.07438615078	-12.1990315031	-58.3431561911	26.4197850395
21	2.56373678205	1.42004547293	-0.55733981425	4.04337685362	-3.18610589882	3.39341817431	-0.961998056301	-0.675460488209	0.0491794537069	1.31279178574	0.142727454687	-1.47162190529	-0.902099423602	-1.013808513	1.28651376547	1.33125458497	0.360065595384	-0.358335680976	1.12234923726	-0.0338783463486	1.14873687024	-37.3397906011	-54.767484731	-14.6689258361
22	8.36405200871	-1.80839774268	-3.36752960787	7.43784033497	0.183575609403	8.05572297036	-0.223964381701	0.322639982803	1.84953871289	0.0604108373613	-0.787694065069	-1.15061145315	0.729896782319	0.842540347799	0.532202148885	0.982497693597	0.0731742750022	-0.263273757204	1.73313975845	0.72874609312	1.85009257387	-17.9236123117	-56.0586522467	-34.9391769592
23	2.06054457834	-3.50328639684	-0.943740438025	5.92585283468	0.826675204686	7.14700218065	-0.420205029526	-0.20710064449	0.309865241982	-0.154219948529	0.180105553997	-0.56541591226	0.0383108356185	1.11857987667	-0.0369123853118	0.909165517855	-0.156496905051	-0.190073007779	1.66906327718	0.576829238884	1.87993452911	-14.5948335546	-51.4556450107	-37.5734937364
24	5.07494654455	0.170108881322	2.60654253145	0.54742243415	1.22717183969	5.43436964996	0.257458137293	1.09210234941	0.727198184107	-1.72200602222	-0.0581060290793	0.168052883885	0.222894146729	0.464618783023	-0.189676358894	1.35295682109	-0.0390961894446	0.0977972755431	2.02944544841	0.832137905828	2.18754531217	-7.3006115333	-49.3685492604	-42.1517590932
25	6.79503758225	-7.21494752883	2.39880486284	7.71615622896	-2.57031857675	0.855947901627	0.296213196838	0.223566103327	0.633535074649	-0.857282439377	-1.08796584974	-3.24642941486	-0.436887719753	1.72936284283	1.66003929364	1.07553580703	0.0493933312982	0.267693953705	2.25546307932	1.12649695901	2.80708829998	-10.8985883389	-43.6165146982	-48.9270136699
26	5.62246191872	-1.05567310688	6.93222907224	2.37759420876	-2.19030381046	8.94777855223	0.906740388139	-1.4490717906	-2.14465514925	-1.14566707608	-1.11992761933	-1.98005771023	0.348078015804	0.656353308145	0.569021509914	1.23917891808	0.189535770356	0.267717178345	2.16750211227	1.28351884926	2.10713297177	-16.7380581227	-41.9458818591	-53.9383691024
27	4.92346743995	-5.07966330502	6.30669427042	5.34951013393	-6.31392679572	8.23353638938	-1.24101330638	-1.81578712383	0.734034842668	-0.134501856534	0.852529486408	-2.04669520647	-0.409204907387	0.221512753866	1.78846358139	1.25668401606	-0.0204654866802	0.373744478233	1.90081118452	0.449471536711	2.39409356334	-6.38208316915	-40.3963375649	-55.6073368889
28	9.38269373816	-2.77333538442	0.38105846669	3.43277146478	1.88216427629	4.27691492213	-0.124956879247	0.583086190783	0.614938344705	-1.80414342257	-0.307322933476	-0.318431573931	1.35573258716	1.72109296679	0.603251194033	1.71436082852	0.609276072444	-0.0191986475953	2.12889245469	0.651184666657	1.5908110957	-27.8890217962	-45.7536634815	-58.3014440605
29	2.68225211393	1.44452509608	-0.395491847846	2.7598513007	0.238439568425	0.171462211795	0.159829061939	-0.0154341425954	-0.6493209942	-0.629567735612	-1.19176996033	-0.656383360157	-0.965778915474	2.03840006841	0.52802066595	1.83448443966	0.414846625629	-0.105267349845	2.20047460507	0.746619863742	1.12692850317	-28.3529257095	-48.5232548376	-63.4304968483
30	2.18235592541	1.26249553477	-1.59295382996	3.2314561179	-2.41133952054	2.49173744765	0.282636026168	1.37037603254	-0.0706630966367	-1.82801488657	-0.710181271721	0.142566704816	0.526894469809	0.212426154087	0.34632164098	1.76142118986	0.455267682751	-0.391154281172	1.79599280142	0.103173981875	1.16761460481	-35.2792734472	-57.8752514398	-57.4253834971
31	1.84959540602	0.711615785357	-0.633309855336	5.0055802481	0.264973626797	0.259692090019	-0.0727244746909	-0.766946682764	-0.185761810266	-0.853820307882	0.76725738471	1.57417110036	-0.409420955247	-1.62652683534	0.380400978842	1.52443424772	1.61094294536	-0.911147421385	2.36942869907	0.403163656254	0.676714301914	-27.4688304285	-59.3753423566	-50.205924325
32	2.41069010176	2.09298637859	0.209891487211	6.04688456068	3.2891652676	9.85037023159	0.045200344017	0.429389496643	-0.148047944624	-1.13605422681	-0.425688853265	-0.0606345411073	1.52417370495	0.400673229699	0.239642840158	1.35259808405	0.39772664815	-0.33400820511	1.12545369719	0.0784888921493	1.26310679391	-31.8698061942	-66.9346559731	-44.6213629088
33	4.50789373622	-1.62538377362	-2.05731142816	5.69150441446	-4.1911248478	6.35510442254	0.0542314940299	-0.902439949991	-1.09144940922	-0.577101712183	-1.06761740616	-0.387815830382	-0.0947445516577	1.16071116933	0.790448165524	0.916359917295	0.210889602571	-0.385243694265	1.07917356552	0.210406451376	1.457065127	-27.6656433734	-66.0644530445	-29.0811293452
34	8.00995897348	4.33691857934	1.87231937412	8.16655423553	-1.78118115693	9.69498804579	-0.553422329573	-0.485165489036	-0.793803019923	-0.494356577376	0.227189778311	0.23899006744	0.000198337810099	-1.37831573245	0.208603366912	1.0311586402	0.174632718369	-0.26710349038	1.08504950554	-0.10322319577	1.43073336171	-51.863804436	-55.4274444384	-32.7011888781
35	2.78087105008	-0.954726855403	0.779699869624	4.79383298788	-1.72159764525	4.79426506735	-0.447727438062	0.0722748517433	0.312014489936	-0.117855677502	0.293725279163	-0.0599937604293	-0.27782076743	-0.141745014475	0.225454527793	0.875770414401	0.126677014365	-0.454444987423	0.928927835418	0.00486654411685	1.22109282236	-46.1378727371	-44.9711854562	-30.5917335917
36	4.18940449989	-0.947682601469	2.15879238757	0.757706310235	-2.36538244862	7.15824848204	-0.186719465788	-0.419440408082	0.762589214383	1.1720086429	-0.0468897849885	-0.843464999145	-1.96233534956	-0.602434123164	0.26152858497	1.55251734899	0.165759257937	-0.717450860779	0.940583926245	-0.00335625043197	1.53042027667	-46.5768477908	-28.9942193365	-33.5931784701
37	6.5199938272	4.37356726048	-5.61861199719	3.80427829982	-4.35321172286	5.22384272213	0.519053480741	0.169409302557	2.29338784981	-1.59019630486	1.42305216318	0.42863611524	-1.6857062033	2.44416116907	-1.45922224571	2.03725755534	-0.540599060148	-0.753896623739	2.06476967686	0.349311217501	2.49135795365	-35.5405346645	-27.7908346419	-28.3524275186
38	6.04152077925	-1.6983057344	3.65839559083	5.5657682999	-5.96097167487	6.98000854216	-1.03870265249	-0.368649976405	2.68669057739	3.41205890959	0.358058156333	-0.812521378066	-2.64415157953	-0.123145028571	1.44716974665	2.24710450538	0.0334902810378	-0.621344336366	0.879477365544	-0.0937830501669	2.21909388443	-45.3760416329	-27.0675381697	-19.1538552742
39	7.02683198594	1.20755122716	-3.13140973792	6.42372609978	-3.24082830481	8.54084069561	-1.25001432646	-0.491442900655	1.68135619917	1.18807750781	0.229617144629	-0.720073398583	-1.78574875751	-0.00553924830448	0.520484091437	2.03789840249	0.121047374721	-0.973822508168	1.45147220735	-0.0879510056142	1.81353103672	-36.6245478794	-41.7059073828	-16.4613747758
40	1.97136747213	1.23175517302	-2.80479208525	0.819343337962	-2.22293141974	7.83164188697	2.69240140089	1.894598931	-0.981465565423	-2.53637221862	-2.69492477883	1.85005143961	2.91120062109	4.03983351003	-0.929370698617	2.15922949443	0.245891732389	-0.464827379394	0.996358275186	-0.308086679508	1.17655274488	-42.3731475293	-35.2680431205	-8.43399291229

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 4:51)
2	X-RAY DIFFRACTION	2	(chain A and resid 52:107)
3	X-RAY DIFFRACTION	3	(chain A and resid 108:124)
4	X-RAY DIFFRACTION	4	(chain A and resid 125:153)
5	X-RAY DIFFRACTION	5	(chain A and resid 169:184)
6	X-RAY DIFFRACTION	6	(chain A and resid 185:251)
7	X-RAY DIFFRACTION	7	(chain A and resid 252:277)
8	X-RAY DIFFRACTION	8	(chain A and resid 278:289)
9	X-RAY DIFFRACTION	9	(chain A and resid 290:310)
10	X-RAY DIFFRACTION	10	(chain A and resid 311:346)
11	X-RAY DIFFRACTION	11	(chain A and resid 347:391)
12	X-RAY DIFFRACTION	12	(chain A and resid 392:408)
13	X-RAY DIFFRACTION	13	(chain A and resid 409:416)
14	X-RAY DIFFRACTION	14	(chain A and resid 417:447)
15	X-RAY DIFFRACTION	15	(chain A and resid 448:551)
16	X-RAY DIFFRACTION	16	(chain A and resid 552:576)
17	X-RAY DIFFRACTION	17	(chain A and resid 577:587)
18	X-RAY DIFFRACTION	18	(chain A and resid 588:640)
19	X-RAY DIFFRACTION	19	(chain A and resid 641:668)
20	X-RAY DIFFRACTION	20	(chain A and resid 669:675)
21	X-RAY DIFFRACTION	21	(chain B and resid 4:27)
22	X-RAY DIFFRACTION	22	(chain B and resid 28:48)
23	X-RAY DIFFRACTION	23	(chain B and resid 49:87)
24	X-RAY DIFFRACTION	24	(chain B and resid 88:112)
25	X-RAY DIFFRACTION	25	(chain B and resid 113:140)
26	X-RAY DIFFRACTION	26	(chain B and resid 141:184)
27	X-RAY DIFFRACTION	27	(chain B and resid 185:198)
28	X-RAY DIFFRACTION	28	(chain B and resid 199:239)
29	X-RAY DIFFRACTION	29	(chain B and resid 240:262)
30	X-RAY DIFFRACTION	30	(chain B and resid 263:308)
31	X-RAY DIFFRACTION	31	(chain B and resid 309:315)
32	X-RAY DIFFRACTION	32	(chain B and resid 316:371)
33	X-RAY DIFFRACTION	33	(chain B and resid 372:403)
34	X-RAY DIFFRACTION	34	(chain B and resid 404:425)
35	X-RAY DIFFRACTION	35	(chain B and resid 426:571)
36	X-RAY DIFFRACTION	36	(chain B and resid 572:605)
37	X-RAY DIFFRACTION	37	(chain B and resid 606:615)
38	X-RAY DIFFRACTION	38	(chain B and resid 616:632)
39	X-RAY DIFFRACTION	39	(chain B and resid 633:667)
40	X-RAY DIFFRACTION	40	(chain B and resid 668:675)

+
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