PDB-8oj9: Arabidopsis thaliana Phosphoenolpyruvate carboxylase PPC1 free form

ID or keywords:

Entry

Database: PDB / ID: 8oj9

Title

Arabidopsis thaliana Phosphoenolpyruvate carboxylase PPC1 free form

Components

Phosphoenolpyruvate carboxylase 1

Keywords

PLANT PROTEIN / Phosphoenolpyruvate carboxylase / Citric acid cycle / TCA cycle / photosynthesis

Function / homology

Function and homology information

phosphoenolpyruvate carboxylase / phosphoenolpyruvate carboxylase activity / leaf development / carbon fixation / apoplast / cellular response to phosphate starvation / photosynthesis / tricarboxylic acid cycle / chloroplast / protein tetramerization ...
Similarity search - Function

Biological species

Arabidopsis thaliana (thale cress)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.24638283547 Å

Authors

Haesaerts, S. / Loris, R. / Larsen, P.B.

Funding support

United States,

Belgium, 2items

Citation

Journal: To Be Published
Title: Amino acid changes that deregulate PHOSPHOENOLPYRUVATE CARBOXYLASE in plants
Authors: Meyer, T.J. / Sheng, J. / Haesaerts, S. / Frausto, K. / O'Leary, S. / Loris, R. / Larsen, P.B.

History

Deposition	Mar 24, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 12, 2023	Provider: repository / Type: Initial release
Revision 1.1	Jun 19, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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 viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8oj9.cif.gz	1.3 MB	Display	PDBx/mmCIF format
PDB format	pdb8oj9.ent.gz	979.4 KB	Display	PDB format
PDBx/mmJSON format	8oj9.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8oj9_validation.pdf.gz	455.1 KB	Display	wwPDB validaton report
Full document	8oj9_full_validation.pdf.gz	487.1 KB	Display
Data in XML	8oj9_validation.xml.gz	91.7 KB	Display
Data in CIF	8oj9_validation.cif.gz	123.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oj/8oj9 ftp://data.pdbj.org/pub/pdb/validation_reports/oj/8oj9	HTTPS FTP

-
Related structure data

Related structure data	8cj5C 8cj8C 8ojeC 8ojfC 8ojqC 8ojyC 8ojzC 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
Related items in Molecule of the Month	#154 - Oct 2012 Citric Acid Cycle similarity (1) #50 - Feb 2004 Glycolytic Enzymes similarity (1)

Deposited unit

A: Phosphoenolpyruvate carboxylase 1

B: Phosphoenolpyruvate carboxylase 1

C: Phosphoenolpyruvate carboxylase 1

334 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Phosphoenolpyruvate carboxylase 1

B: Phosphoenolpyruvate carboxylase 1

A: Phosphoenolpyruvate carboxylase 1

B: Phosphoenolpyruvate carboxylase 1

defined by author
Evidence: gel filtration, Generated by symmetry (crystallographic 2-fold) from chains A and B
446 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Phosphoenolpyruvate carboxylase 1

defined by author
Evidence: gel filtration, Generated by symmetry from chain C
446 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	244.350, 244.350, 397.070
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	98
Space group name H-M	I4₁22
Space group name Hall	I4bw2bw
Symmetry operation	#1: x,y,z #2: -y+1/2,x,z+3/4 #3: y+1/2,-x,z+3/4 #4: x+1/2,-y,-z+3/4 #5: -x+1/2,y,-z+3/4 #6: -x,-y,z #7: y,x,-z #8: -y,-x,-z #9: x+1/2,y+1/2,z+1/2 #10: -y+1,x+1/2,z+5/4 #11: y+1,-x+1/2,z+5/4 #12: x+1,-y+1/2,-z+5/4 #13: -x+1,y+1/2,-z+5/4 #14: -x+1/2,-y+1/2,z+1/2 #15: y+1/2,x+1/2,-z+1/2 #16: -y+1/2,-x+1/2,-z+1/2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1
3	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	LEU	LEU	GLU	GLU	(chain 'A' and (resid 6 through 320 or resid 322...	A	A	6 - 320	13 - 327
1	2	LEU	LEU	SER	SER	(chain 'A' and (resid 6 through 320 or resid 322...	A	A	322 - 346	329 - 353
1	3	LYS	LYS	ILE	ILE	(chain 'A' and (resid 6 through 320 or resid 322...	A	A	359 - 595	366 - 602
1	4	SER	SER	HIS	HIS	(chain 'A' and (resid 6 through 320 or resid 322...	A	A	598 - 635	605 - 642
1	5	GLY	GLY	TRP	TRP	(chain 'A' and (resid 6 through 320 or resid 322...	A	A	638 - 709	645 - 716
1	6	ALA	ALA	LYS	LYS	(chain 'A' and (resid 6 through 320 or resid 322...	A	A	711 - 923	718 - 930
1	7	PRO	PRO	GLY	GLY	(chain 'A' and (resid 6 through 320 or resid 322...	A	A	931 - 967	938 - 974
2	8	LEU	LEU	GLU	GLU	(chain 'B' and (resid 6 through 320 or resid 322...	B	B	6 - 320	13 - 327
2	9	LEU	LEU	SER	SER	(chain 'B' and (resid 6 through 320 or resid 322...	B	B	322 - 346	329 - 353
2	10	LYS	LYS	ILE	ILE	(chain 'B' and (resid 6 through 320 or resid 322...	B	B	359 - 595	366 - 602
2	11	SER	SER	HIS	HIS	(chain 'B' and (resid 6 through 320 or resid 322...	B	B	598 - 635	605 - 642
2	12	GLY	GLY	TRP	TRP	(chain 'B' and (resid 6 through 320 or resid 322...	B	B	638 - 709	645 - 716
2	13	ALA	ALA	LYS	LYS	(chain 'B' and (resid 6 through 320 or resid 322...	B	B	711 - 923	718 - 930
2	14	PRO	PRO	GLY	GLY	(chain 'B' and (resid 6 through 320 or resid 322...	B	B	931 - 967	938 - 974
3	15	LEU	LEU	GLU	GLU	(chain 'C' and (resid 6 through 320 or resid 322...	C	C	6 - 320	13 - 327
3	16	LEU	LEU	SER	SER	(chain 'C' and (resid 6 through 320 or resid 322...	C	C	322 - 346	329 - 353
3	17	LYS	LYS	ILE	ILE	(chain 'C' and (resid 6 through 320 or resid 322...	C	C	359 - 595	366 - 602
3	18	SER	SER	HIS	HIS	(chain 'C' and (resid 6 through 320 or resid 322...	C	C	598 - 635	605 - 642
3	19	GLY	GLY	TRP	TRP	(chain 'C' and (resid 6 through 320 or resid 322...	C	C	638 - 709	645 - 716
3	20	ALA	ALA	LYS	LYS	(chain 'C' and (resid 6 through 320 or resid 322...	C	C	711 - 923	718 - 930
3	21	PRO	PRO	GLY	GLY	(chain 'C' and (resid 6 through 320 or resid 322...	C	C	931 - 967	938 - 974

#1: Protein	Phosphoenolpyruvate carboxylase 1 / AtPPC1 / PEPC 1 / PEPCase 1 / 107-kDa PEPC polypeptide Mass: 111398.164 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PPC1, p107, At1g53310, F12M16.21 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q9MAH0, phosphoenolpyruvate carboxylase

#1: Protein

Phosphoenolpyruvate carboxylase 1 / AtPPC1 / PEPC 1 / PEPCase 1 / 107-kDa PEPC polypeptide

Mass: 111398.164 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Arabidopsis thaliana (thale cress) / Gene: PPC1, p107, At1g53310, F12M16.21 / Production host:

Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9MAH0, phosphoenolpyruvate carboxylase

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 4.43 Å³/Da / Density % sol: 72.26 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion / pH: 6.5 Details: 0.05 M Cesium chloride, 0.1 M MES monohydrate pH 6.5, 30% v/v Jeffamine M-600

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.981 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 7, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.981 Å / Relative weight: 1
Reflection	Resolution: 3.245→48.505 Å / Num. obs: 94348 / % possible obs: 99.7 % / Redundancy: 22.4 % / B_iso Wilson estimate: 112.658543113 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.303 / Net I/σ(I): 9.21
Reflection shell	Resolution: 3.25→3.44 Å / Redundancy: 22.47 % / R_merge(I) obs: 2.84 / Num. unique obs: 14811 / CC_1/2: 0.73 / % possible all: 98.6

-
Processing

Software

Name	Version	Classification
PHENIX	1.11.1_2575	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.24638283547→48.5040153818 Å / SU ML: 0.58887701714 / Cross valid method: FREE R-VALUE / σ(F): 1.32666189489 / Phase error: 37.0214826818
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.264048215651	4677	5.00155061971 %
R_work	0.227732156196	88834	-
obs	0.229578194941	93511	99.1569995546 %

Solvent computation

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

Displacement parameters

B_iso mean: 124.14468808 Å²

Refinement step

Cycle: LAST / Resolution: 3.24638283547→48.5040153818 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	22716	0	0	0	22716

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.00566550496125	23280
X-RAY DIFFRACTION	f_angle_d	0.781896662177	31523
X-RAY DIFFRACTION	f_chiral_restr	0.0448642229817	3488
X-RAY DIFFRACTION	f_plane_restr	0.00502266455223	4103
X-RAY DIFFRACTION	f_dihedral_angle_d	13.6824732265	14228

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 (%)
3.2464-3.2833	0.579568778944	145	0.598578235073	2740	X-RAY DIFFRACTION	93.4261658031
3.2833-3.3219	0.461369736436	153	0.476659886743	2937	X-RAY DIFFRACTION	99.4528484068
3.3219-3.3624	0.464763793203	155	0.441232346437	2922	X-RAY DIFFRACTION	99.4184168013
3.3624-3.4049	0.447130908559	155	0.408668335549	2946	X-RAY DIFFRACTION	99.4866859159
3.4049-3.4497	0.417252316156	155	0.393450433076	2954	X-RAY DIFFRACTION	99.5517130964
3.4497-3.497	0.406661423303	154	0.367986182649	2920	X-RAY DIFFRACTION	99.2253066495
3.497-3.5469	0.381401103719	155	0.361789622181	2923	X-RAY DIFFRACTION	99.4186046512
3.5469-3.5998	0.378754198262	157	0.352846944156	2963	X-RAY DIFFRACTION	99.5215311005
3.5998-3.6561	0.395761109818	156	0.343981653018	2957	X-RAY DIFFRACTION	99.871671479
3.6561-3.716	0.372281422243	156	0.336280632778	2966	X-RAY DIFFRACTION	99.7762863535
3.716-3.78	0.309697107509	153	0.28280483241	2915	X-RAY DIFFRACTION	99.4489465154
3.78-3.8488	0.303688407083	156	0.268094700907	2956	X-RAY DIFFRACTION	99.6796925048
3.8488-3.9227	0.270095250177	155	0.244945549766	2948	X-RAY DIFFRACTION	99.6467565832
3.9227-4.0028	0.228958204062	154	0.22454020136	2955	X-RAY DIFFRACTION	99.8394348105
4.0028-4.0898	0.235688847998	157	0.213511125183	2971	X-RAY DIFFRACTION	99.9041839668
4.0898-4.1849	0.249456261133	156	0.209329226069	2967	X-RAY DIFFRACTION	99.7763578275
4.1849-4.2895	0.246873793808	156	0.211962724715	2946	X-RAY DIFFRACTION	99.6786632391
4.2895-4.4054	0.237187366558	157	0.199799048554	2973	X-RAY DIFFRACTION	99.6180776575
4.4054-4.5349	0.223044046281	157	0.197831019638	3000	X-RAY DIFFRACTION	99.8734577665
4.5349-4.6812	0.260527040008	154	0.185215249555	2946	X-RAY DIFFRACTION	99.7425997426
4.6812-4.8483	0.216744995699	156	0.176436929727	2956	X-RAY DIFFRACTION	99.3614303959
4.8483-5.0422	0.242094586205	158	0.176605273761	2998	X-RAY DIFFRACTION	99.6212121212
5.0422-5.2715	0.189922305326	156	0.17894658445	2980	X-RAY DIFFRACTION	99.7455470738
5.2715-5.549	0.209732926344	158	0.188180262083	2988	X-RAY DIFFRACTION	99.4310998736
5.549-5.8961	0.258628592842	157	0.208008994898	2982	X-RAY DIFFRACTION	99.6824388695
5.8961-6.3505	0.280030833132	156	0.210434581502	3014	X-RAY DIFFRACTION	99.7168921044
6.3505-6.9878	0.267532718383	159	0.214283359956	3027	X-RAY DIFFRACTION	99.5003123048
6.9878-7.9951	0.219542399195	160	0.184352520745	3031	X-RAY DIFFRACTION	99.6564647096
7.9951-10.0582	0.199270561102	162	0.153528530956	3072	X-RAY DIFFRACTION	99.5996304281
10.0582-48.504	0.232446326098	159	0.206005406901	2981	X-RAY DIFFRACTION	92.5434718538

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	4.50278829345	-1.69044580814	-0.94573152979	1.90440527529	1.02759432364	2.39328497215	-0.245940046322	-0.672534821979	-0.15957424606	0.704955165979	0.195673549673	0.666502183288	0.0544750536863	-1.21445146656	0.119695462247	1.399411465	-0.0316248799758	0.0671634752212	1.30779621446	0.106215575212	0.983323207625	71.6988208104	96.9651196876	300.719709834
2	3.10618487638	-1.29947328891	-3.02392203612	-0.113540762324	0.680628729299	1.6035601328	1.18987124027	-0.823108999078	0.586856101953	0.0707664441108	-0.975288182796	-0.326013861899	-0.703712992411	-0.18910298161	-0.0961374109366	1.92367137294	0.251736959226	-0.0982318232317	0.791449229078	0.0256515504357	0.95337230015	85.1957196354	104.845871512	308.112012994
3	1.74035921102	-1.08631205237	0.54480483188	1.1802755057	-1.08504945883	2.87272815094	0.0220878919389	-0.357616575717	0.346484223279	0.286776944727	-0.319559389667	-0.456704987673	-1.24336994899	0.154660068669	0.235407782546	1.20446740525	0.0253062441428	-0.0389981834293	0.497426135244	-0.0637632495448	0.798662585909	108.946562023	95.1913722003	303.098456562
4	1.46859785134	-0.57711413553	-0.144202608282	3.57724753654	-1.93867670444	3.64496098769	-0.159141564092	0.0584390204522	0.0725310523006	0.398497298791	0.29744755545	-0.247653868111	-1.38277267246	-0.420229560585	-0.109288555015	0.945687288567	-0.00623709177119	0.170214908537	0.362033103604	-0.150679118122	0.813977595453	101.573175395	103.592211286	282.27208876
5	2.67101027634	0.220656301377	-1.0758608341	3.69212789194	2.96887634586	5.48796939239	0.187133291141	0.265733891529	0.603578314122	0.0692193673082	-0.0784287849782	0.519267740921	-1.10016875234	-1.07540178583	-0.177409296351	1.12430928085	0.397305253581	-0.0310797570114	1.26858112985	0.109416358967	0.799116172849	70.3988285625	107.407624531	281.163058827
6	6.15650850097	-0.400556919288	0.773910231677	5.93148351767	1.25397433677	7.30036099838	0.206036644438	1.14374344755	1.68671958852	0.361516158611	0.385572459385	-0.205431173951	-2.40978784795	0.246922395798	-0.531548951283	2.00266137927	0.323464213168	0.329626805738	1.4102589586	0.0412171539929	1.48653037927	70.9363912956	123.149319602	301.600674469
7	2.7353431584	-1.50869845802	-0.425977235021	5.19885573688	-0.932402785548	4.54062458706	0.453482911454	-0.0591049063085	-0.512918725874	-0.136423705871	-0.0879474697024	-0.194702929581	0.549318257736	-0.408501346519	-0.29445076935	1.0089461952	-0.290568559895	-0.205194555858	0.667889078377	0.0345184555925	0.951625824268	105.20537852	64.175067191	326.456251864
8	0.570567156311	-2.02704418772	-1.9409863529	3.40934828696	3.22826531155	4.21321711738	-0.172390848602	-0.369449935419	0.211791599878	0.83327345126	0.0699278088038	0.265313188	0.201961310185	-0.683346868322	0.134055928005	1.12704229198	-0.1722289056	-0.00748444967006	1.18705943555	0.167900845218	0.861540812646	95.110843333	86.1801657865	330.917259759
9	4.81760499858	1.16095644903	1.73915799606	1.75715238797	0.0423174223262	2.36606208168	0.218518359014	0.190693063836	-0.146465795129	0.169105328267	-0.177117422706	-0.00930269927901	-0.684144088663	-0.398697047135	-0.120531537006	1.51554350915	0.0431151750815	-0.00418869825211	1.06470073086	-0.152554376942	0.724371807035	93.3546585358	100.314671782	337.513583329
10	3.18758464766	-1.21563629635	3.29968275149	0.812819329138	-0.629495743494	3.48855285119	-0.609038056118	-0.0957127477222	1.15005135669	-0.110301016554	0.0253194047577	-0.457320094359	-0.99974472909	0.461708797657	0.380388141708	2.03854069258	0.133115490641	-0.0186814462566	1.40727649689	0.00182112888073	1.04555400474	96.6970026218	115.928059916	323.014174463
11	3.14863305352	-0.822820899665	1.58148679979	2.13188241236	1.0749828778	1.99804160351	0.273471841634	0.347025113006	0.0106604566598	0.441997672298	-0.391677759012	-0.073760360156	-0.161613113607	0.171168892115	0.143882657381	1.628524025	-0.262835026556	0.035013081567	0.712280136333	-0.0437128473815	0.770053633023	103.176756247	101.76756035	349.987170114
12	3.10495075736	-1.15151502768	-2.07618938079	1.40297612895	1.21400764365	4.16489415364	-0.0588629159392	-0.225065915365	-0.208438287604	1.04128136634	0.0788252386182	-0.114300772648	0.271034668633	0.0812945877512	-0.0535504226417	1.54270208745	-0.40305825852	-0.231127375968	0.647059361331	0.107244060409	0.854111473438	107.329575507	70.4695296756	351.079707144
13	7.95058915887	0.0863528305852	-0.430469230878	6.42550482703	-0.698490472359	7.96501115976	0.765111192092	0.0843865064689	0.948657785579	1.51379713042	-0.335729801782	-1.60635111773	-0.00492576637252	1.92012162018	-0.35078634227	1.06500924183	-0.119163136696	-0.319974993689	1.05282562824	-0.0286491194132	1.13954961151	123.003114004	71.1236734806	330.747493357
14	2.90420761235	-1.04472365717	-1.00012915113	5.85414462304	1.6459995359	5.62425601267	-0.190391598316	0.143896411115	0.326410680058	-0.333948082193	0.193153791443	-0.304185405056	-0.855380797397	0.109168937815	0.0571791527451	0.554866727881	0.21847154426	-0.00100887341826	0.6745720638	-0.0103980303757	0.832294159989	139.113764061	180.218627306	208.83493872
15	1.55286112677	-1.34484728865	3.07735557566	1.44727135033	-1.93723439007	5.01895838678	0.0606789716185	-0.15790316332	0.188066614074	0.128253932235	-0.297957490266	-0.0684750051632	-0.136256556558	-0.27184615191	0.261048744862	0.673611379091	0.163940401366	0.120948616013	0.863774995471	-0.0863863721973	0.867686139936	149.077708593	158.171146207	213.284788774
16	2.17982299691	-2.17295091047	-3.42956248653	1.38758648335	0.979752794951	4.37141625536	0.1917708408	0.769896789501	-0.151477306789	-0.0528458530606	-0.51306015044	0.056976905213	0.313915853871	-1.04757676571	0.287591574369	0.802969153437	-0.0467784026853	-0.085267991877	1.20561537696	-0.182174345386	0.91674649651	149.034513849	135.521810281	211.882216572
17	1.45592683738	-0.768453932084	-0.973491971099	0.833546761844	0.177585052693	0.356272362198	0.125006593081	0.355918380598	-0.628470657259	-0.0291460019235	-0.165650277295	0.0330502893522	0.245794930229	-0.492029734299	0.0493244986158	0.686085499357	0.0382364948687	-0.0494257626887	1.03218989085	-0.0450354533457	0.881828201686	140.949018436	142.654322626	232.306954864
18	3.9926214816	0.0131393182584	3.37256405418	3.44670433625	-0.278814025366	5.7492799019	0.369833773671	-0.43464845079	-0.0858987351843	0.141257213289	-0.0903398436071	0.417872439075	0.0520563060229	-0.709882058287	-0.212952913015	0.584970953304	0.109606267684	0.117975628259	0.637498518081	-0.00143336037045	0.702135037646	137.10705875	173.236176984	236.239912869
19	5.60449249449	0.758906455713	0.32776136899	4.15683920365	-0.0106047939577	6.4423382308	0.0974869048606	0.416882599902	-0.48644682434	-0.117327603752	0.0936871807303	0.861250150121	-0.0220486804761	-1.15841269985	-0.129765502489	0.595386564151	0.244241470412	-0.0490914787459	0.834770166245	-0.115176626499	0.966589153167	126.730655894	174.945998885	214.924379131

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 6 through 163 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 164 through 247 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 248 through 367 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 368 through 728 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 729 through 909 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 910 through 967 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 6 through 114 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 115 through 247 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 248 through 296 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 297 through 365 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 366 through 728 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 729 through 909 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 910 through 967 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 6 through 114 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 115 through 247 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 248 through 365 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 366 through 728 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 729 through 880 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 881 through 967 )

-
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