PDB-8cj5: Arabidopsis thaliana Phosphoenolpyruvate carboxylase PPC1 A651V m...

ID or keywords:

Entry

Database: PDB / ID: 8cj5

Title

Arabidopsis thaliana Phosphoenolpyruvate carboxylase PPC1 A651V mutant with bound phosphate

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 / apoplast / carbon fixation / cellular response to phosphate starvation / photosynthesis / tricarboxylic acid cycle / protein tetramerization / nucleus / cytosol
Similarity search - Function

Biological species

Arabidopsis thaliana (thale cress)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.00135289121 Å

Authors

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

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	Feb 12, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 21, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8cj5.cif.gz	881.2 KB	Display	PDBx/mmCIF format
PDB format	pdb8cj5.ent.gz	619.1 KB	Display	PDB format
PDBx/mmJSON format	8cj5.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8cj5_validation.pdf.gz	919.4 KB	Display	wwPDB validaton report
Full document	8cj5_full_validation.pdf.gz	951 KB	Display
Data in XML	8cj5_validation.xml.gz	61.6 KB	Display
Data in CIF	8cj5_validation.cif.gz	83.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cj/8cj5 ftp://data.pdbj.org/pub/pdb/validation_reports/cj/8cj5	HTTPS FTP

-
Related structure data

Related structure data	8cj8C 8oj9C 8ojeC 8ojfC 8ojqC 8ojyC 8ojzC 8qtmC 8qx1C 8qx3C 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

hetero molecules

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

1

A: Phosphoenolpyruvate carboxylase 1

B: Phosphoenolpyruvate carboxylase 1

hetero molecules

A: Phosphoenolpyruvate carboxylase 1

B: Phosphoenolpyruvate carboxylase 1

hetero molecules

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

Unit cell

Length a, b, c (Å)	128.830, 156.620, 142.950
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2
Space group name Hall	P22ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x+1/2,y+1/2,-z #4: -x,-y,z

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	TYR	TYR	SER	SER	(chain 'A' and ((resid 33 through 35 and (name N...	A	A	33 - 99	40 - 106
2	2	MET	MET	LYS	LYS	(chain 'A' and ((resid 33 through 35 and (name N...	A	A	101 - 121	108 - 128
1	3	SER	SER	THR	THR	(chain 'A' and ((resid 33 through 35 and (name N...	A	A	137 - 300	144 - 307
2	4	ASP	ASP	ARG	ARG	(chain 'A' and ((resid 33 through 35 and (name N...	A	A	302 - 336	309 - 343
1	5	ALA	ALA	VAL	VAL	(chain 'A' and ((resid 33 through 35 and (name N...	A	A	339 - 447	346 - 454
2	6	LEU	LEU	GLU	GLU	(chain 'A' and ((resid 33 through 35 and (name N...	A	A	449 - 480	456 - 487
1	7	ARG	ARG	PHE	PHE	(chain 'A' and ((resid 33 through 35 and (name N...	A	A	482 - 677	489 - 684
2	8	GLU	GLU	PHE	PHE	(chain 'A' and ((resid 33 through 35 and (name N...	A	A	680 - 738	687 - 745
1	9	LEU	LEU	PRO	PRO	(chain 'A' and ((resid 33 through 35 and (name N...	A	A	740 - 756	747 - 763
2	10	GLY	GLY	ILE	ILE	(chain 'A' and ((resid 33 through 35 and (name N...	A	A	764 - 794	771 - 801
1	11	HIS	HIS	HIS	HIS	(chain 'A' and ((resid 33 through 35 and (name N...	A	A	796 - 873	803 - 880
2	12	GLN	GLN	THR	THR	(chain 'A' and ((resid 33 through 35 and (name N...	A	A	885 - 916	892 - 923
1	13	LYS	LYS	LYS	LYS	(chain 'A' and ((resid 33 through 35 and (name N...	A	A	930 - 933	937 - 940
2	14	LEU	LEU	GLY	GLY	(chain 'A' and ((resid 33 through 35 and (name N...	A	A	935 - 967	942 - 974
1	15	TYR	TYR	SER	SER	(chain 'B' and ((resid 33 through 35 and (name N...	B	B	33 - 99	40 - 106
2	16	MET	MET	LYS	LYS	(chain 'B' and ((resid 33 through 35 and (name N...	B	B	101 - 121	108 - 128
1	17	SER	SER	THR	THR	(chain 'B' and ((resid 33 through 35 and (name N...	B	B	137 - 300	144 - 307
2	18	ASP	ASP	ARG	ARG	(chain 'B' and ((resid 33 through 35 and (name N...	B	B	302 - 336	309 - 343
1	19	ALA	ALA	VAL	VAL	(chain 'B' and ((resid 33 through 35 and (name N...	B	B	339 - 447	346 - 454
2	20	LEU	LEU	GLU	GLU	(chain 'B' and ((resid 33 through 35 and (name N...	B	B	449 - 480	456 - 487
1	21	ARG	ARG	PHE	PHE	(chain 'B' and ((resid 33 through 35 and (name N...	B	B	482 - 677	489 - 684
2	22	GLU	GLU	PHE	PHE	(chain 'B' and ((resid 33 through 35 and (name N...	B	B	680 - 738	687 - 745
1	23	LEU	LEU	PRO	PRO	(chain 'B' and ((resid 33 through 35 and (name N...	B	B	740 - 756	747 - 763
2	24	GLY	GLY	ILE	ILE	(chain 'B' and ((resid 33 through 35 and (name N...	B	B	764 - 794	771 - 801
1	25	HIS	HIS	HIS	HIS	(chain 'B' and ((resid 33 through 35 and (name N...	B	B	796 - 873	803 - 880
2	26	GLN	GLN	THR	THR	(chain 'B' and ((resid 33 through 35 and (name N...	B	B	885 - 916	892 - 923
1	27	LYS	LYS	LYS	LYS	(chain 'B' and ((resid 33 through 35 and (name N...	B	B	930 - 933	937 - 940
2	28	LEU	LEU	GLY	GLY	(chain 'B' and ((resid 33 through 35 and (name N...	B	B	935 - 967	942 - 974

#1: Protein	Phosphoenolpyruvate carboxylase 1 / AtPPC1 / PEPC 1 / PEPCase 1 / 107-kDa PEPC polypeptide Mass: 111426.219 Da / Num. of mol.: 2 / Mutation: A651V 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
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.24 Å³/Da / Density % sol: 61.99 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion / pH: 6.5 Details: 0.09M Sodium nitrate, 0.09 Sodium phosphate dibasic, 0.09M Ammonium sulfate, 0.1M MES monohydrate pH 6.5, 20% v/v Ethylene glycol; 10 % w/v PEG 8K

-
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: Apr 8, 2022
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→49.04 Å / Num. obs: 58634 / % possible obs: 99.6 % / Redundancy: 10.34 % / B_iso Wilson estimate: 113.969140974 Å² / CC_1/2: 0.996 / R_merge(I) obs: 0.242 / Net I/σ(I): 8.6
Reflection shell	Resolution: 3→3.5 Å / Redundancy: 8.7 % / R_merge(I) obs: 3.867 / Mean I/σ(I) obs: 0.39 / Num. unique obs: 8677 / CC_1/2: 0.838

-
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: 3.00135289121→49.0386618174 Å / SU ML: 0.611432642802 / Cross valid method: FREE R-VALUE / σ(F): 1.32517119902 / Phase error: 32.0447421462
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.265775553378	2841	5.0165983896 %
R_work	0.214557067552	53791	-
obs	0.217167515667	56632	96.7952552686 %

Solvent computation

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

Displacement parameters

B_iso mean: 127.994922724 Å²

Refinement step

Cycle: LAST / Resolution: 3.00135289121→49.0386618174 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14382	0	10	27	14419

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0059754793327	14785
X-RAY DIFFRACTION	f_angle_d	0.849321911069	20039
X-RAY DIFFRACTION	f_chiral_restr	0.0478671715557	2216
X-RAY DIFFRACTION	f_plane_restr	0.00619874841836	2604
X-RAY DIFFRACTION	f_dihedral_angle_d	15.8161531484	8993

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 (%)
3.0014-3.0531	0.75816297402	85	0.609545376403	1506	X-RAY DIFFRACTION	54.8999309869
3.0531-3.1086	0.555600225447	126	0.491419377876	2350	X-RAY DIFFRACTION	85.5267702936
3.1086-3.1684	0.435768606697	140	0.423691751284	2642	X-RAY DIFFRACTION	96.4298093588
3.1684-3.233	0.414569608272	142	0.382138248897	2704	X-RAY DIFFRACTION	99.4062172546
3.233-3.3033	0.38741797901	146	0.344853824504	2758	X-RAY DIFFRACTION	99.8624484182
3.3033-3.3802	0.372328447105	144	0.324440646816	2744	X-RAY DIFFRACTION	99.9307958478
3.3802-3.4647	0.38772042577	144	0.304523286253	2732	X-RAY DIFFRACTION	100
3.4647-3.5583	0.329645035484	146	0.292795913686	2758	X-RAY DIFFRACTION	99.8968008256
3.5583-3.663	0.324190098582	145	0.282300674851	2754	X-RAY DIFFRACTION	99.8966230186
3.663-3.7812	0.305053297809	144	0.26174612192	2753	X-RAY DIFFRACTION	100
3.7812-3.9163	0.306336781819	146	0.244696819319	2766	X-RAY DIFFRACTION	99.9656711294
3.9163-4.073	0.288870323265	146	0.211601837212	2775	X-RAY DIFFRACTION	100
4.073-4.2583	0.238308779753	145	0.196155389484	2743	X-RAY DIFFRACTION	99.9653859467
4.2583-4.4826	0.205716388157	146	0.179808978036	2791	X-RAY DIFFRACTION	100
4.4826-4.7633	0.221851011884	147	0.173146218642	2776	X-RAY DIFFRACTION	100
4.7633-5.1307	0.211932308041	147	0.169606805161	2793	X-RAY DIFFRACTION	100
5.1307-5.6463	0.25370679423	148	0.188934841078	2810	X-RAY DIFFRACTION	100
5.6463-6.4618	0.297136568536	147	0.205714165116	2804	X-RAY DIFFRACTION	100
6.4618-8.1351	0.233677007042	151	0.181215593283	2860	X-RAY DIFFRACTION	100
8.1351-49.0386618174	0.215145377723	156	0.175070748927	2972	X-RAY DIFFRACTION	99.5861190704

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	1.69580316109	0.477190097187	-0.193021501433	1.50877965986	-0.0153284240329	0.497659489762	0.0318217649163	-0.703452796235	0.0681627311085	0.330664699858	-0.0372777272196	0.1648261071	0.0442966407728	-0.0249242988968	-0.00906015604774	0.803558520827	-0.034720146924	-0.0763392871673	0.869153325425	0.0745786300933	0.794334971424	126.219871192	57.5027759102	169.95498038
2	1.36461105489	-0.376192307961	-0.227985436238	1.72824460597	0.172284024526	0.453418210017	0.0840124022442	-0.0465112189726	0.0118940473522	-0.0194055032807	-0.0624091974751	-0.212539993903	0.0550267421286	-0.0610259507738	-0.0184724109883	0.626425182439	-0.0571039724829	-0.050647038039	0.628993827241	0.03981900606	0.638031669658	148.281326237	62.7435589658	146.109079376
3	3.90556905667	-0.190964329889	0.482500905131	1.29998504521	-0.255495379923	0.98618765484	0.058501706173	-0.26426685047	-0.556724708038	0.146970787475	-0.0469512421711	-0.227522984236	0.203776598911	0.090099707588	-0.00591209059307	0.77790789631	-0.0610971335333	-0.0994321951127	0.683172856671	0.207557630402	0.849562931001	134.130077069	35.6438847991	164.642799383
4	1.40446774362	-0.521178065296	-0.320471100318	1.45608800767	-0.219315756368	1.84722633928	0.705958429367	1.4927637504	0.426095842675	-0.812280118561	-0.402988488445	-0.0810555887407	-0.375830826167	0.242447291642	-0.279866549714	1.5812936988	0.688103832585	0.318247516078	1.92434129248	0.414324316055	1.26142842685	149.340210177	83.495500982	64.6356858527
5	2.90963711624	-0.886331968095	0.0599810922832	1.94666101556	-0.472802742527	0.831372183933	0.454299883425	0.548576774724	-0.401638565684	-0.224027274595	-0.505414218448	0.266429014484	0.106133403867	0.121963014801	0.0652973737625	1.03794754028	0.213262098269	-0.0344844424017	0.873682866541	-0.14068272426	0.716905245499	139.583501571	63.4571132034	92.2922722671
6	2.10634875284	-1.05584192587	0.293567356193	1.92537034858	-0.358472605143	2.83987973426	0.704833638354	1.19222488605	-0.165317873909	-0.983154078002	-0.7656399123	-0.367189686353	0.351144314211	0.425266641439	0.0351317810793	1.23215517567	0.594788319294	0.0721742189884	1.41598548061	0.0722265493824	1.06818414431	160.011473658	56.0458154758	83.9964105274
7	2.0056703382	0.00220770468936	-0.655453363349	1.00593125952	-0.416810646889	0.919037593372	0.203398386469	0.879926954585	0.0843336966	-0.41156792403	-0.254699287491	-0.853197776918	0.218925796265	0.802129592385	0.0695575030293	1.42542076862	0.557040652187	0.359052797958	2.13240014475	0.305477246129	1.52477231637	169.747393011	75.0849819128	68.79824678

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 28 through 221 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 222 through 706 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 707 through 967 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 33 through 221 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 222 through 519 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 520 through 679 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 680 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://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