PDB-8cj8: Arabidopsis thaliana Phosphoenolpyruvate carboxylase PPC1 mutant ...

ID or keywords:

Entry

Database: PDB / ID: 8cj8

Title

Arabidopsis thaliana Phosphoenolpyruvate carboxylase PPC1 mutant A651V in complex with L-malate

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: 3.48991836749 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	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

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Download

PDBx/mmCIF format	8cj8.cif.gz	1.3 MB	Display	PDBx/mmCIF format
PDB format	pdb8cj8.ent.gz	969.6 KB	Display	PDB format
PDBx/mmJSON format	8cj8.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8cj8_validation.pdf.gz	1.6 MB	Display	wwPDB validaton report
Full document	8cj8_full_validation.pdf.gz	1.7 MB	Display
Data in XML	8cj8_validation.xml.gz	94.6 KB	Display
Data in CIF	8cj8_validation.cif.gz	127 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cj/8cj8 ftp://data.pdbj.org/pub/pdb/validation_reports/cj/8cj8	HTTPS FTP

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Related structure data

Related structure data	8cj5C 8oj9C 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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#154 - Oct 2012 Citric Acid Cycle similarity (1) #190 - Oct 2015 Two-component Systems similarity (1) #50 - Feb 2004 Glycolytic Enzymes similarity (1)

Deposited unit

A: Phosphoenolpyruvate carboxylase 1

B: Phosphoenolpyruvate carboxylase 1

C: Phosphoenolpyruvate carboxylase 1

hetero molecules

335 kDa, 3 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, gel filtration
447 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Phosphoenolpyruvate carboxylase 1

hetero molecules

C: Phosphoenolpyruvate carboxylase 1

hetero molecules

C: Phosphoenolpyruvate carboxylase 1

hetero molecules

C: Phosphoenolpyruvate carboxylase 1

hetero molecules

defined by author
447 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	245.380, 245.380, 397.730
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	ASP	ASP	(chain 'A' and (resid 6 through 320 or resid 322...	A	A	6 - 224	13 - 231
2	2	THR	THR	GLU	GLU	(chain 'A' and (resid 6 through 320 or resid 322...	A	A	229 - 320	236 - 327
3	3	LEU	LEU	SER	SER	(chain 'A' and (resid 6 through 320 or resid 322...	A	A	322 - 346	329 - 353
1	4	ALA	ALA	HIS	HIS	(chain 'A' and (resid 6 through 320 or resid 322...	A	A	351 - 635	358 - 642
2	5	GLY	GLY	TRP	TRP	(chain 'A' and (resid 6 through 320 or resid 322...	A	A	638 - 709	645 - 716
3	6	ALA	ALA	GLU	GLU	(chain 'A' and (resid 6 through 320 or resid 322...	A	A	711 - 847	718 - 854
1	7	LEU	LEU	SER	SER	(chain 'A' and (resid 6 through 320 or resid 322...	A	A	849 - 922	856 - 929
2	8	GLY	GLY	GLY	GLY	(chain 'A' and (resid 6 through 320 or resid 322...	A	A	947 - 967	954 - 974
3	9	LEU	LEU	ASP	ASP	(chain 'B' and (resid 6 through 175 or (resid 176...	B	B	6 - 224	13 - 231
1	10	THR	THR	GLU	GLU	(chain 'B' and (resid 6 through 175 or (resid 176...	B	B	229 - 320	236 - 327
2	11	LEU	LEU	SER	SER	(chain 'B' and (resid 6 through 175 or (resid 176...	B	B	322 - 346	329 - 353
3	12	ALA	ALA	HIS	HIS	(chain 'B' and (resid 6 through 175 or (resid 176...	B	B	351 - 635	358 - 642
1	13	GLY	GLY	TRP	TRP	(chain 'B' and (resid 6 through 175 or (resid 176...	B	B	638 - 709	645 - 716
2	14	ALA	ALA	GLU	GLU	(chain 'B' and (resid 6 through 175 or (resid 176...	B	B	711 - 847	718 - 854
3	15	LEU	LEU	SER	SER	(chain 'B' and (resid 6 through 175 or (resid 176...	B	B	849 - 922	856 - 929
1	16	GLY	GLY	GLY	GLY	(chain 'B' and (resid 6 through 175 or (resid 176...	B	B	947 - 967	954 - 974
2	17	LEU	LEU	ASP	ASP	(chain 'C' and (resid 6 through 175 or (resid 176...	C	C	6 - 224	13 - 231
3	18	THR	THR	GLU	GLU	(chain 'C' and (resid 6 through 175 or (resid 176...	C	C	229 - 320	236 - 327
1	19	LEU	LEU	SER	SER	(chain 'C' and (resid 6 through 175 or (resid 176...	C	C	322 - 346	329 - 353
2	20	ALA	ALA	HIS	HIS	(chain 'C' and (resid 6 through 175 or (resid 176...	C	C	351 - 635	358 - 642
3	21	GLY	GLY	TRP	TRP	(chain 'C' and (resid 6 through 175 or (resid 176...	C	C	638 - 709	645 - 716
1	22	ALA	ALA	GLU	GLU	(chain 'C' and (resid 6 through 175 or (resid 176...	C	C	711 - 847	718 - 854
2	23	LEU	LEU	SER	SER	(chain 'C' and (resid 6 through 175 or (resid 176...	C	C	849 - 922	856 - 929
3	24	GLY	GLY	GLY	GLY	(chain 'C' and (resid 6 through 175 or (resid 176...	C	C	947 - 967	954 - 974

#1: Protein	Phosphoenolpyruvate carboxylase 1 / AtPPC1 / PEPC 1 / PEPCase 1 / 107-kDa PEPC polypeptide Mass: 111426.219 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
#2: Chemical	ChemComp-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate Mass: 134.087 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₄H₆O₅ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 4.6 Å³/Da / Density % sol: 73.25 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion / pH: 6.5 / Details: 30% w/v PEG400; 0,1M MES pH6,5; 0,1M NaAc

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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: 3.48991836749→49.71625 Å / Num. obs: 76655 / % possible obs: 99.5 % / Redundancy: 26.42 % / B_iso Wilson estimate: 114.748850146 Å² / CC_1/2: 0.997 / R_merge(I) obs: 0.45 / Net I/σ(I): 5.32
Reflection shell	Resolution: 3.48991836749→3.7 Å / Redundancy: 24.7 % / R_merge(I) obs: 2.716 / Num. unique obs: 11923 / CC_1/2: 0.791 / % possible all: 79.5

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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: 3.48991836749→49.71625 Å / SU ML: 0.465311401768 / Cross valid method: FREE R-VALUE / σ(F): 1.32982694233 / Phase error: 35.0197887326
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.273937803274	3803	5.01364481299 %
R_work	0.244038741916	72050	-
obs	0.245546637964	75853	98.6564524101 %

Solvent computation

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

Displacement parameters

B_iso mean: 134.733536962 Å²

Refinement step

Cycle: LAST / Resolution: 3.48991836749→49.71625 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	22538	0	58	8	22604

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.00731276816809	23126
X-RAY DIFFRACTION	f_angle_d	1.08644977514	31301
X-RAY DIFFRACTION	f_chiral_restr	0.0619098181735	3458
X-RAY DIFFRACTION	f_plane_restr	0.00771984321279	4071
X-RAY DIFFRACTION	f_dihedral_angle_d	12.8996938672	14066

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 (%)
3.48991836749-3.5341	0.419738860428	125	0.401336272082	2284	X-RAY DIFFRACTION	86.4680545585
3.5341-3.5806	0.389568353242	139	0.366064942239	2645	X-RAY DIFFRACTION	99.2867332382
3.5806-3.6296	0.405616150745	141	0.345512470501	2687	X-RAY DIFFRACTION	99.8235086481
3.6296-3.6814	0.350731270009	140	0.337425836451	2659	X-RAY DIFFRACTION	99.6794871795
3.6814-3.7364	0.372392413609	140	0.327896700253	2660	X-RAY DIFFRACTION	99.6441281139
3.7364-3.7947	0.360494008061	140	0.317290966725	2655	X-RAY DIFFRACTION	99.4308075418
3.7947-3.8569	0.367627802625	138	0.303961357857	2670	X-RAY DIFFRACTION	99.3982300885
3.8569-3.9234	0.304647336652	142	0.287389311012	2664	X-RAY DIFFRACTION	99.2922859165
3.9234-3.9947	0.281777949799	140	0.265716546299	2668	X-RAY DIFFRACTION	99.222614841
3.9947-4.0715	0.296425824452	138	0.260338081021	2645	X-RAY DIFFRACTION	99.357372367
4.0715-4.1546	0.2821518764	142	0.252830203472	2681	X-RAY DIFFRACTION	99.3664202746
4.1546-4.2449	0.300740013976	139	0.25035068218	2647	X-RAY DIFFRACTION	99.1812032752
4.2449-4.3436	0.252545760493	142	0.230769295961	2670	X-RAY DIFFRACTION	99.3639575972
4.3436-4.4521	0.284388391903	141	0.232997579527	2691	X-RAY DIFFRACTION	99.5080815179
4.4521-4.5724	0.253400033778	140	0.227930566182	2662	X-RAY DIFFRACTION	99.5028409091
4.5724-4.7069	0.24524881932	142	0.223117904437	2683	X-RAY DIFFRACTION	99.1575991576
4.7069-4.8587	0.270350595781	141	0.2301360836	2657	X-RAY DIFFRACTION	99.3607954545
4.8587-5.0322	0.274320234633	141	0.216649265582	2682	X-RAY DIFFRACTION	99.2965177629
5.0322-5.2334	0.239748991605	143	0.221421266418	2705	X-RAY DIFFRACTION	99.6152500874
5.2334-5.4713	0.26624753865	140	0.224490985039	2671	X-RAY DIFFRACTION	99.1534391534
5.4713-5.7594	0.303780613182	142	0.236326783542	2707	X-RAY DIFFRACTION	99.4068387997
5.7594-6.1196	0.267311132675	143	0.235690555208	2703	X-RAY DIFFRACTION	99.3715083799
6.1196-6.5912	0.274388794479	145	0.234583134489	2727	X-RAY DIFFRACTION	99.5839112344
6.5912-7.2526	0.307447579631	143	0.22741192707	2723	X-RAY DIFFRACTION	99.5138888889
7.2526-8.2979	0.258200598696	143	0.221587802927	2736	X-RAY DIFFRACTION	99.3101069334
8.2979-10.4386	0.183609048483	145	0.19718029444	2746	X-RAY DIFFRACTION	98.5680190931
10.4386-49.71625	0.24344818814	148	0.224265621431	2722	X-RAY DIFFRACTION	93.2120818448

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	1.7822438362	-0.945642436439	0.467409838402	1.61985508001	0.211679189287	0.683102576502	0.050212216496	-0.45728928522	0.077526689133	0.427636970928	-0.000948431411305	0.178828288551	-0.113948470789	-1.22935520442	-0.0616456461237	1.71253577125	-0.119668262207	-0.0047286826783	1.52353144109	0.15250597794	1.03148396404	74.6317261246	97.7180924623	302.566403594
2	1.79153318994	-0.115113052155	-0.782125616419	0.596776887773	0.449401585249	1.58361783363	0.552104623096	-0.357551411569	0.103146243376	-0.267709016315	-0.153641658548	-0.273270107519	-0.498921184923	-0.506262000716	-0.279061620812	1.67140565362	-0.13268878434	0.0117001758014	0.692107733744	0.158356319882	1.05510765578	102.623872293	98.9546990159	307.28267843
3	1.39941301778	0.940033514564	-0.540751985337	1.74268174749	-1.53270504435	1.48434722139	-0.0229494856555	-0.00531764322946	0.128112801396	0.109598732343	0.0867510184653	-0.181767099967	-0.766389211813	-0.287587789947	-0.0349445688502	1.88073358631	0.243193198717	0.0346465239232	0.612250769797	-0.0140888464169	0.979583246685	101.848154141	103.767540184	283.752948516
4	1.96319360966	-1.11851846446	-0.516580469512	2.29576499299	0.913984115676	2.97566853278	-0.0636142949913	-0.00580849910447	0.525471115694	0.134199988767	0.250960728892	0.281410868926	-0.248418915313	-0.547830152114	-0.291797519027	1.97864062827	0.0859640317113	-0.00185509507457	1.20863769997	0.0817665749298	1.03063028378	70.3193042092	109.568801952	284.693914868
5	2.27970783021	-0.241807115338	0.573965104139	2.68086140413	-1.21835626107	2.3535687276	0.40311657805	-0.345278159108	-0.41126789445	-0.0264607139061	0.137050210347	0.243453505758	0.624739196229	-0.131824294693	-0.483836331031	1.92158452744	-0.246357554158	-0.0665031676511	1.19327693435	0.230034725461	1.11250619983	104.763546512	61.9183638058	327.181264136
6	0.90980570671	-0.896119606875	-1.20589426012	1.92333803619	1.40379624837	1.6377805876	-0.289599944674	-0.520856566936	-0.0910534054232	0.583465739271	0.0729324572775	0.190885618092	0.0360265858278	-0.0341707009936	0.112289317204	1.56121104694	-0.413466366776	-0.146868216949	1.61278375763	0.27411221798	1.29773109207	93.6620842098	82.8615316687	331.834322017
7	0.239557260687	0.0186321106598	0.00992536825759	1.34051746606	1.13301093501	1.34417402086	-0.424744426807	-0.864434884489	0.0532456700708	-0.067486815782	0.678127852135	-0.445053546505	-0.467133902037	-0.116630885853	-0.203103863763	1.72066217625	-0.20173938403	-0.0232309860223	2.07806014529	-0.0329600449843	1.16389501055	101.734192534	99.7133145764	333.483763233
8	1.19299269444	-0.477643102204	1.47297222411	0.598515445272	-0.483497678151	1.60366850761	-0.0481509825315	0.166214658987	0.233715067003	0.294462343013	-0.166391266631	-0.218861216985	-0.18311177087	0.638451153077	0.221541655366	2.05480526247	0.0676586760483	0.00880015416258	1.71325107955	0.063427616514	1.23130938695	102.493421009	105.322268997	346.408782676
9	2.77174187216	-1.46451117011	-0.900108606347	2.6307379229	0.628974835468	3.22266174855	-0.147145642184	-0.630989980499	0.148209796658	0.670417669156	0.117285391237	-0.218974071512	-0.13179205883	-0.101755642826	-0.101958049134	1.76293447826	-0.410237174875	-0.170981009507	1.52669511997	0.0353484462579	1.06068439754	107.361201685	73.5631559845	357.075156423
10	1.91618340402	-0.0563180078942	-0.184701372141	2.04166788423	-0.800822393281	3.50382154322	0.189199392318	-0.394570879153	-0.0818593705456	1.01298597867	0.00143619279391	-0.126156744817	0.259845787882	-0.510400300282	-0.148450254123	1.32703583662	-0.349008817835	-0.0643750842713	1.49451818405	-0.0259909171114	0.833409479007	110.286480663	66.82964478	342.438218817
11	1.0559871774	-0.540537448332	0.28313443975	1.94925503876	-0.495151953374	2.23146634208	0.279679009295	0.0822301128645	0.348435562385	-0.176798880705	-0.346475291293	-0.118145837289	0.0658401341298	-0.349006151541	0.102514261847	0.847357024082	0.199643927053	0.0488315082499	0.629064866278	0.0314270053651	0.840520391413	146.755814164	167.165245129	211.989496566
12	1.14484834907	-0.541152766658	-1.09167796489	0.429719177842	-0.0576075844674	1.95188711885	0.149747785438	0.317348379811	-0.1822756326	0.158201178887	-0.130532257739	0.0489462628798	0.612746665631	-0.294908115399	-0.0566554330089	1.14369316367	-0.304779396555	-0.111410415284	0.669401847582	0.00848450032165	1.03941521316	142.662438274	140.138217733	226.324599332
13	1.5977408121	-0.873302687451	0.719572695436	1.90200993646	-0.693463378767	3.60355066286	0.239011076369	-0.0306331809626	-0.233410471808	0.250320163207	0.160962584443	0.385135286126	-0.169369241842	-1.08109081099	0.106861548336	1.15080906983	0.530968162904	0.192391329694	-0.0747452953654	-0.0991249142874	0.901469934901	136.584646366	174.419149547	232.628596596

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 6 through 202 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 203 through 365 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 366 through 728 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 729 through 967 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 6 through 87 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 88 through 221 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 222 through 325 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 326 through 706 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 707 through 849 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 850 through 967 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 6 through 266 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 267 through 706 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 707 through 967 )

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