PDB-8ojz: Arabidopsis thaliana Phosphoenolpyruvate carboxylase 1 (PPC1) G67...

ID or keywords:

Entry

Database: PDB / ID: 8ojz

Title

Arabidopsis thaliana Phosphoenolpyruvate carboxylase 1 (PPC1) G678S mutant

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: 3.24781103461 Å

Authors

Loris, R. / Haesaerts, S. / 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. / Fausto, K. / O'Leary, S. / Loris, R. / Larsen, P.B.

History

Deposition	Mar 25, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 3, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8ojz.cif.gz	882.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8ojz.ent.gz	620.1 KB	Display	PDB format
PDBx/mmJSON format	8ojz.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8ojz_validation.pdf.gz	462 KB	Display	wwPDB validaton report
Full document	8ojz_full_validation.pdf.gz	502.6 KB	Display
Data in XML	8ojz_validation.xml.gz	63 KB	Display
Data in CIF	8ojz_validation.cif.gz	84.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oj/8ojz ftp://data.pdbj.org/pub/pdb/validation_reports/oj/8ojz	HTTPS FTP

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Related structure data

Related structure data	8cj5C 8cj8C 8oj9C 8ojeC 8ojfC 8ojqC 8ojyC 80jg 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) #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)	128.270, 160.280, 141.300
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	LYS	LYS	(chain 'A' and (resid 33 through 121 or resid 137...	A	A	33 - 121	40 - 128
1	2	SER	SER	THR	THR	(chain 'A' and (resid 33 through 121 or resid 137...	A	A	137 - 300	144 - 307
1	3	ASP	ASP	ALA	ALA	(chain 'A' and (resid 33 through 121 or resid 137...	A	A	302 - 604	309 - 611
1	4	LEU	LEU	PRO	PRO	(chain 'A' and (resid 33 through 121 or resid 137...	A	A	607 - 756	614 - 763
1	5	GLY	GLY	ILE	ILE	(chain 'A' and (resid 33 through 121 or resid 137...	A	A	764 - 794	771 - 801
1	6	HIS	HIS	HIS	HIS	(chain 'A' and (resid 33 through 121 or resid 137...	A	A	796 - 873	803 - 880
1	7	GLN	GLN	THR	THR	(chain 'A' and (resid 33 through 121 or resid 137...	A	A	885 - 916	892 - 923
1	8	LYS	LYS	GLY	GLY	(chain 'A' and (resid 33 through 121 or resid 137...	A	A	930 - 967	937 - 974
2	9	TYR	TYR	LYS	LYS	(chain 'B' and (resid 33 or (resid 34 through 35...	B	B	33 - 121	40 - 128
2	10	SER	SER	THR	THR	(chain 'B' and (resid 33 or (resid 34 through 35...	B	B	137 - 300	144 - 307
2	11	ASP	ASP	ALA	ALA	(chain 'B' and (resid 33 or (resid 34 through 35...	B	B	302 - 604	309 - 611
2	12	LEU	LEU	PRO	PRO	(chain 'B' and (resid 33 or (resid 34 through 35...	B	B	607 - 756	614 - 763
2	13	GLY	GLY	ILE	ILE	(chain 'B' and (resid 33 or (resid 34 through 35...	B	B	764 - 794	771 - 801
2	14	HIS	HIS	HIS	HIS	(chain 'B' and (resid 33 or (resid 34 through 35...	B	B	796 - 873	803 - 880
2	15	GLN	GLN	THR	THR	(chain 'B' and (resid 33 or (resid 34 through 35...	B	B	885 - 916	892 - 923
2	16	LYS	LYS	GLY	GLY	(chain 'B' and (resid 33 or (resid 34 through 35...	B	B	930 - 967	937 - 974

#1: Protein	Phosphoenolpyruvate carboxylase 1 / AtPPC1 / PEPC 1 / PEPCase 1 / 107-kDa PEPC polypeptide Mass: 111428.188 Da / Num. of mol.: 2 / Mutation: G678S 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
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.26 Å³/Da / Density % sol: 62.26 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.09M Sodium nitrate, 0.09 Sodium phosphate dibasic, 0.09M Ammonium sulfate, 0.1M MES monohydrate pH6.5, 20% v/v Ethylene glycol; 10 % w/v PEG 8K

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.981 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 19, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.981 Å / Relative weight: 1
Reflection	Resolution: 3.24781103461→49.3195390826 Å / Num. obs: 46684 / % possible obs: 99.5 % / Redundancy: 13.52 % / B_iso Wilson estimate: 112.469871245 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.241 / Net I/σ(I): 8.43
Reflection shell	Resolution: 3.24781103461→3.44 Å / Redundancy: 14 % / R_merge(I) obs: 3.044 / Mean I/σ(I) obs: 0.83 / Num. unique obs: 7212 / CC_1/2: 0.491 / % possible all: 97.2

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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: 3.24781103461→49.3195390826 Å / SU ML: 0.503330922496 / Cross valid method: FREE R-VALUE / σ(F): 1.3358637312 / Phase error: 28.693031822
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.261072179645	2322	5.00280087905 %
R_work	0.220320678354	44092	-
obs	0.222337246982	46414	99.4642551003 %

Solvent computation

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

Displacement parameters

B_iso mean: 136.006903806 Å²

Refinement step

Cycle: LAST / Resolution: 3.24781103461→49.3195390826 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14388	0	10	35	14433

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.00599100139067	14734
X-RAY DIFFRACTION	f_angle_d	0.839629936399	19960
X-RAY DIFFRACTION	f_chiral_restr	0.0477008707817	2207
X-RAY DIFFRACTION	f_plane_restr	0.00617859869395	2590
X-RAY DIFFRACTION	f_dihedral_angle_d	15.9690543143	8947

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 (%)
3.24781103461-3.3141	0.37191366662	125	0.366138159375	2383	X-RAY DIFFRACTION	92.4097273397
3.3141-3.3861	0.354664021488	136	0.334952243462	2572	X-RAY DIFFRACTION	99.8525073746
3.3861-3.4649	0.380564047994	135	0.325846600631	2559	X-RAY DIFFRACTION	99.9628942486
3.4649-3.5515	0.347312778449	135	0.323299406618	2568	X-RAY DIFFRACTION	99.7785160576
3.5515-3.6475	0.346030016852	135	0.331825789004	2569	X-RAY DIFFRACTION	99.6682639145
3.6475-3.7548	0.365075410004	135	0.339140608811	2565	X-RAY DIFFRACTION	99.7045790251
3.7548-3.8759	0.3161220263	136	0.256716232493	2587	X-RAY DIFFRACTION	99.9266055046
3.8759-4.0144	0.290669844674	137	0.230863407258	2593	X-RAY DIFFRACTION	100
4.0144-4.1751	0.242346090634	135	0.201795269124	2569	X-RAY DIFFRACTION	100
4.1751-4.365	0.218144741461	136	0.181967579132	2588	X-RAY DIFFRACTION	99.9266324285
4.365-4.5949	0.214836365053	138	0.178715584573	2609	X-RAY DIFFRACTION	99.9636098981
4.5949-4.8826	0.237423956587	136	0.162751206299	2600	X-RAY DIFFRACTION	100
4.8826-5.2592	0.233754663948	137	0.172755899226	2603	X-RAY DIFFRACTION	100
5.2592-5.7877	0.272342398125	139	0.193903682255	2633	X-RAY DIFFRACTION	100
5.7877-6.6235	0.267484412006	138	0.211629916894	2626	X-RAY DIFFRACTION	99.9638336347
6.6235-8.3384	0.212937870132	141	0.199908886648	2683	X-RAY DIFFRACTION	100
8.3384-49.3195390826	0.238113967788	148	0.208541201547	2785	X-RAY DIFFRACTION	99.694085656

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	2.26023107681	-1.80712104203	1.14655039595	5.57485812859	-2.00155374028	2.33092402959	0.258844065364	-0.890108239681	0.0698583690361	0.443090275948	-0.437220064814	1.4466111732	0.217498329658	0.178287703882	0.115383988579	1.21030363251	-0.353369296921	0.187384017406	1.28389030591	-0.00662392613782	0.896423707628	111.792478751	48.2977845865	173.01592362
2	1.46624215112	-0.258441816173	-1.00374509754	1.45316588645	-0.822856215326	1.18602491661	0.152799211955	-0.120702724551	0.0818212212369	0.262483408946	-0.00349228864109	-0.0200704330005	0.0359128053662	-0.0151166986101	-0.0127875619108	0.852613167361	-0.0594656933575	-0.0787258041421	0.688019385828	-0.0069047179521	0.688733981247	130.375118172	64.0425388019	162.231623231
3	1.52557828565	-0.0602101610382	0.365156658305	1.66384082709	0.146423024614	1.83605304305	0.0600990467762	-0.19036128096	-0.234184789267	-0.320217050064	0.0453846502553	0.0811864001514	0.0311448298189	-0.417930745669	-0.210531528045	0.679299894149	0.129336653519	-0.364791184009	0.657572534039	-0.0502951469666	0.934432401194	146.151599246	68.9357996094	153.922058912
4	1.812436777	0.390619409046	0.580356327528	2.99039376601	-0.0137740641908	0.549143553259	-0.174037335347	0.311047462579	0.653218463851	-0.5363469017	0.195358730167	0.359781536882	-0.323618404519	0.050482001286	-0.0364399350644	0.72028591783	-0.0709822025768	0.0950634833121	0.647832591275	-0.00407617584388	0.819204932307	140.897524575	87.3437271784	139.781414666
5	3.61523000893	1.870041761	0.533936753156	3.69570983674	0.160580440222	4.18068719849	-0.588867470487	0.562323661508	0.563622314551	-0.465070581939	-0.00680042770428	0.293508075644	0.508936780442	0.301792306995	0.417547421699	0.620001049987	-0.0689072693838	0.300483548477	0.668309226722	-0.0619529337176	0.638464385926	144.693771944	83.4841600683	139.715662603
6	0.90785150079	-0.612608878055	-0.441715278473	1.02177766308	-0.222421461211	0.706788433425	-0.133595285449	0.231844288164	-0.411917093235	-0.168562379401	0.111980846551	-0.248535247844	0.309457373279	-0.0300892119169	0.0457770218224	0.580223510942	-0.0480772364574	0.0375101787349	0.621549181628	-0.0466180149258	0.7710097163	152.981276104	50.674060231	136.110011734
7	1.43541592711	0.666383985154	-0.6852625926	1.2780344721	-0.285659651906	0.0829047432554	-0.0402873043118	-0.0325833262026	-0.117413735976	0.136381674727	-0.0927586845756	-0.338867329148	0.0453504222092	0.217266496212	0.0280652818966	0.830451401658	0.00656673754573	-0.137840601245	0.730820273375	0.114058238527	0.771907923152	146.158292361	44.3542507544	162.630662335
8	3.29342562045	-1.08120783227	1.39685443508	0.366492588675	-0.463405311415	1.03404114629	0.524023228196	-0.749264628793	-0.964081334365	0.115248687395	-0.250169436024	0.301275318069	0.754764660392	-0.0626587631038	-0.0840549578225	0.972282043582	-0.160431116713	-0.130901384058	0.953562653238	0.36728910936	0.981748162032	127.671033386	36.2841810875	170.547322031
9	1.87146845841	0.863940905539	-0.303579866717	2.44618488623	0.443053921251	1.65448907143	-0.36325476366	0.377601043257	0.206912379698	-0.0070736566607	0.13925314463	-0.432436826675	-0.472897598016	0.372980402207	-0.0449289844358	0.546675469723	-0.132724312508	-0.0688799037668	0.640562212114	0.117944472038	0.622439760825	113.521508901	43.1223815089	150.833757343
10	1.33783944994	0.571541265682	-0.560634257125	2.20094749494	-0.068030780891	0.0598777706284	0.59712952759	0.745194670343	0.198333886685	-0.700239038253	-0.554065350928	0.0559227982529	-0.0427403040193	-0.138318503249	0.0931738993186	1.6726052081	0.502260155128	0.136109817306	1.54088266994	0.186262170293	1.0996906321	141.046217738	76.6299333206	73.8553153345
11	2.43042849958	-1.64129345202	0.385987061715	3.1239285306	-0.747351039886	1.37367525253	0.220418185283	-0.0142106961789	-0.137402491229	0.330940989	-0.458517950048	-0.114064654554	0.0787510562634	0.101330899328	0.286405737896	1.00304787519	0.121739354215	0.052626125095	1.03265059904	-0.00171985894766	0.743658683405	148.895563793	58.043763633	94.6615238537
12	0.276959984758	0.282689629884	-0.782315525933	1.03275165691	-1.04716107379	0.06167577235	0.219449633032	0.955313855694	-0.0261897459835	-0.126863507248	-0.288662339156	-0.908525046158	0.374189932208	0.184795928431	0.0244413438757	1.56110161734	0.520123718217	0.30654522202	1.87370515635	0.180541606163	1.59287019446	165.887991094	70.0919085368	68.7632959042

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 31 through 87 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 88 through 247 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 248 through 296 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 297 through 365 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 366 through 430 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 431 through 605 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 606 through 831 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 832 through 908 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 909 through 967 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 33 through 365 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 366 through 605 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 606 through 967 )

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