PDB-8ojf: Arabidopsis thaliana Phosphoenolpyruvate carboxylase PPC1 with bo...

ID or keywords:

Entry

Database: PDB / ID: 8ojf

Title

Arabidopsis thaliana Phosphoenolpyruvate carboxylase PPC1 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 /

carbon fixation /

apoplast / 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: 3.0368376252 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	May 31, 2023	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8ojf.cif.gz	871.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8ojf.ent.gz	614.7 KB	Display	PDB format
PDBx/mmJSON format	8ojf.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oj/8ojf ftp://data.pdbj.org/pub/pdb/validation_reports/oj/8ojf	HTTPS FTP

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Related structure data

Related structure data	8cj5C 8cj8C 8oj9C 8ojeC 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) #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)	127.220, 158.170, 141.020
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:

Dom-ID	Component-ID	Ens-ID	Selection details	Auth asym-ID	Auth seq-ID
1	1	1	(chain 'A' and (resid 33 through 121 or resid 137...	A	33 - 121
1	2	1	(chain 'A' and (resid 33 through 121 or resid 137...	A	137 - 300
1	3	1	(chain 'A' and (resid 33 through 121 or resid 137...	A	302 - 604
1	4	1	(chain 'A' and (resid 33 through 121 or resid 137...	A	607 - 756
1	5	1	(chain 'A' and (resid 33 through 121 or resid 137...	A	764 - 794
1	6	1	(chain 'A' and (resid 33 through 121 or resid 137...	A	796 - 873
1	7	1	(chain 'A' and (resid 33 through 121 or resid 137...	A	887 - 916
1	8	1	(chain 'A' and (resid 33 through 121 or resid 137...	A	930 - 967
2	9	1	(chain 'B' and (resid 33 or (resid 34 through 35...	B	33 - 121
2	10	1	(chain 'B' and (resid 33 or (resid 34 through 35...	B	137 - 300
2	11	1	(chain 'B' and (resid 33 or (resid 34 through 35...	B	302 - 604
2	12	1	(chain 'B' and (resid 33 or (resid 34 through 35...	B	607 - 756
2	13	1	(chain 'B' and (resid 33 or (resid 34 through 35...	B	764 - 794
2	14	1	(chain 'B' and (resid 33 or (resid 34 through 35...	B	796 - 873
2	15	1	(chain 'B' and (resid 33 or (resid 34 through 35...	B	887 - 916
2	16	1	(chain 'B' and (resid 33 or (resid 34 through 35...	B	930 - 967

#1: Protein	Phosphoenolpyruvate carboxylase 1 / / AtPPC1 / PEPC 1 / PEPCase 1 / 107-kDa PEPC polypeptide Mass: 111398.164 Da / Num. of mol.: 2 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 / Phosphate Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 18 / 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: 3.18 Å³/Da / Density % sol: 61.37 %
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

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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 18, 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: 3.029→48.8 Å / Num. obs: 55586 / % possible obs: 99.8 % / Redundancy: 13.74 % / B_iso Wilson estimate: 114.572419455 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.152 / Net I/σ(I): 10.86
Reflection shell	Resolution: 3.029→3.22 Å / Redundancy: 13.96 % / R_merge(I) obs: 2.63 / Num. unique obs: 8756 / CC_1/2: 0.36 / % possible all: 89.9

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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: 3.0368376252→48.7063417119 Å / SU ML: 0.48126573983 / Cross valid method: FREE R-VALUE / σ(F): 1.33789407038 / Phase error: 28.2293480275
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.242683220805	2774	5.00252470605 %
R_work	0.202838068279	52678	-
obs	0.20485384429	55452	99.7391945609 %

Solvent computation

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

Displacement parameters

B_iso mean: 137.299495629 Å²

Refinement step

Cycle: LAST / Resolution: 3.0368376252→48.7063417119 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14334	0	17	18	14369

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.00622026349698	14683
X-RAY DIFFRACTION	f_angle_d	0.878339136228	19900
X-RAY DIFFRACTION	f_chiral_restr	0.0496529516366	2203
X-RAY DIFFRACTION	f_plane_restr	0.00583744075515	2584
X-RAY DIFFRACTION	f_dihedral_angle_d	15.685314078	8898

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 (%)
3.0368376252-3.0892	0.434829121564	132	0.400023017142	2485	X-RAY DIFFRACTION	95.3022578296
3.0892-3.1454	0.40985502996	136	0.37032480568	2587	X-RAY DIFFRACTION	99.9632892805
3.1454-3.2058	0.320530549471	138	0.324816230291	2614	X-RAY DIFFRACTION	99.9636759898
3.2058-3.2713	0.364110426927	138	0.301480225838	2616	X-RAY DIFFRACTION	100
3.2713-3.3424	0.326880497074	137	0.291333066512	2604	X-RAY DIFFRACTION	99.9635302699
3.3424-3.4201	0.301996614869	136	0.28622227828	2590	X-RAY DIFFRACTION	100
3.4201-3.5056	0.321296307154	138	0.280963783052	2629	X-RAY DIFFRACTION	99.9638728324
3.5056-3.6004	0.269442134498	138	0.255857410939	2612	X-RAY DIFFRACTION	100
3.6004-3.7063	0.273042895296	138	0.22544965164	2615	X-RAY DIFFRACTION	99.9274047187
3.7063-3.8259	0.300262520874	137	0.229832379383	2612	X-RAY DIFFRACTION	100
3.8259-3.9625	0.255871178627	138	0.213240331433	2628	X-RAY DIFFRACTION	100
3.9625-4.1211	0.25628525511	138	0.192097724952	2623	X-RAY DIFFRACTION	100
4.1211-4.3086	0.202629913932	139	0.178296059009	2630	X-RAY DIFFRACTION	100
4.3086-4.5356	0.215133697348	139	0.169160208003	2647	X-RAY DIFFRACTION	100
4.5356-4.8195	0.192696277543	139	0.159537777314	2636	X-RAY DIFFRACTION	100
4.8195-5.1912	0.237922371492	140	0.168546256398	2651	X-RAY DIFFRACTION	100
5.1912-5.7129	0.26067068819	140	0.194720057708	2664	X-RAY DIFFRACTION	100
5.7129-6.5379	0.256098817781	141	0.205960416972	2690	X-RAY DIFFRACTION	100
6.5379-8.2306	0.199667083976	143	0.182174723939	2717	X-RAY DIFFRACTION	100
8.2306-48.70633	0.215162984338	149	0.184389600271	2828	X-RAY DIFFRACTION	99.6652159357

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	0.758680586947	-0.278862613022	-0.33105869481	1.06902801938	0.0859364181906	0.515414329535	-0.0153827459458	-0.383670340918	-0.0643951973051	0.342005351926	-0.0434729664092	0.238866039303	0.0856043055645	-0.0708981032049	0.0610908834331	1.00626508959	-0.0712504438756	-0.0473908257932	0.954751599264	0.0645261607994	0.831327656663	124.750305721	58.5035908194	167.577170789
2	1.20245593669	-0.189854884807	-0.305802823167	2.06893360233	0.184557509863	0.459572883534	0.0653057863719	0.0050168992269	-0.0716678148276	-0.0427060054845	-0.00223233102792	-0.172901935699	0.104871965551	-0.0481761264951	-0.0525909947897	0.799197204957	-0.0450777425045	-0.0599511283289	0.77493010995	0.0221999773375	0.774059135141	146.939405147	63.0337879852	144.136722939
3	2.58592340454	0.0112488068845	0.210188497561	1.27023502032	-0.128235440084	0.935861973049	0.0927898243136	-0.210966281754	-0.46712917889	0.249821995066	-0.0915476149715	-0.18232744583	0.393096016235	0.138259317511	0.0309184294669	0.998275744131	-0.0723055014717	-0.1497524884	0.807835424081	0.216405096505	1.04710297674	132.76428516	36.809126951	162.928850831
4	0.547093567729	-0.502056377699	-0.348463365911	0.806981408652	-0.283128969435	1.06648166989	0.571645745826	0.963038152529	0.201537394962	-1.02207612412	-0.64419511184	-0.386442725653	-0.123035696734	0.360101220511	0.0972394081398	1.65752982032	0.395908476747	0.167737494868	1.93830224517	0.35313772486	1.47111760556	147.586792037	83.2439738451	63.6149062779
5	2.17886047227	-1.15815478297	0.251300691045	2.00270688285	-0.463586501266	1.22786052786	0.289917058321	0.309495508511	-0.127307996381	0.0677955926901	-0.430749207937	0.0479318251863	0.165782599947	0.182926524812	0.131756695548	1.13747267252	0.0295745772676	0.000450660339309	1.1546205927	-0.0478313150322	1.02335932462	142.164745764	61.4235248538	90.9584363857
6	0.674111599184	0.265274388888	-0.0366350783373	0.673365828992	-0.786518732554	1.0583458884	0.275885513388	0.923467277599	0.229973876235	-0.566069703956	-0.304382758096	-1.00825573109	0.257570212158	0.69101726601	0.00106208107933	1.36907993346	0.40358005947	0.352551188926	2.21472974143	0.227355696466	1.78997850844	165.28724729	70.2375938886	68.5947576147

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 31 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 605 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 606 through 967 )

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