PDB-4bxh: Resolving the activation site of positive regulators in plant pho...

Basic information

• Entry: Database: PDB / ID: 4bxh
• Title: Resolving the activation site of positive regulators in plant phosphoenolpyruvate carboxylase
• Components: (C4 PHOSPHOENOLPYRUVATE CARBOXYLASE) x 2
• Keywords: LYASE / ALLOSTERIC REGULATION / C4 PHOTOSYNTHETIC PATHWAY / CO2 FIXATION / GLUCOSE 6-PHOSPHATE / SULFATE BINDING SITE

Function / homology

Function:

C4 photosynthesis / phosphoenolpyruvate carboxylase / phosphoenolpyruvate carboxylase activity / leaf development / apoplast / carbon fixation / tricarboxylic acid cycle / chloroplast / cytosol

Domain/homology:

Phosphoenolpyruvate carboxylase, Lys active site / Phosphoenolpyruvate carboxylase / Phosphoenolpyruvate carboxylase, bacterial/plant-type / Phosphoenolpyruvate carboxylase, His active site / Phosphoenolpyruvate carboxylase / Phosphoenolpyruvate carboxylase active site 2. / Phosphoenolpyruvate carboxylase active site 1. / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily

Component:

C4 phosphoenolpyruvate carboxylase

• Biological species: FLAVERIA TRINERVIA (plant)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
• Authors: Schlieper, D. / Foerster, K. / Paulus, J.K. / Groth, G.
• Citation: Journal: Mol.Plant / Year: 2014; Title: Resolving the Activation Site of Positive Regulators in Plant Phosphoenolpyruvate Carboxylase.; Authors: Schlieper, D. / Foerster, K. / Paulus, J.K. / Groth, G.

History

Deposition	Jul 11, 2013	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 2, 2013	Provider: repository / Type: Initial release
Revision 1.1	Dec 4, 2013	Group: Database references / Source and taxonomy / Structure summary
Revision 1.2	Feb 5, 2014	Group: Database references
Revision 1.3	Dec 20, 2023	Group: Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

• Remark 700: SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

Assembly

Deposited unit

A: C4 PHOSPHOENOLPYRUVATE CARBOXYLASE

B: C4 PHOSPHOENOLPYRUVATE CARBOXYLASE

hetero molecules

Summary:

• 227 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	227,412	8
Polymers	226,971	2
Non-polymers	440	6
Water	14,988	832

1

A: C4 PHOSPHOENOLPYRUVATE CARBOXYLASE

B: C4 PHOSPHOENOLPYRUVATE CARBOXYLASE

hetero molecules

A: C4 PHOSPHOENOLPYRUVATE CARBOXYLASE

B: C4 PHOSPHOENOLPYRUVATE CARBOXYLASE

hetero molecules

Summary:

• defined by author
• 455 kDa, 4 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	454,823	16
Polymers	453,942	4
Non-polymers	881	12
Water	72	4

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_655	-x+1,-y,z	1

2

A: C4 PHOSPHOENOLPYRUVATE CARBOXYLASE

hetero molecules

A: C4 PHOSPHOENOLPYRUVATE CARBOXYLASE

hetero molecules

Summary:

• defined by software
• 227 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	227,414	8
Polymers	226,973	2
Non-polymers	440	6
Water	36	2

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_655	-x+1,-y,z	1

Calculated values:

Buried area	7380 Å2
ΔGint	-20.3 kcal/mol
Surface area	69040 Å2
Method	PISA

3

B: C4 PHOSPHOENOLPYRUVATE CARBOXYLASE

hetero molecules

B: C4 PHOSPHOENOLPYRUVATE CARBOXYLASE

hetero molecules

Summary:

• defined by software
• 227 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	227,410	8
Polymers	226,969	2
Non-polymers	440	6
Water	36	2

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_655	-x+1,-y,z	1

Calculated values:

Buried area	7350 Å2
ΔGint	-20.7 kcal/mol
Surface area	69160 Å2
Method	PISA

Unit cell

Length a, b, c (Å)	162.918, 122.857, 131.540
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P21212

Components

#1: Protein

A C4 PHOSPHOENOLPYRUVATE CARBOXYLASE / C4 PEPC / C4 PEPCASE / PPCA / PHOTOSYNTHETIC PEPCASE

Details:

Mass: 113486.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) FLAVERIA TRINERVIA (plant) / Plasmid: PETEV16B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P30694, phosphoenolpyruvate carboxylase

#2: Protein

B C4 PHOSPHOENOLPYRUVATE CARBOXYLASE / C4 PEPC / C4 PEPCASE / PPCA / PHOTOSYNTHETIC PEPCASE

Details:

Mass: 113484.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) FLAVERIA TRINERVIA (plant) / Plasmid: PETEV16B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P30694, phosphoenolpyruvate carboxylase

#3: Chemical

A-1002 A-1003 B-1002 B-1003
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL

Details:

Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆O₂

#4: Chemical

A-1004 B-1004 ChemComp-SO4 / SULFATE ION

Details:

Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄

#5: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 832 / Source method: isolated from a natural source / Formula: H₂O

Experimental details

Experiment

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

Sample preparation

• Crystal: Density Matthews: 2.98 ų/Da / Density % sol: 58.33 % / Description: NONE
• Crystal grow: pH: 5.6 ; Details: 0.1 M TRI-SODIUM CITRATE (PH 5.6/NAOH), 15 % (W/V) PEG4000 AND 0.2 M AMMONIUM SULFATE

Data collection

• Diffraction: Mean temperature: 100 K
• Diffraction source: Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625
• Detector: Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 3, 2012 / Details: MIRRORS
• Radiation: Monochromator: SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 0.97625 Å / Relative weight: 1
• Reflection: Resolution: 2.24→41 Å / Num. obs: 124109 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / B_iso Wilson estimate: 52 Ų / R_merge(I) obs: 0.05 / Net I/σ(I): 12.6
• Reflection shell: Resolution: 2.24→2.36 Å / Redundancy: 4.6 % / R_merge(I) obs: 0.39 / Mean I/σ(I) obs: 2 / % possible all: 99.9

Processing

Software

Name	Version	Classification
REFMAC	5.7.0032	refinement
XDS		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZGE

3zge

Resolution: 2.24→41 Å / Cor.coef. F_o:F_c: 0.962 / Cor.coef. F_o:F_c free: 0.946 / SU B: 9.492 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.203 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.21006	2590	2 %	RANDOM
Rwork	0.17672	-	-	-
obs	0.17741	124109	99.64 %	-

• Solvent computation: Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 45.475 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	3.28 Å2	0 Å2	0 Å2
2-	-	-1.55 Å2	0 Å2
3-	-	-	-1.73 Å2

Refinement step

Cycle: LAST / Resolution: 2.24→41 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14899	0	26	832	15757

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.019	15287
X-RAY DIFFRACTION	r_bond_other_d	0.005	0.02	14688
X-RAY DIFFRACTION	r_angle_refined_deg	1.797	1.971	20682
X-RAY DIFFRACTION	r_angle_other_deg	1.059	3	33810
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.931	5	1864
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.442	23.704	737
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.848	15	2743
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.423	15	128
X-RAY DIFFRACTION	r_chiral_restr	0.1	0.2	2280
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.021	17130
X-RAY DIFFRACTION	r_gen_planes_other	0.005	0.02	3490
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	2.579	2.979	7432
X-RAY DIFFRACTION	r_mcbond_other	2.579	2.979	7431
X-RAY DIFFRACTION	r_mcangle_it	3.688	4.454	9280
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	3.598	3.318	7855
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.24→2.298 Å / Total num. of bins used: 20

	Rfactor	Num. reflection	% reflection
Rfree	0.285	207	-
Rwork	0.246	9046	-
obs	-	-	99.77 %

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	1.5243	-0.6415	0.0606	1.4941	-0.056	0.5922	-0.0767	-0.0876	-0.1617	0.1731	0.0844	-0.1842	0.0562	0.0981	-0.0077	0.0994	-0.0587	-0.0064	0.1818	-0.0143	0.1256	98.216	10.776	101.681
2	0.3765	0.1326	-0.1077	1.0026	-0.5005	0.6609	-0.028	0.0607	-0.0149	-0.1876	0.0225	0.1065	0.0216	-0.0575	0.0055	0.0672	-0.0087	-0.0257	0.1316	0.0268	0.0445	83.426	27.473	79.13
3	1.9775	-0.5265	-0.1699	2.3305	0.0729	1.1301	-0.0483	0.1014	-0.0134	0.0001	-0.0432	-0.3115	-0.1242	0.1721	0.0915	0.0642	-0.0907	-0.0302	0.1939	0.0178	0.0762	111.407	30.236	100.305
4	1.9062	0.6437	0.0071	0.9652	0.0217	0.5563	-0.0613	0.2209	-0.076	-0.1104	0.0608	0.1841	0.0326	-0.1369	0.0005	0.1024	0.0397	0.0099	0.1081	0.0073	0.131	69.024	15.942	135.834
5	0.2482	-0.0712	-0.0189	1.1825	0.5039	0.3924	0.0144	-0.0238	-0.0945	0.1985	0.0308	-0.0767	0.0761	0.0372	-0.0453	0.0498	0.0062	-0.0127	0.018	0.0126	0.0549	88.789	26.579	158.189
6	2.2517	0.6019	-0.4381	1.337	-0.0868	0.9902	-0.0265	0.0537	0.0675	-0.0749	-0.0124	0.2328	-0.1304	-0.1329	0.0389	0.0959	0.079	0.0007	0.0736	0.0151	0.06	63.054	38.517	137.251

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	8 - 230
2	X-RAY DIFFRACTION	2	A	231 - 704
3	X-RAY DIFFRACTION	3	A	705 - 966
4	X-RAY DIFFRACTION	4	B	8 - 230
5	X-RAY DIFFRACTION	5	B	231 - 704
6	X-RAY DIFFRACTION	6	B	705 - 966