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Basic information

Entry
Database: PDB / ID: 4bxc
TitleResolving the activation site of positive regulators in plant phosphoenolpyruvate carboxylase
ComponentsC4 PHOSPHOENOLPYRUVATE CARBOXYLASE
KeywordsLYASE / ALLOSTERIC REGULATION / C4 PHOTOSYNTHETIC PATHWAY / CO2 FIXATION / SULFATE BINDING SITE
Function / homology
Function and homology information


C4 photosynthesis / phosphoenolpyruvate carboxylase / phosphoenolpyruvate carboxylase activity / carbon fixation / tricarboxylic acid cycle / cytoplasm
Similarity search - Function
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
Similarity search - Domain/homology
6-O-phosphono-alpha-D-glucopyranose / C4 phosphoenolpyruvate carboxylase
Similarity search - Component
Biological speciesFlaveria trinervia (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.86 Å
AuthorsSchlieper, D. / Foerster, K. / Paulus, J.K. / Groth, G.
CitationJournal: 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
DepositionJul 10, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2013Group: Derived calculations / Other
Revision 1.2Feb 5, 2014Group: Database references
Revision 1.3Jul 1, 2015Group: Data collection
Revision 1.4Mar 7, 2018Group: Data collection / Source and taxonomy / Category: diffrn_source / entity_src_gen
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_gene_src_scientific_name ..._diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.5Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.6Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... 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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: C4 PHOSPHOENOLPYRUVATE CARBOXYLASE
B: C4 PHOSPHOENOLPYRUVATE CARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,9329
Polymers226,9732
Non-polymers9597
Water23413
1
A: C4 PHOSPHOENOLPYRUVATE CARBOXYLASE
B: C4 PHOSPHOENOLPYRUVATE CARBOXYLASE
hetero molecules

A: C4 PHOSPHOENOLPYRUVATE CARBOXYLASE
B: C4 PHOSPHOENOLPYRUVATE CARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)455,86418
Polymers453,9464
Non-polymers1,91714
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area14000 Å2
ΔGint26 kcal/mol
Surface area167420 Å2
MethodPISA
2
B: C4 PHOSPHOENOLPYRUVATE CARBOXYLASE
hetero molecules

B: C4 PHOSPHOENOLPYRUVATE CARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,8108
Polymers226,9732
Non-polymers8376
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area7590 Å2
ΔGint-25.8 kcal/mol
Surface area69320 Å2
MethodPISA
3
A: C4 PHOSPHOENOLPYRUVATE CARBOXYLASE
hetero molecules

A: C4 PHOSPHOENOLPYRUVATE CARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,05410
Polymers226,9732
Non-polymers1,0818
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area8060 Å2
ΔGint-15.5 kcal/mol
Surface area68310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.413, 121.232, 132.186
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein C4 PHOSPHOENOLPYRUVATE CARBOXYLASE / C4 PEPC / C4 PEPCASE / PPCA / PHOTOSYNTHETIC PEPCASE


Mass: 113486.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flaveria trinervia (plant) / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P30694, phosphoenolpyruvate carboxylase
#2: Sugar ChemComp-G6P / 6-O-phosphono-alpha-D-glucopyranose / ALPHA-D-GLUCOSE-6-PHOSPHATE / 6-O-phosphono-alpha-D-glucose / 6-O-phosphono-D-glucose / 6-O-phosphono-glucose


Type: D-saccharide, alpha linking / Mass: 260.136 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
a-D-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 18 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.15 Å3/Da / Density % sol: 61 % / Description: NONE
Crystal growpH: 5.6
Details: 0.1 M TRI-SODIUM CITRATE (PH 5.6/NAOH), 15 % (W/V) PEG4000 AND 0.2 M AMMONIUM SULFATE; SOAKED WITH 200 MM GLUCOSE 6-PHOSPHATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1.23953
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.23953 Å / Relative weight: 1
ReflectionResolution: 2.84→51.9 Å / Num. obs: 60347 / % possible obs: 99.7 % / Observed criterion σ(I): 1.9 / Redundancy: 6.6 % / Biso Wilson estimate: 74.3 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.4
Reflection shellResolution: 2.84→2.99 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 1.9 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZGE

3zge


Resolution: 2.86→50.68 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.936 / SU B: 29.512 / SU ML: 0.253 / Cross valid method: THROUGHOUT / ESU R: 2.487 / ESU R Free: 0.316 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.22067 1257 2 %RANDOM
Rwork0.18403 ---
obs0.18478 60347 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 71.067 Å2
Baniso -1Baniso -2Baniso -3
1-3.86 Å20 Å20 Å2
2---2.22 Å20 Å2
3----1.64 Å2
Refinement stepCycle: LAST / Resolution: 2.86→50.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14846 0 58 13 14917
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01915207
X-RAY DIFFRACTIONr_bond_other_d0.0040.0214518
X-RAY DIFFRACTIONr_angle_refined_deg1.6191.97420571
X-RAY DIFFRACTIONr_angle_other_deg0.918333405
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4651842
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.31423.678726
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.491152674
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.02715127
X-RAY DIFFRACTIONr_chiral_restr0.0820.22280
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02116969
X-RAY DIFFRACTIONr_gen_planes_other0.0030.023454
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8813.9397415
X-RAY DIFFRACTIONr_mcbond_other2.883.9387414
X-RAY DIFFRACTIONr_mcangle_it4.5685.8899238
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.5194.3197792
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.86→2.934 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 102 -
Rwork0.277 4409 -
obs--99.69 %
Refinement TLS params.

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

IDL11 (°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)
12.3793-0.3812-0.03581.10130.3030.4752-0.0645-0.2420.30710.19750.02830.26410.0385-0.12990.03620.4401-0.0639-0.04030.0991-0.0040.3341-12.502-15.59961.897
20.50380.1042-0.07532.02781.16151.06250.04760.11070.2498-0.29580.0464-0.1701-0.24-0.0104-0.09390.28720.00860.01680.05880.05970.16897.42-26.72839.346
33.7374-1.24570.91161.9083-0.34961.5389-0.17460.12870.09980.07910.00480.2780.2855-0.07650.16980.3928-0.11480.02540.03830.00550.0876-18.688-38.20359.093
41.62910.5575-0.54191.8368-0.30780.7023-0.0372-0.00970.3774-0.22040.1226-0.31320.07010.1057-0.08550.41590.1318-0.00620.3288-0.07810.372316.865-10.46695.214
50.9895-0.1874-0.13441.8022-1.10811.9325-0.0369-0.1010.11060.2296-0.02330.1443-0.1380.1020.06030.29750.04150.04570.18510.04480.09872.237-27.534117.798
63.66621.0287-0.04013.66650.2041.886-0.1804-0.47860.064-0.0094-0.089-0.52690.30640.34220.26940.30590.23240.08010.33730.03780.159330.561-29.34197.691
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 226
2X-RAY DIFFRACTION2A229 - 707
3X-RAY DIFFRACTION3A708 - 966
4X-RAY DIFFRACTION4B7 - 226
5X-RAY DIFFRACTION5B229 - 704
6X-RAY DIFFRACTION6B705 - 966

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