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- PDB-6v3o: Crystal structure of the T-state of maize C4-phosphoenolpyruvate ... -

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Basic information

Entry
Database: PDB / ID: 6v3o
TitleCrystal structure of the T-state of maize C4-phosphoenolpyruvate carboxylase in complex with citrate
ComponentsPhosphoenolpyruvate carboxylase
KeywordsLYASE / C4 metabolism / allosteric regulation / R and T states / Plant Protein
Function / homology
Function and homology information


response to cytokinin / phosphoenolpyruvate carboxylase / phosphoenolpyruvate carboxylase activity / response to nitrate / leaf development / response to ammonium ion / carbon fixation / photosynthesis / tricarboxylic acid cycle / cytosol / 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
CITRATE ANION / Phosphoenolpyruvate carboxylase 1 / phosphoenolpyruvate carboxylase
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.909 Å
AuthorsCarrizosa-Carbajal, E.I. / Munoz-Clares, R.A. / Gonzalez-Segura, L.
Funding support Mexico, 1items
OrganizationGrant numberCountry
Programa de Apoyo a Proyectos de Investigacion e Innovacion Tecnologica (PAPIIT)IN227920 Mexico
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: Two new T-state crystal structures of maize C 4 -phosphoenolpyruvate carboxylase reveal and suggest novel structural features of the allosteric regulation and carboxylation step.
Authors: Carrizosa-Carbajal, E.I. / Gonzalez-Segura, L. / Munoz-Clares, R.A.
History
DepositionNov 26, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2023Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2May 17, 2023Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.grant_number
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Sep 11, 2024Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphoenolpyruvate carboxylase
B: Phosphoenolpyruvate carboxylase
C: Phosphoenolpyruvate carboxylase
D: Phosphoenolpyruvate carboxylase
E: Phosphoenolpyruvate carboxylase
F: Phosphoenolpyruvate carboxylase
G: Phosphoenolpyruvate carboxylase
H: Phosphoenolpyruvate carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)879,42439
Polymers875,8728
Non-polymers3,55231
Water1086
1
A: Phosphoenolpyruvate carboxylase
B: Phosphoenolpyruvate carboxylase
C: Phosphoenolpyruvate carboxylase
D: Phosphoenolpyruvate carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)439,77319
Polymers437,9364
Non-polymers1,83715
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15860 Å2
ΔGint-170 kcal/mol
Surface area136390 Å2
MethodPISA
2
E: Phosphoenolpyruvate carboxylase
F: Phosphoenolpyruvate carboxylase
G: Phosphoenolpyruvate carboxylase
H: Phosphoenolpyruvate carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)439,65120
Polymers437,9364
Non-polymers1,71516
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16440 Å2
ΔGint-230 kcal/mol
Surface area135430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.692, 217.976, 173.569
Angle α, β, γ (deg.)90.000, 91.050, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Phosphoenolpyruvate carboxylase


Mass: 109484.016 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: ppc1 / Plasmid: pET32-ZmPEPC-C4 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / Variant (production host): RIL
References: UniProt: Q84KR7, UniProt: P04711*PLUS, phosphoenolpyruvate carboxylase

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Non-polymers , 5 types, 37 molecules

#2: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H5O7
#4: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.04 Å3/Da / Density % sol: 59.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M TRI-SODIUM CITRATE/KOH, 0.2M AMMONIUM SULFATE, 12% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.909→49.2 Å / Num. obs: 225088 / % possible obs: 98.46 % / Redundancy: 3.3 % / CC1/2: 0.65 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.08 / Net I/σ(I): 5.9
Reflection shellResolution: 2.91→3.07 Å / Rmerge(I) obs: 0.523 / Num. unique obs: 103014

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
SCALA3.3.20data scaling
PHASER2.5.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6U2T

6u2t


Resolution: 2.909→49.198 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2495 11280 5.01 %
Rwork0.2184 213771 -
obs0.2199 225051 98.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 124.39 Å2 / Biso mean: 60.6344 Å2 / Biso min: 34.53 Å2
Refinement stepCycle: final / Resolution: 2.909→49.198 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms59474 0 208 6 59688
Biso mean--69.8 44.57 -
Num. residues----7480
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.909-2.94210.37153060.3193573779
2.9421-2.97670.3363910.27557121100
2.9767-3.0130.32613780.27227228100
3.013-3.05110.30893460.2696722599
3.0511-3.09130.29753530.2588717099
3.0913-3.13360.31283810.2637721499
3.1336-3.17840.29514080.2648711099
3.1784-3.22580.33333900.2703709899
3.2258-3.27620.29223560.2642720998
3.2762-3.32990.32073920.2636703898
3.3299-3.38730.2893380.2582707198
3.3873-3.44890.29483830.2583706597
3.4489-3.51520.29773810.2521707898
3.5152-3.58690.27073580.23547174100
3.5869-3.66490.25334170.2327161100
3.6649-3.75010.2553950.23257247100
3.7501-3.84390.28273610.23367222100
3.8439-3.94780.2513660.2317263100
3.9478-4.06390.25113590.21827194100
4.0639-4.1950.24753900.21637200100
4.195-4.34480.24174140.209717899
4.3448-4.51870.25913620.21017215100
4.5187-4.72420.24513880.2064716699
4.7242-4.9730.24413400.2023713698
4.973-5.28430.22053870.2063704697
5.2843-5.69170.24623930.21057248100
5.6917-6.26350.23823840.22087252100
6.2635-7.16740.2213950.19537253100
7.1674-9.02110.16073570.1529725699
9.0211-49.1980.16474110.1511719698

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