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- PDB-6u2t: Crystal structure of the T-state of maize C4-phosphoenolpyruvate ... -

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Basic information

Entry
Database: PDB / ID: 6u2t
TitleCrystal structure of the T-state of maize C4-phosphoenolpyruvate carboxylase in complex with malate
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 / tricarboxylic acid cycle / photosynthesis / 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
D-MALATE / Phosphoenolpyruvate carboxylase 1 / phosphoenolpyruvate carboxylase
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsCarrizosa-Carbajal, E.l. / Munoz-Clares, R.A. / Gonzalez-Segura, L.
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
DepositionAug 20, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Sep 11, 2024Group: Database references / Category: citation / citation_author
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 / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoenolpyruvate carboxylase
B: Phosphoenolpyruvate carboxylase
C: Phosphoenolpyruvate carboxylase
D: Phosphoenolpyruvate carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)439,62120
Polymers437,9364
Non-polymers1,68516
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14630 Å2
ΔGint-204 kcal/mol
Surface area132630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.940, 140.931, 376.401
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Phosphoenolpyruvate carboxylase


Mass: 109484.016 Da / Num. of mol.: 4
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
#2: Chemical
ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6O5
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
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: 3.15 Å3/Da / Density % sol: 60.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M TRI-SODIUM CITRATE//KOH, 0.2M AMMONIUM SULFATE, 14% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.8→188.201 Å / Num. all: 129366 / Num. obs: 129366 / % possible obs: 95.3 % / Redundancy: 3.6 % / Biso Wilson estimate: 56.79 Å2 / Rpim(I) all: 0.046 / Rrim(I) all: 0.095 / Rsym value: 0.082 / Net I/av σ(I): 7.3 / Net I/σ(I): 10.5 / Num. measured all: 471354
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.8-2.953.60.4041.867401187540.2260.4660.4043.295.5
2.95-3.133.40.2792.561214179660.1610.3240.2794.396.3
3.13-3.353.80.1823.763487168970.0980.2080.1826.596.4
3.35-3.613.70.1245.358572157450.0680.1420.1249.396.4
3.61-3.963.60.097.352663144570.0510.1030.0912.296
3.96-4.433.60.0689.546764129800.0380.0790.06815.595
4.43-5.113.80.0581143777114520.0320.0660.05817.794.7
5.11-6.263.60.0610.83408495850.0340.0690.0614.493.2
6.26-8.853.90.04214.22876674270.0230.0480.04218.892.8
8.85-48.3563.60.03514.21462641030.0210.040.03525.690.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.8 Å48.36 Å
Translation2.8 Å48.36 Å

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
SCALA3.3.20data scaling
PHASER2.5.1phasing
PDB_EXTRACT3.25data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VYJ

5vyj


Resolution: 2.8→48.356 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2256 6535 5.06 %RANDOM
Rwork0.1826 122719 --
obs0.1848 129254 94.51 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 132.48 Å2 / Biso mean: 54.4582 Å2 / Biso min: 22.11 Å2
Refinement stepCycle: final / Resolution: 2.8→48.356 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29172 0 97 57 29326
Biso mean--83.3 40.41 -
Num. residues----3671
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8002-2.8320.33912170.2776381189
2.832-2.86530.31652240.2527412197
2.8653-2.90020.27482080.2343412897
2.9002-2.93690.29612110.2335414997
2.9369-2.97560.30172390.2326414097
2.9756-3.01630.28692290.2292407696
3.0163-3.05940.28142000.223417096
3.0594-3.10510.312380.238397895
3.1051-3.15360.28832120.2424412696
3.1536-3.20530.29882280.2302411096
3.2053-3.26050.26162060.2208414296
3.2605-3.31980.27072230.2044407996
3.3198-3.38360.26112050.2045413896
3.3836-3.45270.24062020.1987416896
3.4527-3.52770.252100.2055411896
3.5277-3.60980.2722140.1971412896
3.6098-3.70.24472310.197411496
3.7-3.80.23542300.1795410095
3.8-3.91180.24122430.1769409196
3.9118-4.0380.19562160.1736407695
4.038-4.18220.20822220.1634408494
4.1822-4.34960.21592140.1584410495
4.3496-4.54740.18521950.1544410494
4.5474-4.7870.18372040.1505408194
4.787-5.08660.18832160.1529408394
5.0866-5.47880.21222070.1638411993
5.4788-6.02920.2351890.1779403792
6.0292-6.89950.19712370.1814401492
6.8995-8.68450.182210.1459407491
8.6845-48.3560.16172440.1542405688

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