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- PDB-5vyj: Crystal structure of the photosynthetic phosphoenolpyruvate carbo... -

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Basic information

Entry
Database: PDB / ID: 5vyj
TitleCrystal structure of the photosynthetic phosphoenolpyruvate carboxylase isoenzyme from maize in complex with Gly
ComponentsPhosphoenolpyruvate carboxylase
KeywordsLYASE / PEPC-C4 / C4 metabolism / allosteric activator
Function / homology
Function and homology information


response to cytokinin / phosphoenolpyruvate carboxylase / phosphoenolpyruvate carboxylase activity / response to nitrate / leaf development / response to ammonium ion / apoplast / carbon fixation / photosynthesis / tricarboxylic acid cycle ...response to cytokinin / phosphoenolpyruvate carboxylase / phosphoenolpyruvate carboxylase activity / response to nitrate / leaf development / response to ammonium ion / apoplast / carbon fixation / photosynthesis / tricarboxylic acid cycle / chloroplast / cytosol
Similarity search - Function
Phosphoenolpyruvate/pyruvate domain / 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. / de novo design (two linked rop proteins) / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily ...Phosphoenolpyruvate/pyruvate domain / 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. / de novo design (two linked rop proteins) / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / GLYCINE / Phosphoenolpyruvate carboxylase 1 / phosphoenolpyruvate carboxylase
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsGonzalez-Segura, L. / Guemez-Toro, R. / Munoz-Clares, R.A.
Funding support Mexico, 1items
OrganizationGrant numberCountry
PAPIITIN216911 Mexico
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Identification of the allosteric site for neutral amino acids in the maize C4isozyme of phosphoenolpyruvate carboxylase: The critical role of Ser-100.
Authors: Gonzalez-Segura, L. / Mujica-Jimenez, C. / Juarez-Diaz, J.A. / Guemez-Toro, R. / Martinez-Castilla, L.P. / Munoz-Clares, R.A.
History
DepositionMay 25, 2017Deposition site: RCSB / Processing site: RCSB
SupersessionJun 28, 2017ID: 4UOL
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.2May 23, 2018Group: Data collection / 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jun 13, 2018Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.grant_number
Revision 1.4Jul 11, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.5Oct 4, 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)439,07922
Polymers437,9364
Non-polymers1,14318
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14920 Å2
ΔGint9 kcal/mol
Surface area132420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.950, 167.240, 242.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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 (E. coli) / Strain (production host): BL21 / Variant (production host): RIL
References: UniProt: Q84KR7, UniProt: P04711*PLUS, phosphoenolpyruvate carboxylase
#2: Chemical
ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H5NO2
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H3O2

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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: 3.65 Å3/Da / Density % sol: 66.26 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M SODIUM ACETATE TRIHYDRATE, 0.1 M TRIS HYDROCHLORIDE PH 8.5, 15% (W/V) PEG 4000, 0.1M POTASSIUM/SODIUM TARTRATE-4-HYDRATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.3→57.08 Å / Num. obs: 90116 / % possible obs: 93.2 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.2
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.8 / % possible all: 62.2

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
XDSdata scaling
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JQO

1jqo


Resolution: 3.3→57.079 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2527 4510 5.01 %
Rwork0.2096 --
obs0.2118 89996 93.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.3→57.079 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29262 0 77 0 29339
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00729941
X-RAY DIFFRACTIONf_angle_d1.00140527
X-RAY DIFFRACTIONf_dihedral_angle_d14.63311324
X-RAY DIFFRACTIONf_chiral_restr0.0654473
X-RAY DIFFRACTIONf_plane_restr0.0045299
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3003-3.33780.3631960.30161662X-RAY DIFFRACTION55
3.3378-3.3770.28231130.27751895X-RAY DIFFRACTION63
3.377-3.41820.32021100.2822090X-RAY DIFFRACTION69
3.4182-3.46150.37931090.30542199X-RAY DIFFRACTION74
3.4615-3.5070.32811220.27342415X-RAY DIFFRACTION79
3.507-3.55510.31471260.26822556X-RAY DIFFRACTION84
3.5551-3.60580.28651470.26132642X-RAY DIFFRACTION89
3.6058-3.65970.36161330.32492802X-RAY DIFFRACTION92
3.6597-3.71680.38741550.32572954X-RAY DIFFRACTION97
3.7168-3.77780.29041490.2483035X-RAY DIFFRACTION100
3.7778-3.84290.27191560.24243042X-RAY DIFFRACTION100
3.8429-3.91280.37241550.29972952X-RAY DIFFRACTION97
3.9128-3.9880.29541660.22912994X-RAY DIFFRACTION99
3.988-4.06940.21741430.19723036X-RAY DIFFRACTION100
4.0694-4.15780.23321700.19353017X-RAY DIFFRACTION100
4.1578-4.25450.19411440.18013077X-RAY DIFFRACTION100
4.2545-4.36090.2451480.17963043X-RAY DIFFRACTION100
4.3609-4.47870.20681570.18473053X-RAY DIFFRACTION100
4.4787-4.61050.22361680.18573041X-RAY DIFFRACTION100
4.6105-4.75920.25481630.17313058X-RAY DIFFRACTION100
4.7592-4.92920.21641700.17343037X-RAY DIFFRACTION100
4.9292-5.12650.24931690.17733026X-RAY DIFFRACTION100
5.1265-5.35960.21161740.17863074X-RAY DIFFRACTION100
5.3596-5.6420.24271620.18563063X-RAY DIFFRACTION100
5.642-5.99510.24971640.18473066X-RAY DIFFRACTION100
5.9951-6.45740.22231760.17733080X-RAY DIFFRACTION100
6.4574-7.10610.2251580.1653125X-RAY DIFFRACTION100
7.1061-8.13190.21921480.14593125X-RAY DIFFRACTION100
8.1319-10.23570.14361740.13073128X-RAY DIFFRACTION100
10.2357-57.08730.20441850.19523199X-RAY DIFFRACTION97
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)
10.1904-0.03870.01340.24630.03250.20210.0130.02020.0033-0.18370.03090.08560.2377-0.3053-0.3045-0.2133-0.5936-0.0008-0.54420.17090.122420.9279-77.42070.7206
20.27270.0388-0.00230.2857-0.10420.2523-0.01-0.1788-0.06070.27520.0309-0.1587-0.2975-0.01640.1156-0.0558-0.03470.0404-0.09470.0055-0.103640.6942-29.68517.1472
30.1944-0.06460.14880.49360.06210.44330.047-0.06950.0469-0.0291-0.0373-0.13630.3341-0.1850.04-0.08250.03120.23620.0621-0.14490.028541.9446-53.9988-65.889
40.4568-0.0872-0.3150.44340.14680.6640.00160.212-0.1590.2026-0.13040.1893-0.2087-0.6612-0.3317-0.15940.35860.08460.0588-0.10320.107421.6864-6.4464-49.8963
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 35:970)
2X-RAY DIFFRACTION2(chain B and resseq 36:970)
3X-RAY DIFFRACTION3(chain C and resseq 36:970)
4X-RAY DIFFRACTION4(chain D and resseq 36:970)

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