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- PDB-6mgi: Photosynthetic phosphoenolpyruvate carboxylase isoenzyme from mai... -

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Basic information

Entry
Database: PDB / ID: 6mgi
TitlePhotosynthetic phosphoenolpyruvate carboxylase isoenzyme from maize complexed with the allosteric activator glucose-6-phosphate in its allosteric site
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 / carbon fixation / photosynthesis / tricarboxylic acid cycle / 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
6-O-phosphono-alpha-D-glucopyranose / GLYCINE / 2-PHOSPHOGLYCOLIC ACID / Phosphoenolpyruvate carboxylase 1 / phosphoenolpyruvate carboxylase
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.986 Å
AuthorsGonzalez-Segura, L. / Munoz-Clares, R.A.
Funding support Mexico, 1items
OrganizationGrant numberCountry
Programa de Apoyo a Proyectos de Investigacion e Innovacion TecnologicaIN216911 Mexico
CitationJournal: Biochem.J. / Year: 2020
Title: Structural and biochemical evidence of the glucose 6-phosphate-allosteric site of maize C4-phosphoenolpyruvate carboxylase: its importance in the overall enzyme kinetics.
Authors: Munoz-Clares, R.A. / Gonzalez-Segura, L. / Juarez-Diaz, J.A. / Mujica-Jimenez, C.
History
DepositionSep 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Author supporting evidence / Data collection / Derived calculations
Category: pdbx_audit_support / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_assembly_prop.value ..._pdbx_audit_support.funding_organization / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.matrix[1][1] / _pdbx_struct_oper_list.matrix[2][2] / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.vector[1] / _pdbx_struct_oper_list.vector[3]
Revision 1.2Jun 24, 2020Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / 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_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 11, 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,50716
Polymers218,9682
Non-polymers1,53914
Water37821
1
A: Phosphoenolpyruvate carboxylase
B: Phosphoenolpyruvate carboxylase
hetero molecules

A: Phosphoenolpyruvate carboxylase
B: Phosphoenolpyruvate carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)441,01432
Polymers437,9364
Non-polymers3,07828
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area23590 Å2
ΔGint41 kcal/mol
Surface area129170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.087, 170.679, 244.622
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Phosphoenolpyruvate carboxylase /


Mass: 109484.016 Da / Num. of mol.: 2
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
#3: 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 , 5 types, 33 molecules

#2: Chemical ChemComp-GLY / GLYCINE / Glycine


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5NO2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PGA / 2-PHOSPHOGLYCOLIC ACID


Mass: 156.031 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5O6P
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 3.63 Å3/Da / Density % sol: 66.09 %
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: 19-ID / Wavelength: 0.9792372 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792372 Å / Relative weight: 1
ReflectionResolution: 2.986→29.618 Å / Num. obs: 62876 / % possible obs: 97.11 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 12.1
Reflection shellResolution: 2.986→3.15 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.506 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 8596 / % possible all: 97.11

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VYJ

5vyj


Resolution: 2.986→29.618 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.65
RfactorNum. reflection% reflection
Rfree0.2435 3167 5.04 %
Rwork0.2083 --
obs0.21 62789 97.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.986→29.618 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14563 0 96 21 14680
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00314955
X-RAY DIFFRACTIONf_angle_d0.5720242
X-RAY DIFFRACTIONf_dihedral_angle_d3.819080
X-RAY DIFFRACTIONf_chiral_restr0.0382243
X-RAY DIFFRACTIONf_plane_restr0.0042628
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9862-3.03070.381180.34591965X-RAY DIFFRACTION75
3.0307-3.0780.37811310.31842618X-RAY DIFFRACTION99
3.078-3.12840.34221510.30642573X-RAY DIFFRACTION99
3.1284-3.18230.35941290.29452657X-RAY DIFFRACTION99
3.1823-3.24010.32781390.28312580X-RAY DIFFRACTION99
3.2401-3.30240.30291490.28492602X-RAY DIFFRACTION99
3.3024-3.36970.31781370.25912629X-RAY DIFFRACTION99
3.3697-3.44280.31351250.25552614X-RAY DIFFRACTION99
3.4428-3.52280.29641460.25082611X-RAY DIFFRACTION99
3.5228-3.61070.29621210.2312631X-RAY DIFFRACTION98
3.6107-3.70820.26751470.22272627X-RAY DIFFRACTION98
3.7082-3.81710.25221270.22122624X-RAY DIFFRACTION99
3.8171-3.940.24261400.21292618X-RAY DIFFRACTION99
3.94-4.08050.24351370.20012623X-RAY DIFFRACTION98
4.0805-4.24340.2091420.18662598X-RAY DIFFRACTION98
4.2434-4.4360.20641370.17732606X-RAY DIFFRACTION98
4.436-4.6690.22971500.18522611X-RAY DIFFRACTION98
4.669-4.96020.1821310.17642634X-RAY DIFFRACTION98
4.9602-5.34120.22811460.18432605X-RAY DIFFRACTION98
5.3412-5.87490.22511450.18862613X-RAY DIFFRACTION97
5.8749-6.71630.23871500.19292631X-RAY DIFFRACTION97
6.7163-8.42940.16861270.15752638X-RAY DIFFRACTION96
8.4294-29.61950.17871420.15372714X-RAY DIFFRACTION96

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