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- PDB-5fdn: Crystal structure of phosphoenolpyruvate carboxylase from Arabido... -

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Basic information

Entry
Database: PDB / ID: 5fdn
TitleCrystal structure of phosphoenolpyruvate carboxylase from Arabidopsis thaliana in complex with aspartate and citrate
ComponentsPhosphoenolpyruvate carboxylase 3
KeywordsLYASE / Carboxylase Inhibitor PEPC Functional tetramer
Function / homology
Function and homology information


phosphoenolpyruvate carboxylase / phosphoenolpyruvate carboxylase activity / leaf development / carbon fixation / apoplast / photosynthesis / tricarboxylic acid cycle / chloroplast / cytosol
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
ASPARTIC ACID / CITRATE ANION / Phosphoenolpyruvate carboxylase 3
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsConnell, M.B. / Lee, M.J.Y. / Plaxton, W.C. / Jia, Z.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN203705-2013 Canada
CitationJournal: To Be Published
Title: Crystal structure of phosphoenolpyruvate carboxylase from Arabidopsis thaliana in complex with aspartate and citrate
Authors: Connell, M.B. / Lee, M.J.Y. / Plaxton, W.C. / Jia, Z.
History
DepositionDec 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphoenolpyruvate carboxylase 3
B: Phosphoenolpyruvate carboxylase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,3226
Polymers224,6782
Non-polymers6444
Water28,8421601
1
A: Phosphoenolpyruvate carboxylase 3
B: Phosphoenolpyruvate carboxylase 3
hetero molecules

A: Phosphoenolpyruvate carboxylase 3
B: Phosphoenolpyruvate carboxylase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)450,64512
Polymers449,3564
Non-polymers1,2898
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x+1/2,-y+1/2,z1
Unit cell
Length a, b, c (Å)264.260, 268.130, 77.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-1129-

HOH

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Components

#1: Protein Phosphoenolpyruvate carboxylase 3 / / PEPCase 3


Mass: 112338.984 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PPC3, PEPC, PPC, At3g14940, K15M2.8 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q84VW9, phosphoenolpyruvate carboxylase
#2: Chemical ChemComp-ASP / ASPARTIC ACID / Aspartic acid


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H7NO4
#3: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1601 / 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: 3.07 Å3/Da / Density % sol: 59.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 6% PEG 6000, 100 mM sodium citrate pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03323 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03323 Å / Relative weight: 1
ReflectionResolution: 2.2→48.87 Å / Num. obs: 140308 / % possible obs: 100 % / Redundancy: 7.4 % / Rsym value: 0.076 / Net I/σ(I): 19.41
Reflection shellResolution: 2.2→2.5 Å / Redundancy: 7.52 % / Rmerge(I) obs: 0.239 / Mean I/σ(I) obs: 8.48 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
Blu-Icedata collection
XDSdata reduction
PHASERphasing
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→48.87 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1925 2013 1.43 %
Rwork0.1731 --
obs0.1734 140290 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→48.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14573 0 44 1601 16218
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00814911
X-RAY DIFFRACTIONf_angle_d0.94720176
X-RAY DIFFRACTIONf_dihedral_angle_d13.9259062
X-RAY DIFFRACTIONf_chiral_restr0.0482234
X-RAY DIFFRACTIONf_plane_restr0.0052620
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2550.22281500.19689770X-RAY DIFFRACTION100
2.255-2.3160.23311370.19529807X-RAY DIFFRACTION100
2.316-2.38420.20591410.19279759X-RAY DIFFRACTION100
2.3842-2.46110.25671430.19179818X-RAY DIFFRACTION100
2.4611-2.54910.26561420.19179782X-RAY DIFFRACTION100
2.5491-2.65110.1951460.18849798X-RAY DIFFRACTION100
2.6511-2.77180.25131410.18749826X-RAY DIFFRACTION100
2.7718-2.91790.21421440.18619846X-RAY DIFFRACTION100
2.9179-3.10070.19421410.18389849X-RAY DIFFRACTION100
3.1007-3.340.19771460.17599862X-RAY DIFFRACTION100
3.34-3.6760.20951430.16549901X-RAY DIFFRACTION100
3.676-4.20770.15491440.14829924X-RAY DIFFRACTION100
4.2077-5.30030.14591440.14610017X-RAY DIFFRACTION100
5.3003-48.88130.15611510.171910318X-RAY DIFFRACTION100

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