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- PDB-6h7g: Crystal structure of redox-sensitive phosphoribulokinase (PRK) fr... -

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Basic information

Entry
Database: PDB / ID: 6h7g
TitleCrystal structure of redox-sensitive phosphoribulokinase (PRK) from the green algae Chlamydomonas reinhardtii
ComponentsPhosphoribulokinase, chloroplastic
KeywordsPHOTOSYNTHESIS / Transferase / ATP binding / kinase activity
Function / homology
Function and homology information


phosphoribulokinase / phosphoribulokinase activity / supramolecular complex / stromule / reductive pentose-phosphate cycle / response to cold / chloroplast / disordered domain specific binding / phosphorylation / enzyme binding ...phosphoribulokinase / phosphoribulokinase activity / supramolecular complex / stromule / reductive pentose-phosphate cycle / response to cold / chloroplast / disordered domain specific binding / phosphorylation / enzyme binding / protein homodimerization activity / ATP binding
Similarity search - Function
Phosphoribulokinase signature. / Phosphoribulokinase / Phosphoribulokinase/uridine kinase / Phosphoribulokinase / Uridine kinase family / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Phosphoribulokinase, chloroplastic
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsFermani, S. / Sparla, F. / Gurrieri, L. / Demitri, N. / Polentarutti, M. / Falini, G. / Trost, P. / Lemaire, S.D.
Funding support Italy, 1items
OrganizationGrant numberCountry
FARB2012-University of Bologna Italy
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: ArabidopsisandChlamydomonasphosphoribulokinase crystal structures complete the redox structural proteome of the Calvin-Benson cycle.
Authors: Gurrieri, L. / Del Giudice, A. / Demitri, N. / Falini, G. / Pavel, N.V. / Zaffagnini, M. / Polentarutti, M. / Crozet, P. / Marchand, C.H. / Henri, J. / Trost, P. / Lemaire, S.D. / Sparla, F. / Fermani, S.
History
DepositionJul 31, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.title
Revision 1.2Apr 24, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 17, 2024Group: 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

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Assembly

Deposited unit
A: Phosphoribulokinase, chloroplastic
B: Phosphoribulokinase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,8194
Polymers77,6272
Non-polymers1922
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, The assembly was also confirmed by gel filtration and DLS (Rh about 4.5)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-30 kcal/mol
Surface area29330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.679, 83.549, 133.146
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 Phosphoribulokinase, chloroplastic / / PRKase / Phosphopentokinase


Mass: 38813.543 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: PRKA / Organ: chloroplast / Plasmid: pET-28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P19824, phosphoribulokinase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.65 Å3/Da / Density % sol: 53.6 % / Description: needle-like
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 22 % w/v PEG MME 5K, 0.1 M MES, pH 6.5, 0.2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.24 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 15, 2015
RadiationMonochromator: Si(111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.24 Å / Relative weight: 1
ReflectionResolution: 2.6→44.38 Å / Num. obs: 27230 / % possible obs: 99.6 % / Observed criterion σ(F): 3 / Redundancy: 5.1 % / Biso Wilson estimate: 58.95 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 13.6
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3280 / CC1/2: 0.743 / Rsym value: 0.77 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B3F
Resolution: 2.6→39.859 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.86
RfactorNum. reflection% reflection
Rfree0.2619 1378 5.07 %
Rwork0.2272 --
obs0.2291 27162 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→39.859 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5319 0 10 31 5360
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045442
X-RAY DIFFRACTIONf_angle_d0.9157349
X-RAY DIFFRACTIONf_dihedral_angle_d4.1743307
X-RAY DIFFRACTIONf_chiral_restr0.052802
X-RAY DIFFRACTIONf_plane_restr0.006948
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6001-2.6930.33881440.31282522X-RAY DIFFRACTION100
2.693-2.80080.351400.32392552X-RAY DIFFRACTION100
2.8008-2.92820.36761350.33142529X-RAY DIFFRACTION99
2.9282-3.08250.27831440.28132566X-RAY DIFFRACTION100
3.0825-3.27560.32311150.26322565X-RAY DIFFRACTION100
3.2756-3.52830.29111390.25612570X-RAY DIFFRACTION100
3.5283-3.88310.26811220.22962550X-RAY DIFFRACTION98
3.8831-4.44440.25931580.20262559X-RAY DIFFRACTION99
4.4444-5.5970.21561280.18742634X-RAY DIFFRACTION99
5.597-39.86340.21421530.18962737X-RAY DIFFRACTION99

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