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- PDB-6kev: Reduced phosphoribulokinase from Synechococcus elongatus PCC 7942... -

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Basic information

Entry
Database: PDB / ID: 6kev
TitleReduced phosphoribulokinase from Synechococcus elongatus PCC 7942 complexed with adenosine diphosphate and glucose 6-phosphate
ComponentsPhosphoribulokinase
KeywordsTRANSFERASE / phosphoribulokinase / adenosine diphosphate / glucose 6-phosphate
Function / homology
Function and homology information


phosphoribulokinase / phosphoribulokinase activity / carbohydrate metabolic process / 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
ADENOSINE-5'-DIPHOSPHATE / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 6-O-phosphono-alpha-D-glucopyranose / Phosphoribulokinase
Similarity search - Component
Biological speciesSynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5061389246 Å
AuthorsYu, A. / Xie, Y. / Li, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31770778 China
CitationJournal: Plant Cell / Year: 2020
Title: Photosynthetic Phosphoribulokinase Structures: Enzymatic Mechanisms and the Redox Regulation of the Calvin-Benson-Bassham Cycle.
Authors: Yu, A. / Xie, Y. / Pan, X. / Zhang, H. / Cao, P. / Su, X. / Chang, W. / Li, M.
History
DepositionJul 5, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1May 20, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jul 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoribulokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8624
Polymers39,0201
Non-polymers8423
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area650 Å2
ΔGint-4 kcal/mol
Surface area15100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.415, 77.104, 94.405
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

#1: Protein Phosphoribulokinase /


Mass: 39020.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus (strain PCC 7942) (bacteria)
Strain: PCC 7942 / Gene: Synpcc7942_0977 / Production host: Escherichia coli (E. coli) / References: UniProt: Q31PL2, phosphoribulokinase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Sugar ChemComp-G6P / 6-O-phosphono-alpha-D-glucopyranose


Type: D-saccharide, alpha linking / Mass: 260.136 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
a-D-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL / Dithiothreitol


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.34 Å3/Da / Density % sol: 47.37 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.02 M magnesium chloride hexahydrate, 0.05 M MES monohydrate pH6.0, 15% v/v 2-propanol, 10mM adenosine diphosphate, 10mM glucose 6-phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.5→29.14 Å / Num. obs: 12171 / % possible obs: 100 % / Redundancy: 12.2 % / Biso Wilson estimate: 43.7292263371 Å2 / Net I/σ(I): 18.4
Reflection shellResolution: 2.5→2.59 Å / Num. unique obs: 1187

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5061389246→29.1352375049 Å / SU ML: 0.298114043027 / Cross valid method: FREE R-VALUE / σ(F): 1.34365868481 / Phase error: 24.4554813273
RfactorNum. reflection% reflection
Rfree0.222948224709 607 5.04027235739 %
Rwork0.189604799391 --
obs0.191333603136 12043 99.013401299 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 47.4564802544 Å2
Refinement stepCycle: LAST / Resolution: 2.5061389246→29.1352375049 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2540 0 51 60 2651
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00369208982722645
X-RAY DIFFRACTIONf_angle_d0.7318343946443588
X-RAY DIFFRACTIONf_chiral_restr0.264225186544396
X-RAY DIFFRACTIONf_plane_restr0.00350428408085460
X-RAY DIFFRACTIONf_dihedral_angle_d19.5539645631010
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7582-3.15690.2649648090191480.2172237925912829X-RAY DIFFRACTION99.8993288591
3.1569-3.97570.2290585484171460.1902354476112874X-RAY DIFFRACTION99.8677248677

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