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- PDB-6kez: Crystal structure of GAPDH/CP12/PRK complex from Arabidopsis thaliana -

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Basic information

Entry
Database: PDB / ID: 6kez
TitleCrystal structure of GAPDH/CP12/PRK complex from Arabidopsis thaliana
Components
  • Calvin cycle protein CP12-2
  • Glyceraldehyde-3-phosphate dehydrogenase GAPA1
  • Phosphoribulokinase
KeywordsOXIDOREDUCTASE/TRANSFERASE/PROTEIN BINDING / glyceraldehyde-2-phosphate dehydrogenase / phosphoribulokinase / CP12 chloroplast / OXIDOREDUCTASE-TRANSFERASE-PROTEIN BINDING complex
Function / homology
Function and homology information


peptide cross-linking via L-cystine / phosphoribulokinase / phosphoribulokinase activity / negative regulation of reductive pentose-phosphate cycle / supramolecular complex / cellular response to anoxia / glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) / stromule / salicylic acid binding / glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) activity ...peptide cross-linking via L-cystine / phosphoribulokinase / phosphoribulokinase activity / negative regulation of reductive pentose-phosphate cycle / supramolecular complex / cellular response to anoxia / glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) / stromule / salicylic acid binding / glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) activity / chloroplast membrane / thylakoid / response to sucrose / apoplast / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / reductive pentose-phosphate cycle / chloroplast envelope / chloroplast stroma / cellular response to cold / chloroplast thylakoid membrane / nickel cation binding / response to light stimulus / chloroplast / response to cold / glucose metabolic process / NAD binding / disordered domain specific binding / NADP binding / cellular response to heat / protein-containing complex assembly / protein-macromolecule adaptor activity / protein homotetramerization / copper ion binding / mRNA binding / protein-containing complex binding / enzyme binding / protein homodimerization activity / protein-containing complex / ATP binding / identical protein binding / nucleus / cytosol
Similarity search - Function
Phosphoribulokinase signature. / Phosphoribulokinase / Calvin cycle protein CP12-like / CP12 domain / CP12 domain / CP12 / Phosphoribulokinase/uridine kinase / Phosphoribulokinase / Uridine kinase family / Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, active site ...Phosphoribulokinase signature. / Phosphoribulokinase / Calvin cycle protein CP12-like / CP12 domain / CP12 domain / CP12 / Phosphoribulokinase/uridine kinase / Phosphoribulokinase / Uridine kinase family / Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain / Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain / Glyceraldehyde/Erythrose phosphate dehydrogenase family / Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Phosphoribulokinase, chloroplastic / Glyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic / Calvin cycle protein CP12-2, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 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 1.2Nov 22, 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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glyceraldehyde-3-phosphate dehydrogenase GAPA1
B: Glyceraldehyde-3-phosphate dehydrogenase GAPA1
C: Glyceraldehyde-3-phosphate dehydrogenase GAPA1
D: Glyceraldehyde-3-phosphate dehydrogenase GAPA1
E: Glyceraldehyde-3-phosphate dehydrogenase GAPA1
F: Glyceraldehyde-3-phosphate dehydrogenase GAPA1
G: Glyceraldehyde-3-phosphate dehydrogenase GAPA1
H: Glyceraldehyde-3-phosphate dehydrogenase GAPA1
I: Phosphoribulokinase
K: Phosphoribulokinase
J: Phosphoribulokinase
L: Phosphoribulokinase
M: Calvin cycle protein CP12-2
N: Calvin cycle protein CP12-2
O: Calvin cycle protein CP12-2
P: Calvin cycle protein CP12-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)490,27724
Polymers484,96916
Non-polymers5,3078
Water66737
1
A: Glyceraldehyde-3-phosphate dehydrogenase GAPA1
B: Glyceraldehyde-3-phosphate dehydrogenase GAPA1
C: Glyceraldehyde-3-phosphate dehydrogenase GAPA1
D: Glyceraldehyde-3-phosphate dehydrogenase GAPA1
I: Phosphoribulokinase
K: Phosphoribulokinase
O: Calvin cycle protein CP12-2
P: Calvin cycle protein CP12-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)245,13812
Polymers242,4858
Non-polymers2,6544
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30620 Å2
ΔGint-179 kcal/mol
Surface area78620 Å2
MethodPISA
2
E: Glyceraldehyde-3-phosphate dehydrogenase GAPA1
F: Glyceraldehyde-3-phosphate dehydrogenase GAPA1
G: Glyceraldehyde-3-phosphate dehydrogenase GAPA1
H: Glyceraldehyde-3-phosphate dehydrogenase GAPA1
J: Phosphoribulokinase
L: Phosphoribulokinase
M: Calvin cycle protein CP12-2
N: Calvin cycle protein CP12-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)245,13812
Polymers242,4858
Non-polymers2,6544
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30750 Å2
ΔGint-169 kcal/mol
Surface area80250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.813, 204.734, 157.036
Angle α, β, γ (deg.)90.000, 106.880, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Glyceraldehyde-3-phosphate dehydrogenase GAPA1 / GAPDH / NADP-dependent glyceraldehydephosphate dehydrogenase A subunit 1


Mass: 36592.750 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: GAPA1, GAPA, At3g26650, MLJ15.4, MLJ15_5 / Production host: Escherichia coli (E. coli)
References: UniProt: P25856, glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating)
#2: Protein
Phosphoribulokinase / PRKase / Phosphopentokinase


Mass: 39514.785 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At1g32060, T12O21.4 / Production host: Escherichia coli (E. coli) / References: UniProt: P25697, phosphoribulokinase
#3: Protein
Calvin cycle protein CP12-2 / CP12 domain-containing protein 2 / Chloroplast protein 12-2


Mass: 8542.076 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CP12-2, At3g62410, T12C14.110 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9LZP9
#4: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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 Å3/Da / Density % sol: 58.97 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 100mM HEPES, pH7.5, 100mM KCl, 15% polyethylene glycol 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 68615 / % possible obs: 97.8 % / Redundancy: 3.3 % / Biso Wilson estimate: 55.99606247 Å2 / Rmerge(I) obs: 0.123 / Net I/σ(I): 7.56
Reflection shellResolution: 3.5→3.56 Å / Rmerge(I) obs: 0.554 / Num. unique obs: 3452

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RVD, 6KEW

3rvd

6kew


Resolution: 3.5→50 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2868 --
Rwork0.2465 --
obs-63151 87.32 %
Refinement stepCycle: LAST / Resolution: 3.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms33437 0 352 37 33826
LS refinement shellResolution: 3.497→3.622 Å /
Num. reflection% reflection
obs2386 33.97 %

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