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- PDB-7zq3: Crystal structure of photosynthetic glyceraldehyde-3-phosphate de... -

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Basic information

Entry
Database: PDB / ID: 7zq3
TitleCrystal structure of photosynthetic glyceraldehyde-3-phosphate dehydrogenase from Chlamydomonas reinhardtii (CrGAPA) complexed with NADP+
ComponentsGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
KeywordsOXIDOREDUCTASE / Rossman-fold domain / Calvin-Benson cycle / pyridin dinucleotide cofactors.
Function / homology
Function and homology information


supramolecular complex / glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) activity / reductive pentose-phosphate cycle / chloroplast / kinase binding / glucose metabolic process / NAD binding / NADP binding / identical protein binding
Similarity search - Function
Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde-3-phosphate dehydrogenase, type I / 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 ...Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde-3-phosphate dehydrogenase, type I / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsFermani, S. / Zaffagnini, M. / Lemaire, S.D. / Falini, G. / Fanti, S. / Rossi, J.
Funding support Italy, 1items
OrganizationGrant numberCountry
Not funded Italy
CitationJournal: Redox Biol / Year: 2022
Title: Structural snapshots of nitrosoglutathione binding and reactivity underlying S-nitrosylation of photosynthetic GAPDH.
Authors: Mattioli, E.J. / Rossi, J. / Meloni, M. / De Mia, M. / Marchand, C.H. / Tagliani, A. / Fanti, S. / Falini, G. / Trost, P. / Lemaire, S.D. / Fermani, S. / Calvaresi, M. / Zaffagnini, M.
History
DepositionApr 29, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
O: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
R: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,20711
Polymers76,0432
Non-polymers2,1639
Water12,845713
1
O: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
R: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
hetero molecules

O: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
R: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,41322
Polymers152,0874
Non-polymers4,32718
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_445-x-1/2,-y-1/2,z1
Buried area22080 Å2
ΔGint-313 kcal/mol
Surface area47860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.984, 148.511, 74.055
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11R-790-

HOH

21R-830-

HOH

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Components

#1: Protein Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic / NADP-dependent glyceraldehydephosphate dehydrogenase subunit A


Mass: 38021.664 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Cell: Chloroplast / Gene: GAPA / Production host: Escherichia coli (E. coli)
References: UniProt: P50362, glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating)
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 713 / 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: 2.71 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.2-1.6 M (NH4)2SO4, 0.1 M Tris-HCl / PH range: 7.5-8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 12, 2015
RadiationMonochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→46.74 Å / Num. obs: 124828 / % possible obs: 100 % / Redundancy: 13.1 % / CC1/2: 0.995 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.043 / Rrim(I) all: 0.157 / Net I/σ(I): 10.6 / Num. measured all: 1629730 / Scaling rejects: 2073
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.5-1.5313.30.8128167961380.9170.2280.844399.9
8.22-46.7412.60.11107748530.9890.0310.11418.799.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.9 Å46.74 Å
Translation5.9 Å46.74 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
PHENIX1.19rc7-4070refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RM4

1rm4


Resolution: 1.5→46.74 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0.02 / Phase error: 20.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.205 11862 4.9 %
Rwork0.1869 230326 -
obs0.1877 124793 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.47 Å2 / Biso mean: 20.725 Å2 / Biso min: 8.01 Å2
Refinement stepCycle: final / Resolution: 1.5→46.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5255 0 131 713 6099
Biso mean--21.75 32.81 -
Num. residues----687
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.5-1.520.24884250.238376248049
1.52-1.530.26894360.222876738109
1.53-1.550.28064180.223276828100
1.55-1.570.27823380.220276818019
1.57-1.590.25184170.214776728089
1.59-1.620.23693770.211776868063
1.62-1.640.23664030.20876618064
1.64-1.660.23893870.206876668053
1.66-1.690.25024100.218277068116
1.69-1.720.24794640.203275838047
1.72-1.750.25344490.210176178066
1.75-1.780.21113990.191476608059
1.78-1.810.1973850.186677158100
1.81-1.850.23073680.189376548022
1.85-1.890.24583930.186877138106
1.89-1.930.22573940.188776608054
1.93-1.980.22233960.182677198115
1.98-2.040.19813940.182176478041
2.04-2.10.21474450.180276948139
2.1-2.160.2083600.181776598019
2.16-2.240.20923340.176877568090
2.24-2.330.19414060.180176698075
2.33-2.440.20973700.184877118081
2.44-2.560.21864360.183376298065
2.56-2.730.1863760.185477078083
2.73-2.940.2124220.192176598081
2.94-3.230.2083630.183176938056
3.23-3.70.17513170.176477718088
3.7-4.660.15573830.169877008083
4.66-46.740.18573970.19176598056

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