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- PDB-3k2b: Crystal structure of photosynthetic A4 isoform glyceraldehyde-3-p... -

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Basic information

Entry
Database: PDB / ID: 3k2b
TitleCrystal structure of photosynthetic A4 isoform glyceraldehyde-3-phosphate dehydrogenase complexed with NAD, from Arabidopsis thaliana
ComponentsGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
KeywordsOXIDOREDUCTASE / Rossmann fold / Calvin cycle / Chloroplast / Membrane / NADP / Transit peptide
Function / homology
Function and homology information


supramolecular complex / glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) / stromule / salicylic acid binding / glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) activity / chloroplast membrane / response to sucrose / apoplast / reductive pentose-phosphate cycle / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity ...supramolecular complex / glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) / stromule / salicylic acid binding / glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) activity / chloroplast membrane / response to sucrose / apoplast / reductive pentose-phosphate cycle / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / chloroplast envelope / chloroplast stroma / chloroplast thylakoid membrane / response to light stimulus / response to cold / chloroplast / glucose metabolic process / NAD binding / disordered domain specific binding / NADP binding / protein homotetramerization / mRNA binding / protein homodimerization activity / identical protein binding / cytosol
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 Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Glyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsFermani, S. / Falini, G. / Thumiger, A. / Sparla, F. / Marri, L. / Trost, P.
Citation
Journal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Structure of photosynthetic glyceraldehyde-3-phosphate dehydrogenase (isoform A4) from Arabidopsis thaliana in complex with NAD
Authors: Fermani, S. / Sparla, F. / Marri, L. / Thumiger, A. / Pupillo, P. / Falini, G. / Trost, P.
#1: Journal: Plant Physiol. / Year: 2005
Title: Reconstitution and properties of the recombinant glyceraldehyde-3-phosphate dehydrogenase/CP12/phosphoribulokinase supramolecular complex of Arabidopsis
Authors: Marri, L. / Trost, P. / Pupillo, P. / Sparla, F.
History
DepositionSep 29, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 2, 2012Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
B: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
C: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
D: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
E: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
F: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
G: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
H: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
O: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
Q: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)374,87365
Polymers363,91610
Non-polymers10,95755
Water15,889882
1
A: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
B: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
C: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
D: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,04527
Polymers145,5664
Non-polymers4,47923
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14570 Å2
ΔGint-95 kcal/mol
Surface area45800 Å2
MethodPISA
2
E: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
F: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
G: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
H: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,66123
Polymers145,5664
Non-polymers4,09519
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14320 Å2
ΔGint-93 kcal/mol
Surface area45450 Å2
MethodPISA
3
O: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
Q: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)150,33330
Polymers145,5664
Non-polymers4,76726
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area14550 Å2
ΔGint-103 kcal/mol
Surface area44880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.738, 188.625, 314.129
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11B-382-

HOH

21D-359-

HOH

31H-669-

HOH

41Q-342-

HOH

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Components

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


Mass: 36391.570 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: GAPA / Plasmid: pET 28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P25856, glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating)
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 45 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 882 / 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: 59.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 2.4M ammonium sulphate, 0.1M sodium citrate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 9, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.6→95.3 Å / Num. all: 136899 / Num. obs: 131352 / % possible obs: 96.1 % / Observed criterion σ(F): 3 / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 40.5 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 12.7
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3 % / Rmerge(I) obs: 0.697 / Mean I/σ(I) obs: 1.2 / Num. unique all: 10346 / Rsym value: 0.697 / % possible all: 76.4

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Processing

Software
NameVersionClassification
DNAdata collection
EPMRphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NBO

1nbo


Resolution: 2.6→94.22 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2920354.69 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.289 6671 5.1 %RANDOM
Rwork0.237 ---
all0.239 136963 --
obs0.237 131352 95.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 63.3778 Å2 / ksol: 0.362364 e/Å3
Displacement parametersBiso mean: 59.8 Å2
Baniso -1Baniso -2Baniso -3
1-22.55 Å20 Å20 Å2
2---7.99 Å20 Å2
3----14.55 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.66 Å0.58 Å
Refinement stepCycle: LAST / Resolution: 2.6→94.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25525 0 665 882 27072
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_improper_angle_d0.88
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.412 885 4.9 %
Rwork0.389 17328 -
obs-18213 80.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4nad.paramnad.top

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