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- PDB-2pkr: Crystal structure of (A+CTE)4 chimeric form of photosyntetic glyc... -

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Basic information

Entry
Database: PDB / ID: 2pkr
TitleCrystal structure of (A+CTE)4 chimeric form of photosyntetic glyceraldehyde-3-phosphate dehydrogenase, complexed with NADP
ComponentsGlyceraldehyde-3-phosphate dehydrogenase Aor
KeywordsOXIDOREDUCTASE / chimeric protein / Rossmann fold / NADP complex
Function / homology
Function and homology information


glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) activity / reductive pentose-phosphate cycle / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / chloroplast / glucose metabolic process / NAD binding / NADP 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 Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
Similarity search - Component
Biological speciesSpinacia oleracea (spinach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsFermani, S. / Falini, G. / Ripamonti, A.
Citation
Journal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Molecular mechanism of thioredoxin regulation in photosynthetic A2B2-glyceraldehyde-3-phosphate dehydrogenase.
Authors: Fermani, S. / Sparla, F. / Falini, G. / Martelli, P.L. / Casadio, R. / Pupillo, P. / Ripamonti, A. / Trost, P.
#1: Journal: J.Mol.Biol. / Year: 2004
Title: Coenzyme Site-directed Mutants of Photosynthetic A4-GAPDH Show Selectively Reduced NADPH-dependent Catalysis, Similar to Regulatory AB-GAPDH Inhibited by Oxidized Thioredoxin.
Authors: Sparla, F. / Fermani, S. / Falini, G. / Zaffagnini, M. / Ripamonti, A. / Sabatino, P. / Pupillo, P. / Trost, P.
#2: Journal: Biochemistry / Year: 2003
Title: Coenzyme Specificity of Photosynthetic Glyceraldehyde-3-phosphate Dehydrogenase Interpreted by the Crystal Structure of A4 Isoform Complexed with NAD.
Authors: Falini, G. / Fermani, S. / Ripamonti, A. / Sabatino, P. / Sparla, F. / Pupillo, P. / Trost, P.
#3: Journal: J.Mol.Biol. / Year: 2001
Title: Crystal structure of the non-regulatory A4 isoform of spinach chloroplast glyceraldehyde-3-phosphate dehydrogenase complexed with NADP.
Authors: Fermani, S. / Ripamonti, A. / Sabatino, P. / Zanotti, G. / Scagliarini, S. / Sparla, F. / Trost, P. / Pupillo, P.
History
DepositionApr 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 12, 2014Group: Structure summary
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Aug 30, 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
Revision 1.6Mar 13, 2024Group: Source and taxonomy / Category: entity_src_gen
Revision 1.7Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE Database reference was not available at the time of processing.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
O: Glyceraldehyde-3-phosphate dehydrogenase Aor
R: Glyceraldehyde-3-phosphate dehydrogenase Aor
P: Glyceraldehyde-3-phosphate dehydrogenase Aor
Q: Glyceraldehyde-3-phosphate dehydrogenase Aor
A: Glyceraldehyde-3-phosphate dehydrogenase Aor
B: Glyceraldehyde-3-phosphate dehydrogenase Aor
C: Glyceraldehyde-3-phosphate dehydrogenase Aor
D: Glyceraldehyde-3-phosphate dehydrogenase Aor
H: Glyceraldehyde-3-phosphate dehydrogenase Aor
I: Glyceraldehyde-3-phosphate dehydrogenase Aor
L: Glyceraldehyde-3-phosphate dehydrogenase Aor
M: Glyceraldehyde-3-phosphate dehydrogenase Aor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)483,81958
Polymers471,60712
Non-polymers12,21146
Water18010
1
O: Glyceraldehyde-3-phosphate dehydrogenase Aor
R: Glyceraldehyde-3-phosphate dehydrogenase Aor
P: Glyceraldehyde-3-phosphate dehydrogenase Aor
Q: Glyceraldehyde-3-phosphate dehydrogenase Aor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,43321
Polymers157,2024
Non-polymers4,23117
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Glyceraldehyde-3-phosphate dehydrogenase Aor
B: Glyceraldehyde-3-phosphate dehydrogenase Aor
C: Glyceraldehyde-3-phosphate dehydrogenase Aor
D: Glyceraldehyde-3-phosphate dehydrogenase Aor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,14518
Polymers157,2024
Non-polymers3,94214
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
H: Glyceraldehyde-3-phosphate dehydrogenase Aor
I: Glyceraldehyde-3-phosphate dehydrogenase Aor
L: Glyceraldehyde-3-phosphate dehydrogenase Aor
M: Glyceraldehyde-3-phosphate dehydrogenase Aor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,24119
Polymers157,2024
Non-polymers4,03815
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.377, 217.707, 114.793
Angle α, β, γ (deg.)90.00, 90.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 39300.609 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spinacia oleracea (spinach) / Gene: GAPA / Plasmid: pET-29 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P19866, glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating)
#2: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 34 / Source method: obtained synthetically / Formula: SO4
References: glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating)
#3: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
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: 3.03 Å3/Da / Density % sol: 59.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.5-1.2 M ammonium sulfate, 0.1 M potassium phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 11, 2004 / Details: mirror
RadiationMonochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→72 Å / Num. all: 201038 / Num. obs: 154012 / % possible obs: 76.6 % / Observed criterion σ(F): 3 / Observed criterion σ(I): -3 / Redundancy: 1.4 % / Biso Wilson estimate: 24.6 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 6.5
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 1.5 / Num. unique all: 12396 / Rsym value: 0.336 / % possible all: 62

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Processing

Software
NameVersionClassification
CNS1refinement
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RM4

1rm4


Resolution: 2.4→63.22 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2437968.11 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.258 7785 5.1 %RANDOM
Rwork0.249 ---
obs0.249 153938 76.5 %-
all-201038 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.373755 e/Å3
Displacement parametersBiso mean: 24.6 Å2
Baniso -1Baniso -2Baniso -3
1--8.77 Å20 Å20 Å2
2--11.75 Å20 Å2
3----2.98 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.35 Å
Luzzati d res low-8 Å
Luzzati sigma a0.4 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.4→63.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30492 0 746 10 31248
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_angle_deg2.5
X-RAY DIFFRACTIONc_dihedral_angle_d24.4
X-RAY DIFFRACTIONc_improper_angle_d2.74
X-RAY DIFFRACTIONc_mcbond_it1.091.5
X-RAY DIFFRACTIONc_mcangle_it1.822
X-RAY DIFFRACTIONc_scbond_it1.72
X-RAY DIFFRACTIONc_scangle_it2.52.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.34 1134 5.3 %
Rwork0.326 20131 -
obs-21265 63.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ndp.paramndp.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4water_rep.paramCNS_TOPAAR:water_rep.top

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