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- PDB-2pkq: Crystal structure of the photosynthetic A2B2-glyceraldehyde-3-pho... -

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Basic information

Entry
Database: PDB / ID: 2pkq
TitleCrystal structure of the photosynthetic A2B2-glyceraldehyde-3-phosphate dehydrogenase, complexed with NADP
Components
  • Glyceraldehyde-3-phosphate dehydrogenase A
  • Glyceraldehyde-3-phosphate dehydrogenase B
KeywordsOXIDOREDUCTASE / Rossmann fold / protein-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 B, chloroplastic / Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
Similarity search - Component
Biological speciesSpinacia oleracea (spinach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 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: Dual 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: Derived calculations / 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 1.6Nov 13, 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 B
P: Glyceraldehyde-3-phosphate dehydrogenase A
Q: Glyceraldehyde-3-phosphate dehydrogenase B
R: Glyceraldehyde-3-phosphate dehydrogenase A
S: Glyceraldehyde-3-phosphate dehydrogenase A
T: Glyceraldehyde-3-phosphate dehydrogenase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,89527
Polymers226,9816
Non-polymers5,91321
Water00
1
O: Glyceraldehyde-3-phosphate dehydrogenase B
P: Glyceraldehyde-3-phosphate dehydrogenase A
Q: Glyceraldehyde-3-phosphate dehydrogenase B
R: Glyceraldehyde-3-phosphate dehydrogenase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,16717
Polymers151,3214
Non-polymers3,84613
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20860 Å2
ΔGint-259 kcal/mol
Surface area46110 Å2
MethodPISA, PQS
2
S: Glyceraldehyde-3-phosphate dehydrogenase A
T: Glyceraldehyde-3-phosphate dehydrogenase B
hetero molecules

S: Glyceraldehyde-3-phosphate dehydrogenase A
T: Glyceraldehyde-3-phosphate dehydrogenase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,45520
Polymers151,3214
Non-polymers4,13416
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)186.147, 215.687, 81.469
Angle α, β, γ (deg.)90.00, 102.52, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 39403.957 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: chloroplasts (leaves) / Source: (natural) Spinacia oleracea (spinach)
References: UniProt: P12860, glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating)
#2: Protein Glyceraldehyde-3-phosphate dehydrogenase A / NADP-dependent glyceraldehydephosphate dehydrogenase subunit A


Mass: 36256.391 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: chloroplasts (leaves) / Source: (natural) Spinacia oleracea (spinach)
References: UniProt: P19866, glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating)
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H30N7O17P3
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 3.52 Å3/Da / Density % sol: 65.01 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2.0-2.5 M ammonium sulfate, 0.1 M potassium phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
1,2,31
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID14-210.933
SYNCHROTRONESRF ID14-220.933
SYNCHROTRONELETTRA 5.2R31
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 41CCDMay 3, 2003mirrors
ADSC QUANTUM 42CCDMay 3, 2003mirrors
MAR CCD 165 mm3CCDOct 18, 2003mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Diamond (111), Ge(220)SINGLE WAVELENGTHMx-ray1
2Diamond (111), Ge(220)SINGLE WAVELENGTHMx-ray1
3Silicon (111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9331
211
ReflectionResolution: 3.6→91 Å / Num. all: 36736 / Num. obs: 36699 / % possible obs: 99.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): -3 / Redundancy: 13.4 % / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.359 / Rsym value: 0.359 / Net I/σ(I): 4.5
Reflection shellResolution: 3.6→3.73 Å / Rmerge(I) obs: 0.694 / Mean I/σ(I) obs: 1.5 / Num. unique all: 3647 / Rsym value: 0.694 / % possible all: 99.3

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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: 3.6→90.86 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 5783074.97 / 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
Rfree0.292 1802 5 %RANDOM
Rwork0.261 ---
obs0.261 36271 99.9 %-
all-36736 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.336 Å2 / ksol: 0.344771 e/Å3
Displacement parametersBiso mean: 30.9 Å2
Baniso -1Baniso -2Baniso -3
1-6.13 Å20 Å2-10.38 Å2
2--7 Å20 Å2
3----13.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.56 Å0.48 Å
Luzzati d res low-8 Å
Luzzati sigma a0.65 Å0.58 Å
Refinement stepCycle: LAST / Resolution: 3.6→90.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15477 0 363 0 15840
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_improper_angle_d5.21
X-RAY DIFFRACTIONc_mcbond_it1.111.5
X-RAY DIFFRACTIONc_mcangle_it1.982
X-RAY DIFFRACTIONc_scbond_it1.252
X-RAY DIFFRACTIONc_scangle_it2.132.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3.6→3.83 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.352 286 4.8 %
Rwork0.324 5675 -
obs-5961 99.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ndp.paramndp.top
X-RAY DIFFRACTION3ion.paramion.top

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