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- PDB-1nbo: The dual coenzyme specificity of photosynthetic glyceraldehyde-3-... -

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Basic information

Entry
Database: PDB / ID: 1nbo
TitleThe dual coenzyme specificity of photosynthetic glyceraldehyde-3-phosphate dehydrogenase interpreted by the crystal structure of A4 isoform complexed with NAD
Componentsglyceraldehyde-3-phosphate dehydrogenase A
KeywordsOXIDOREDUCTASE / Rossmann fold
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
Similarity search - Component
Biological speciesSpinacia oleracea (spinach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsFalini, G. / Fermani, S. / Ripamonti, A. / Sabatino, P. / Sparla, F. / Pupillo, P. / Trost, P.
Citation
Journal: Biochemistry / Year: 2003
Title: Dual Coenzyme Specificity of Photosynthetic Glyceraldehyde-3-phosphate Dehydrogenase Interpreted by the Crystal Structure of A(4) Isoform Complexed with NAD
Authors: Falini, G. / Fermani, S. / Ripamonti, A. / Sabatino, P. / Sparla, F. / Pupillo, P. / Trost, P.
#1: 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.
#2: Journal: J.Biol.Chem. / Year: 2002
Title: The C-terminal extension of glyceraldehyde-3-phosphate dehydrogenase subunit B acts as an autoinhibitory domain regulated by thioredoxins and nicotinamide adenine dinucleotide
Authors: Sparla, F. / Pupillo, P. / Trost, P.
#3: Journal: Biochim.Biophys.Acta / Year: 1990
Title: Chloroplast glyceraldehyde-3-phosphate dehydrogenase (NADP): amino acid sequence of the subunits from isoenzyme I and structural relationship with isoenzyme II
Authors: Ferri, G. / Stoppini, M. / Meloni, M. / Zapponi, M.C. / Iadarola, P.
History
DepositionDec 3, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 16, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
O: glyceraldehyde-3-phosphate dehydrogenase A
A: glyceraldehyde-3-phosphate dehydrogenase A
B: glyceraldehyde-3-phosphate dehydrogenase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,52814
Polymers108,7693
Non-polymers2,75911
Water6,467359
1
O: glyceraldehyde-3-phosphate dehydrogenase A
hetero molecules

O: glyceraldehyde-3-phosphate dehydrogenase A
hetero molecules

O: glyceraldehyde-3-phosphate dehydrogenase A
hetero molecules

O: glyceraldehyde-3-phosphate dehydrogenase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,44816
Polymers145,0264
Non-polymers3,42212
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_557-x,y,-z+21
crystal symmetry operation4_567x,-y+1,-z+21
Buried area20940 Å2
ΔGint-289 kcal/mol
Surface area43500 Å2
MethodPISA, PQS
2
A: glyceraldehyde-3-phosphate dehydrogenase A
B: glyceraldehyde-3-phosphate dehydrogenase A
hetero molecules

A: glyceraldehyde-3-phosphate dehydrogenase A
B: glyceraldehyde-3-phosphate dehydrogenase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,83220
Polymers145,0264
Non-polymers3,80616
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_565-x+1/2,-y+3/2,z1
Buried area21460 Å2
ΔGint-345 kcal/mol
Surface area44010 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)140.644, 185.652, 106.446
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Cell settingorthorhombic
Space group name H-MC222
DetailsThe biological assembly is a tetramer generated from the monomer in the asymmetric unit by the operations: -x, y, 2-z and x, 1-y, 2-z and -x, 1-y, z or generated from the dimer in the asymmetric unit by the two fold axis: 1/2-x, 3/2-y, z.

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Components

#1: Protein glyceraldehyde-3-phosphate dehydrogenase A / E.C.1.2.1.13 / NADP-dependent glyceraldehydephosphate dehydrogenase subunit A


Mass: 36256.391 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spinacia oleracea (spinach) / Gene: GapA / Organ: leaves / Organelle: Chloroplast / Plasmid: pET-28 / 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.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.2 Å3/Da / Density % sol: 61.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: ammonium sulfate 2 M, Tris-HCl, 0.1 M, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 293 K / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11 Mammonium sulfate1reservoir
20.1 MTris-HCl1reservoirpH8
310 mg/mlprotein1drop
425 mMTris-HCl1droppH7.5
51 mMNAD1drop

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONELETTRA 5.2R11
SYNCHROTRONELETTRA 5.2R21
Detector
TypeIDDetectorDateDetails
MARRESEARCH1CCDJul 12, 2001mirrors
MARRESEARCH2CCDDec 12, 2001mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHMx-ray1
2Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→90 Å / Num. all: 45974 / Num. obs: 43213 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 8.5 % / Biso Wilson estimate: 25.4 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 26
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.201 / Mean I/σ(I) obs: 9.3 / Rsym value: 0.201 / % possible all: 99.9
Reflection
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 90 Å / Num. obs: 43271 / Num. measured all: 679015
Reflection shell
*PLUS
Highest resolution: 2.6 Å / % possible obs: 99.9 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 9

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JN0

1jn0


Resolution: 2.6→77.2 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.245 2161 5 %RANDOM
Rwork0.203 ---
all-45316 --
obs-43155 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.0324 Å2 / ksol: 0.371898 e/Å3
Displacement parametersBiso mean: 34.9 Å2
Baniso -1Baniso -2Baniso -3
1-10.72 Å20 Å20 Å2
2--1.09 Å20 Å2
3----11.82 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.6→77.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7626 0 172 359 8157
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_mcbond_it1.271.5
X-RAY DIFFRACTIONc_mcangle_it2.112
X-RAY DIFFRACTIONc_scbond_it2.032
X-RAY DIFFRACTIONc_scangle_it2.932.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.288 350 4.9 %
Rwork0.232 6785 -
obs-6785 100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2NAD.PARAMNAD.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 8 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.84
LS refinement shell
*PLUS
Rfactor Rfree: 0.203

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