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- PDB-1rm4: Crystal structure of recombinant photosynthetic glyceraldehyde-3-... -

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Basic information

Entry
Database: PDB / ID: 1rm4
TitleCrystal structure of recombinant photosynthetic glyceraldehyde-3-phosphate dehydrogenase A4 isoform, complexed with NADP
ComponentsGlyceraldehyde 3-phosphate dehydrogenase A
KeywordsOXIDOREDUCTASE / Rossmann fold / GAPDH-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 / chloroplast / glucose metabolic process / NAD binding / NADP binding
Similarity search - Function
Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / 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, type I / Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / 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 Å
AuthorsSparla, F. / Fermani, S. / Falini, G. / Ripamonti, A. / Sabatino, P. / Pupillo, P. / Trost, P.
Citation
Journal: J.Mol.Biol. / Year: 2004
Title: Coenzyme Site-directed Mutants of Photosynthetic A(4)-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.
#1: Journal: Biochemistry / Year: 2003
Title: The 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.
#2: 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
DepositionNov 27, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 23, 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
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)111,77414
Polymers108,7693
Non-polymers3,00511
Water10,611589
1
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)149,16020
Polymers145,0264
Non-polymers4,13416
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_565-x+1/2,-y+3/2,z1
Buried area21660 Å2
ΔGint-327 kcal/mol
Surface area43460 Å2
MethodPISA, PQS
2
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)148,77616
Polymers145,0264
Non-polymers3,75012
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
MethodPQS
Unit cell
Length a, b, c (Å)141.688, 185.365, 106.614
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Cell settingorthorhombic
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11O-7497-

HOH

21O-7611-

HOH

31B-2464-

HOH

41B-2472-

HOH

DetailsThe biological assembly is a tetramer (OPQR) generated from the monomer O by the operations: monomer R -x, y, -z and translation 0, 0, 2; monomer Q x, -y, -z and translation 0, 1, 2; monomer P -x, -y, z and translation 0, 1, 0. A second tetramer is generated from dimer AB by the operations: 1/2-x, 3/2-y, z and translation 0, 0, 0.

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Components

#1: Protein Glyceraldehyde 3-phosphate dehydrogenase A / E.C.1.2.1.13 / photosynthetic glyceraldehyde-3-phosphate dehydrogenase / GAPDH / NADP-dependent ...photosynthetic glyceraldehyde-3-phosphate dehydrogenase / GAPDH / 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: chloroplastsChloroplast / 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 / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 589 / 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: 2.96 Å3/Da / Density % sol: 58.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: ammonium sulphate, Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 19, 2001 / Details: mirrors
RadiationMonochromator: Si crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→76 Å / Num. all: 94456 / Num. obs: 81938 / % possible obs: 52 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 14.2 Å2 / Rsym value: 0.038 / Net I/σ(I): 24.2
Reflection shellResolution: 2→2.07 Å / Mean I/σ(I) obs: 3.8 / Num. unique all: 7906 / Rsym value: 0.115 / % possible all: 37.6

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Processing

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

1jn0


Resolution: 2→69.95 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 4753767.43 / 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
Rfree0.228 4124 5 %RANDOM
Rwork0.204 ---
all0.214 81843 --
obs0.204 81843 86.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 63.3863 Å2 / ksol: 0.394412 e/Å3
Displacement parametersBiso mean: 32 Å2
Baniso -1Baniso -2Baniso -3
1-11.31 Å20 Å20 Å2
2--0.39 Å20 Å2
3----11.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2→69.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7614 0 184 589 8387
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_improper_angle_d5.22
X-RAY DIFFRACTIONc_mcbond_it1.191.5
X-RAY DIFFRACTIONc_mcangle_it1.752
X-RAY DIFFRACTIONc_scbond_it1.852
X-RAY DIFFRACTIONc_scangle_it2.622.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.269 643 4.9 %
Rwork0.249 12462 -
obs-13105 83.9 %
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.PARAMWATER.TOP

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