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- PDB-1rm3: Crystal structure of mutant T33A of photosynthetic glyceraldehyde... -

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Basic information

Entry
Database: PDB / ID: 1rm3
TitleCrystal structure of mutant T33A of 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 / 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: 2.2 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 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / 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 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 16, 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)111,97217
Polymers108,6793
Non-polymers3,29314
Water6,485360
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)149,23222
Polymers144,9054
Non-polymers4,32718
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_655-x+3/2,-y+1/2,z1
Buried area21820 Å2
ΔGint-334 kcal/mol
Surface area43850 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)149,42424
Polymers144,9054
Non-polymers4,51920
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area22320 Å2
ΔGint-333 kcal/mol
Surface area43920 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)142.246, 185.045, 106.282
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-7426-

HOH

21O-7511-

HOH

31A-1428-

HOH

DetailsThe biological assembly is a tetramer (OPQR) generated from the monomer O by the operations: monomer R -x, y, -z and translation 1, 0, 0; monomer Q x, -y, -z and translation 0, 0, 0; monomer P -x, -y, z and translation 1, 0, 0. A second tetramer is generated from dimer AB by the operations: 1/2-x, 3/2-y, z and translation 1, -1, 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: 36226.363 Da / Num. of mol.: 3 / Mutation: T33A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spinacia oleracea (spinach) / Gene: GapA / Organ: leaves / Organelle: chloroplasts / 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.: 11 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 360 / 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 %
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: Jul 17, 2002 / 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: 2.2→91 Å / Num. all: 71278 / Num. obs: 71064 / % possible obs: 54 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 19.3 Å2 / Rsym value: 0.056 / Net I/σ(I): 17.1
Reflection shellResolution: 2.2→2.28 Å / Mean I/σ(I) obs: 3 / Num. unique all: 6926 / Rsym value: 0.222 / % possible all: 98.9

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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: 2.2→33.09 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3849750.98 / 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
Rfree0.237 3602 5.1 %RANDOM
Rwork0.212 ---
all0.231 71033 --
obs0.212 71033 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.1629 Å2 / ksol: 0.372795 e/Å3
Displacement parametersBiso mean: 35.7 Å2
Baniso -1Baniso -2Baniso -3
1-14.86 Å20 Å20 Å2
2---1.39 Å20 Å2
3----13.47 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.2→33.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7620 0 199 360 8179
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_d5.11
X-RAY DIFFRACTIONc_mcbond_it1.211.5
X-RAY DIFFRACTIONc_mcangle_it1.942
X-RAY DIFFRACTIONc_scbond_it1.942
X-RAY DIFFRACTIONc_scangle_it2.752.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.294 573 5 %
Rwork0.26 10996 -
obs-11569 98.6 %
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.PARAMWATER.TOP

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