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- PDB-1dbv: GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE MUTANT WITH ASP 32 REPLA... -

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Basic information

Entry
Database: PDB / ID: 1dbv
TitleGLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE MUTANT WITH ASP 32 REPLACED BY GLY, LEU 187 REPLACED BY ALA, AND PRO 188 REPLACED BY SER COMPLEXED WITH NAD+
ComponentsGLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / NAD(P) SELECTIVITY
Function / homology
Function and homology information


glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / glycolytic process / glucose metabolic process / NAD binding / NADP binding / cytoplasm
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
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsDidierjean, C. / Rahuel-Clermont, S. / Vitoux, B. / Dideberg, O. / Branlant, G. / Aubry, A.
Citation
Journal: J.Mol.Biol. / Year: 1997
Title: A crystallographic comparison between mutated glyceraldehyde-3-phosphate dehydrogenases from Bacillus stearothermophilus complexed with either NAD+ or NADP+.
Authors: Didierjean, C. / Rahuel-Clermont, S. / Vitoux, B. / Dideberg, O. / Branlant, G. / Aubry, A.
#1: Journal: Gene / Year: 1989
Title: Nucleotide Sequence Determination of the DNA Region Coding for Bacillus Stearothermophilus Glyceraldehyde-3-Phosphate Dehydrogenase and of the Flanking DNA Regions Required for its Expression in Escherichia Coli
Authors: Branlant, C. / Oster, T. / Branlant, G.
#2: Journal: J.Mol.Biol. / Year: 1987
Title: Structure of Holo-Glyceraldehyde-3-Phosphate Dehydrogenase from Bacillus Stearothermophilus at 1.8 A Resolution
Authors: Skarzynski, T. / Moody, P.C. / Wonacott, A.J.
History
DepositionDec 20, 1996Processing site: BNL
Revision 1.0Jul 7, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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 / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
O: GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
P: GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
Q: GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
R: GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,94616
Polymers143,5244
Non-polymers3,42212
Water6,918384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21820 Å2
ΔGint-254 kcal/mol
Surface area42130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.950, 124.680, 82.870
Angle α, β, γ (deg.)90.00, 108.63, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.325947, 0.115931, 0.938253), (0.133675, -0.97683, 0.167135), (0.93589, 0.179898, 0.302898)-37.0971, -5.1263, 27.349
2given(-0.993286, -0.115464, 0.007071), (-0.11498, 0.978708, -0.170028), (0.012711, -0.169699, -0.985414)-7.7745, 5.3026, 68.0785
3given(0.316346, 0.007736, -0.948612), (0.003445, -0.99997, -0.007006), (-0.948638, -0.001052, -0.316363)30.0126, 0.3197, 41.4437

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Components

#1: Protein
GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE / GAPDH


Mass: 35880.895 Da / Num. of mol.: 4 / Mutation: D32G, L187A, P188S
Source method: isolated from a genetically manipulated source
Details: COMPLEXED WITH NAD+
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Cellular location: CYTOPLASM / Gene: GAP / Gene (production host): BACILLUS STEAROTHERMOPHILUS / Production host: Escherichia coli (E. coli) / Strain (production host): DF221
References: UniProt: P00362, glyceraldehyde-3-phosphate dehydrogenase (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.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / 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: 2.83 Å3/Da / Density % sol: 56.51 %
Description: THE MUTANT CRYSTALS ARE ISOMORPHOUS TO THE CRYSTALS OF THE WILD-TYPE HOLOENZYME (PDB ENTRY 1GD1).
Crystal growpH: 6.9 / Details: pH 6.9
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17 mg/mlprotein1drop
22 Mammonium sulfate1drop
330 mMNAD(P)+1drop
450 mMphosphate1drop
51 mMEDTA1drop
61 mMdithiothreitol1drop
72.5 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 297 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: MAC Science DIP-2020 / Detector: IMAGE PLATE / Date: Apr 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→15 Å / Num. obs: 45468 / % possible obs: 85 % / Observed criterion σ(I): 0 / Rsym value: 0.07
Reflection
*PLUS
% possible obs: 81 % / Rmerge(I) obs: 0.068

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementResolution: 2.5→8 Å / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.214 4344 8.1 %RANDOM
Rwork0.14 ---
obs0.14 43095 80.6 %-
Displacement parametersBiso mean: 27.5 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10068 0 216 384 10668
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.48
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.5→2.61 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.266 489 7.4 %
Rwork0.201 4327 -
obs--72.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM.NADTOPO.NAD
X-RAY DIFFRACTION3PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.48

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