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- PDB-1nq5: Glyceraldehyde-3-Phosphate Dehydrogenase Mutant With Cys 149 Repl... -

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Basic information

Entry
Database: PDB / ID: 1nq5
TitleGlyceraldehyde-3-Phosphate Dehydrogenase Mutant With Cys 149 Replaced By Ser Complexed With Nad+
ComponentsGlyceraldehyde 3-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / Glycolysis / NAD
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, 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsDidierjean, C. / Corbier, C. / Fatih, M. / Favier, F. / Boschi-Muller, S. / Branlant, G. / Aubry, A.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Crystal structure of two ternary complexes of phosphorylating Glyceraldehyde-3-Phosphate Dehydrogenase from Bacillus stearothermophilus with NAD and D-Glyceraldehyde-3-Phosphate
Authors: Didierjean, C. / Corbier, C. / Fatih, M. / Favier, F. / Boschi-Muller, S. / Branlant, G. / Aubry, A.
History
DepositionJan 21, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2003Provider: 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 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
O: Glyceraldehyde 3-phosphate dehydrogenase
Q: Glyceraldehyde 3-phosphate dehydrogenase
A: Glyceraldehyde 3-phosphate dehydrogenase
C: Glyceraldehyde 3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,93812
Polymers143,9004
Non-polymers3,0388
Water10,881604
1
O: Glyceraldehyde 3-phosphate dehydrogenase
Q: Glyceraldehyde 3-phosphate dehydrogenase
hetero molecules

O: Glyceraldehyde 3-phosphate dehydrogenase
Q: Glyceraldehyde 3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,93812
Polymers143,9004
Non-polymers3,0388
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area21520 Å2
ΔGint-208 kcal/mol
Surface area42570 Å2
MethodPISA, PQS
2
A: Glyceraldehyde 3-phosphate dehydrogenase
C: Glyceraldehyde 3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4696
Polymers71,9502
Non-polymers1,5194
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21510 Å2
ΔGint-209 kcal/mol
Surface area42400 Å2
MethodPISA
3
A: Glyceraldehyde 3-phosphate dehydrogenase
C: Glyceraldehyde 3-phosphate dehydrogenase
hetero molecules

A: Glyceraldehyde 3-phosphate dehydrogenase
C: Glyceraldehyde 3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,93812
Polymers143,9004
Non-polymers3,0388
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)140.480, 87.909, 119.925
Angle α, β, γ (deg.)90.00, 119.00, 90.00
Int Tables number5
Space group name H-MC121
Details: The second part of the first biological tetramer is generated by the symmetry operator (1-x, y, 2-z). / : The second part of the second biological tetramer is generated by the symmetry operator (-x, y, 1-z).

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Components

#1: Protein
Glyceraldehyde 3-phosphate dehydrogenase / / GAPDH


Mass: 35974.984 Da / Num. of mol.: 4 / Mutation: C149S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: GAP / Plasmid: pBluescriptII / Production host: Escherichia coli (E. coli)
References: UniProt: P00362, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 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 / Water


Mass: 18.015 Da / Num. of mol.: 604 / 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: 2.12 Å3/Da / Density % sol: 41.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4000, sodium acetate, Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 8.9
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
210 %(w/v)PEG40001reservoir
31 mMD,L-G3P1drop
41 mMNAD1drop
540 mMTEA1drop
62 mMEDTA1drop
750 mMpotassium phosphate1droppH8.9
1Tris-HCl1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
DetectorType: MAC Science DIP-2030B / Detector: IMAGE PLATE / Date: Oct 15, 1997 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.11→8 Å / Num. all: 71217 / Num. obs: 71217 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.085 / Net I/σ(I): 14
Reflection shellResolution: 2.11→2.18 Å / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3.4 / % possible all: 75.6
Reflection
*PLUS
Num. obs: 71736
Reflection shell
*PLUS
% possible obs: 75.6 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GD1

1gd1


Resolution: 2.11→8 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection
Rfree0.249 7204
Rwork0.198 -
all0.203 71217
obs0.203 71217
Refinement stepCycle: LAST / Resolution: 2.11→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10100 0 196 604 10900
LS refinement shellResolution: 2.11→2.18 Å
RfactorNum. reflection
Rfree0.315 592
Rwork0.254 -
obs-5443
Refinement
*PLUS
% reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.005
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg1.4
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_deg24.7
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_deg0.9

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