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- PDB-1gad: COMPARISON OF THE STRUCTURES OF WILD TYPE AND A N313T MUTANT OF E... -

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Basic information

Entry
Database: PDB / ID: 1gad
TitleCOMPARISON OF THE STRUCTURES OF WILD TYPE AND A N313T MUTANT OF ESCHERICHIA COLI GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASES: IMPLICATION FOR NAD BINDING AND COOPERATIVITY
ComponentsD-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE (ALDEHYDE(D)-NAD+(A))
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 / identical protein binding / membrane / cytosol
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 A
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsDuee, E. / Olivier-Deyris, L. / Fanchon, E. / Corbier, C. / Branlant, G. / Dideberg, O.
Citation
Journal: J.Mol.Biol. / Year: 1996
Title: Comparison of the structures of wild-type and a N313T mutant of Escherichia coli glyceraldehyde 3-phosphate dehydrogenases: implication for NAD binding and cooperativity.
Authors: Duee, E. / Olivier-Deyris, L. / Fanchon, E. / Corbier, C. / Branlant, G. / Dideberg, O.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1995
Title: Crystallization and Preliminary X-Ray Diffraction Studies of Escherichia Coli Glyceraldehyde-3-Phosphate Dehydrogenase
Authors: Olivier, L. / Buisson, G. / Fanchon, E. / Corbier, C. / Branlant, G. / Dideberg, O.
#2: Journal: Eur.J.Biochem. / Year: 1985
Title: Nucleotide Sequence of the Escherichia Coli Gap Gene. Different Evolutionary Behavior of the Nad+ Binding Domain and of the Catalytic Domain of D-Glyceraldehyde-3-Phosphate Dehydrogenase
Authors: Branlant, G. / Branlant, C.
History
DepositionOct 24, 1995Processing site: BNL
Revision 1.0Mar 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)72,2194
Polymers70,8922
Non-polymers1,3272
Water5,224290
1
O: D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
P: D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
hetero molecules

O: D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
P: D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,4398
Polymers141,7854
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area19610 Å2
ΔGint-119 kcal/mol
Surface area43630 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)79.140, 189.560, 122.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11O-471-

HOH

DetailsTHE MOLECULAR TWO-FOLD SYMMETRY AXIS R COINCIDES WITH A CRYSTALLOGRAPHIC TWO-FOLD SYMMETRY AXIS PARALLEL TO THE B AXIS. THE COMPLETE TETRAMER IS GENERATED FROM THE ASYMMETRIC UNIT BY THE CRYSTALLOGRAPHIC SYMMETRY OPERATION: - X , Y , 1/2 -Z.

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Components

#1: Protein D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE


Mass: 35446.238 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: WILD TYPE, HOLO FORM / Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PBR322 / Gene (production host): ESCHERICHIA COLI GAPA / Production host: Escherichia coli (E. coli) / Strain (production host): DF221 (GAPDH-)
References: UniProt: P0A9B2, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.23 Å3/Da / Density % sol: 61.93 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.35 Mtris-sodium citrate1reservoir
21 mMEDTA1reservoir
31 mMdithiothreitol1reservoir
40.1 mMazide1reservoir
50.3 mMNAD1reservoir
6100 mMHEPES1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.8→8 Å / Num. obs: 62943 / % possible obs: 74.8 % / Observed criterion σ(I): 0
Reflection
*PLUS
Num. obs: 66191 / % possible obs: 69 % / Rmerge(I) obs: 0.065
Reflection shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 2 Å / % possible obs: 40 %

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Processing

Software
NameClassification
ARP/wARPmodel building
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.8→8 Å / σ(F): 2
Details: ATOMS FOR WHICH NO DENSITY WAS OBSERVED IN THE ELECTRON DENSITY MAP WERE GIVEN AN OCCUPANCY OF 0.0.
RfactorNum. reflection% reflection
Rwork0.197 --
obs0.197 58328 69 %
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4976 0 88 290 5354
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.62
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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