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- PDB-4gpd: THE STRUCTURE OF LOBSTER APO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDRO... -

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Basic information

Entry
Database: PDB / ID: 4gpd
TitleTHE STRUCTURE OF LOBSTER APO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE AT 3.0 ANGSTROMS RESOLUTION
ComponentsAPO-D-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 / 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
Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesHomarus americanus (American lobster)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsGriffith, J.P. / Song, S. / Rossmann, M.G.
Citation
Journal: J.Mol.Biol. / Year: 1980
Title: Structure of lobster apo-D-glyceraldehyde-3-phosphate dehydrogenase at 3.0 A resolution.
Authors: Murthy, M.R. / Garavito, R.M. / Johnson, J.E. / Rossmann, M.G.
#1: Journal: J.Biol.Chem. / Year: 1975
Title: Studies of Asymmetry in the Three-Dimensional Structure of Lobster D-Glyceraldehyde-3-Phosphate Dehydrogenase
Authors: Moras, D. / Olsen, K.W. / Sabesan, M.N. / Buehner, M. / Ford, G.C. / Rossmann, M.G.
#2: Journal: J.Mol.Biol. / Year: 1976
Title: Anion Binding Sites in the Active Center of D-Glyceraldehyde-3-Phosphate Dehydrogenase
Authors: Olsen, K.W. / Garavito, R.M. / Sabesan, M.N. / Rossmann, M.G.
#3: Journal: J.Mol.Biol. / Year: 1976
Title: Studies on Coenzyme Binding to Glyceraldehyde-3-Phosphate Dehydrogenase
Authors: Olsen, K.W. / Garavito, R.M. / Sabesan, M.N. / Rossmann, M.G.
#4: Journal: STRUCTURE AND CONFORMATION OF NUCLEIC ACIDS AND PROTEIN-NUCLEIC ACID INTERACTIONS : PROCEEDINGS OF THE FOURTH ANNUAL HARRY STEENBOCK SYMPOSIUM, JUNE 16-19, 1974, MADISON, WISCONSIN
Year: 1975
Title: A Comparison of the Binding and Function of Nad with Respect to Lactate Dehydrogenase and Glyceraldehyde-3-Phosphate Dehydrogenase
Authors: Rossmann, M.G.
#5: Journal: J.Biol.Chem. / Year: 1975
Title: Sequence Variability and Structure of D-Glyceraldehyde-3-Phosphate Dehydrogenase
Authors: Olsen, K.W. / Moras, D. / Rossmann, M.G. / Harris, J.I.
#6: Journal: J.Mol.Biol. / Year: 1974
Title: Three-Dimensional Structure of D-Glyceraldehyde-3-Phosphate Dehydrogenase
Authors: Buehner, M. / Ford, G.C. / Moras, D. / Olsen, K.W. / Rossmann, M.G.
#7: Journal: J.Mol.Biol. / Year: 1974
Title: Structure Determination of Crystalline Lobster D-Glyceraldehyde-3-Phosphate Dehydrogenase
Authors: Buehner, M. / Ford, G.C. / Moras, D. / Olsen, K.W. / Rossmann, M.G.
#8: Journal: Proc.Natl.Acad.Sci.USA / Year: 1973
Title: D-Glyceraldehyde-3-Phosphate Dehydrogenase, Three-Dimensional Structure and Evolutionary Significance
Authors: Buehner, M. / Ford, G.C. / Moras, D. / Olsen, K.W. / Rossmann, M.G.
#9: Journal: Acta Crystallogr.,Sect.A / Year: 1975
Title: An Application of the Molecular Replacement Technique in Direct Space to a Known Protein Structure
Authors: Argos, P. / Ford, G.C. / Rossmann, M.G.
History
DepositionJan 4, 1988Processing site: BNL
SupersessionJul 12, 1989ID: 2GPD
Revision 1.0Jul 12, 1989Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Remark 700SHEET THE SHEET SUBSTRUCTURE OF THE CATALYTIC DOMAIN IS BIFURCATED. TO REPRESENT THIS FEATURE ...SHEET THE SHEET SUBSTRUCTURE OF THE CATALYTIC DOMAIN IS BIFURCATED. TO REPRESENT THIS FEATURE REDUNDANT SHEETS ARE DEFINED. STRANDS 1-7 OF SHEET C1 ARE IDENTICAL TO STRANDS 1-7 OF SHEET C2.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
1: APO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
2: APO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
3: APO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
4: APO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)143,0324
Polymers143,0324
Non-polymers00
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13300 Å2
ΔGint-54 kcal/mol
Surface area47470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.019, 80.956, 82.545
Angle α, β, γ (deg.)110.85, 71.47, 116.86
Int Tables number1
Space group name H-MP1
Atom site foot note1: SEE REMARK 6.
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.99755, 0.06825, 0.01534), (0.06743, 0.87985, 0.47044), (0.01861, 0.47033, -0.88232)103.10318, -20.02042, 64.92454
2given(-0.34281, 0.20463, -0.91685), (0.20517, -0.93612, -0.28564), (-0.91675, -0.28604, 0.27893)104.43578, 72.71724, 91.16001
3given(0.34413, -0.26927, 0.89948), (-0.27332, -0.94523, -0.1784), (0.89818, -0.18444, -0.39885)4.94277, 93.71841, 20.86403
DetailsTHE TRANSFORMATION PRESENTED AS *MTRIX 1* BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN 2 WHEN APPLIED TO CHAIN 1. THE TRANSFORMATION PRESENTED AS *MTRIX 2* BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN 3 WHEN APPLIED TO CHAIN 1. THE TRANSFORMATION PRESENTED AS *MTRIX 3* BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN 4 WHEN APPLIED TO CHAIN 1.

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Components

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


Mass: 35757.914 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homarus americanus (American lobster)
References: UniProt: P00357, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O
Compound detailsEACH SUBUNIT IS CONSIDERED TO BE COMPRISED OF A COFACTOR BINDING DOMAIN AND A CATALYTIC DOMAIN. THE ...EACH SUBUNIT IS CONSIDERED TO BE COMPRISED OF A COFACTOR BINDING DOMAIN AND A CATALYTIC DOMAIN. THE CHARACTERS B AND C IN THE SHEET IDENTIFIERS ARE USED TO DENOTE WHICH DOMAIN INCLUDES THESE STRUCTURAL FEATURES.
Sequence detailsTHE SEQUENCE GIVEN IN *PIR* SHOWS RESIDUE 6 TO BE ASP. THE DATA PRESENTED IN THIS ENTRY SHOWS ...THE SEQUENCE GIVEN IN *PIR* SHOWS RESIDUE 6 TO BE ASP. THE DATA PRESENTED IN THIS ENTRY SHOWS RESIDUE 6 AS ASN (M. ROSSMANN, PRIVATE COMMUNICATION FROM J. HARRIS).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.17 Å3/Da / Density % sol: 61.26 %
Crystal grow
*PLUS
Method: microdialysis / PH range low: 6.4 / PH range high: 6.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
118 mg/mlprotein11
23.08 Mammonium sulfate12
31 mMEDTA12
41 mMdithiothreitol12
5chloroform12dialyzing medium

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Data collection

Reflection
*PLUS
Highest resolution: 3 Å / Num. obs: 30128 / % possible obs: 86 % / Num. measured all: 56899

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.8→6 Å / σ(I): 3
Details: THE PHASES FOR APO-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE WERE DERIVED BY THE MOLECULAR REPLACEMENT TECHNIQUE. THE INITIAL PHASING MODEL WAS THE HOLO GAPDH ELECTRON DENSITY SUITABLY ...Details: THE PHASES FOR APO-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE WERE DERIVED BY THE MOLECULAR REPLACEMENT TECHNIQUE. THE INITIAL PHASING MODEL WAS THE HOLO GAPDH ELECTRON DENSITY SUITABLY TRANSFORMED TO THE TRICLINIC APO GAPDH CELL. THE KNOWN 222 SYMMETRY OF THE TETRAMERIC MOLECULE WAS USED IN IMPROVING THE PHASES BY ELECTRON DENSITY AVERAGING. THE STRUCTURE WAS FOUND TO BE VERY SIMILAR TO THAT OF THE HOLO ENZYME.
RfactorNum. reflection
obs0.218 27016
Refinement stepCycle: LAST / Resolution: 2.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10028 0 0 122 10150
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 6 Å / Num. reflection obs: 27016 / σ(I): 3 / Rfactor obs: 0.218
Solvent computation
*PLUS
Displacement parameters
*PLUS

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