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- PDB-1gd1: STRUCTURE OF HOLO-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE FROM B... -

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Basic information

Entry
Database: PDB / ID: 1gd1
TitleSTRUCTURE OF HOLO-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE FROM BACILLUS STEAROTHERMOPHILUS AT 1.8 ANGSTROMS RESOLUTION
ComponentsHOLO-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, 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: 1.8 Å
AuthorsSkarzynski, T. / Moody, P.C.E. / Wonacott, A.J.
Citation
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.
#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 Escherichia Coli
Authors: Branlant, C. / Oster, T. / Branlant, G.
#2: Journal: J.Mol.Biol. / Year: 1988
Title: Coenzyme-Induced Conformational Changes in Glyceraldehyde-3-Phosphate Dehydrogenase from Bacillus Stearothermophillus
Authors: Skarzynski, T. / Wonacott, A.J.
#3: Journal: J.Mol.Biol. / Year: 1984
Title: Structural Evidence for Ligand-Induced Sequential Conformational Changes in Glyceraldehyde 3-Phosphate Dehydrogenase
Authors: Leslie, A.G.W. / Wonacott, A.J.
#4: Journal: J.Mol.Biol. / Year: 1983
Title: Coenzyme Binding in Crystals of Glyceraldehyde-3-Phosphate Dehydrogenase
Authors: Leslie, A.G.W. / Wonacott, A.J.
#5: Journal: Philos.Trans.R.Soc.London,Ser.B / Year: 1981
Title: Glyceraldehyde-3-Phosphate Dehydrogenase
Authors: Dalziel, K. / Mcferran, N.V. / Wonacott, A.J.
#6: Journal: Proc.FEBS Meet. / Year: 1978
Title: Enzymes from Thermophilic Bacteria
Authors: Walker, J.E.
#7: Journal: Nature / Year: 1977
Title: Sequence and Structure of D-Glyceraldehyde 3-Phosphate Dehydrogenase from Bacillus Stearothermophilus
Authors: Biesecker, G. / Harris, J.I. / Thierry, J.C. / Walker, J.E. / Wonacott, A.J.
#8: Journal: Biochem.Soc.Trans. / Year: 1977
Title: Coenzyme Binding and Co-Operativity in D-Glyceraldehyde 3-Phosphate Dehydrogenase
Authors: Biesecker, G. / Wonacott, A.J.
#9: Journal: FEBS Lett. / Year: 1971
Title: Glyceraldehyde-3-Phosphate Dehydrogenase from Bacillus Stearothermophilus
Authors: Suzuki, K. / Harris, J.I.
History
DepositionJun 22, 1987Processing site: BNL
Revision 1.0Jan 16, 1988Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 2.0Jul 26, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / atom_sites ...atom_site / atom_sites / database_2 / database_PDB_matrix / pdbx_database_remark / pdbx_database_status / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_ncs_oper / struct_site
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[1][2] / _atom_sites.fract_transf_matrix[1][3] / _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[2][3] / _atom_sites.fract_transf_matrix[3][1] / _atom_sites.fract_transf_matrix[3][2] / _atom_sites.fract_transf_matrix[3][3] / _atom_sites.fract_transf_vector[1] / _atom_sites.fract_transf_vector[2] / _atom_sites.fract_transf_vector[3] / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _database_PDB_matrix.origx[1][1] / _database_PDB_matrix.origx[1][2] / _database_PDB_matrix.origx[1][3] / _database_PDB_matrix.origx[2][1] / _database_PDB_matrix.origx[2][2] / _database_PDB_matrix.origx[2][3] / _database_PDB_matrix.origx[3][1] / _database_PDB_matrix.origx[3][2] / _database_PDB_matrix.origx[3][3] / _database_PDB_matrix.origx_vector[1] / _database_PDB_matrix.origx_vector[2] / _database_PDB_matrix.origx_vector[3] / _pdbx_database_status.process_site / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _struct_ncs_oper.matrix[1][1] / _struct_ncs_oper.matrix[1][2] / _struct_ncs_oper.matrix[1][3] / _struct_ncs_oper.matrix[2][1] / _struct_ncs_oper.matrix[2][2] / _struct_ncs_oper.matrix[2][3] / _struct_ncs_oper.matrix[3][1] / _struct_ncs_oper.matrix[3][2] / _struct_ncs_oper.matrix[3][3] / _struct_ncs_oper.vector[1] / _struct_ncs_oper.vector[2] / _struct_ncs_oper.vector[3] / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Details: Coordinates and associated ncs operations (if present) transformed into standard crystal frame
Provider: repository / Type: Remediation
Revision 2.1Sep 6, 2023Group: Data collection / Refinement description / Category: chem_comp_atom / chem_comp_bond / struct_ncs_oper
Item: _struct_ncs_oper.matrix[1][1] / _struct_ncs_oper.matrix[1][2] ..._struct_ncs_oper.matrix[1][1] / _struct_ncs_oper.matrix[1][2] / _struct_ncs_oper.matrix[1][3] / _struct_ncs_oper.matrix[2][1] / _struct_ncs_oper.matrix[2][2] / _struct_ncs_oper.matrix[2][3] / _struct_ncs_oper.matrix[3][1] / _struct_ncs_oper.matrix[3][2] / _struct_ncs_oper.matrix[3][3] / _struct_ncs_oper.vector[1] / _struct_ncs_oper.vector[2] / _struct_ncs_oper.vector[3]

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)147,38616
Polymers143,9644
Non-polymers3,42212
Water12,034668
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.440, 124.100, 82.540
Angle α, β, γ (deg.)90.00, 108.98, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.32914388, -0.11859551, 0.93679851), (-0.11858943, -0.97903548, -0.16560093), (0.93680779, -0.16561107, 0.30817936)-15.5571, 30.01619, 14.94063
2given(-0.99407439, 0.10828628, 0.00946446), (0.10829182, 0.97895525, 0.17296498), (0.00946596, 0.17298351, -0.98488087)-17.29732, -0.11792, 12.17887
3given(0.32321827, 0.01030923, -0.94626296), (0.0102976, -0.99991977, -0.00736405), (-0.94627374, -0.00737245, -0.32329849)1.55934, 30.16609, 2.50917
DetailsTHE TRANSFORMATION PROVIDED ON THE *MTRIX 1* RECORDS BELOW CORRESPONDS TO A TWO-FOLD ROTATION ABOUT AXIS P OF THE ORTHOGONAL AXIAL SYSTEM DESCRIBED IN REMARK 5 ABOVE AND YIELDS APPROXIMATE COORDINATES FOR CHAIN *P* WHEN APPLIED TO CHAIN *O*. THE TRANSFORMATION PROVIDED ON THE *MTRIX 2* RECORDS BELOW (TWO-FOLD ROTATION ABOUT AXIS Q) YIELDS APPROXIMATE COORDINATES FOR CHAIN *Q* WHEN APPLIED TO CHAIN *O*. THE TRANSFORMATION PROVIDED ON THE *MTRIX 3* RECORDS BELOW (TWO-FOLD ROTATION ABOUT AXIS R) YIELDS APPROXIMATE COORDINATES FOR CHAIN *R* WHEN APPLIED TO CHAIN *O*.

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Components

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


Mass: 35991.047 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Cell line: 293 / Gene: BACILLUS STEAROTHERMOPHILUS / Gene (production host): BACILLUS STEAROTHERMOPHILUS / Strain (production host): 293
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.: 668 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE NUMBERING SCHEME USED IN THIS ENTRY MAXIMIZES THE HOMOLOGY BETWEEN SEQUENCES OF GAPDH FROM ...THE NUMBERING SCHEME USED IN THIS ENTRY MAXIMIZES THE HOMOLOGY BETWEEN SEQUENCES OF GAPDH FROM VARIOUS SOURCES. THE AMINO ACID SEQUENCE USED IS BASED ON THE GENE SEQUENCE (SEE REFERENCE 1 ABOVE) AND CONTAINS 20 DIFFERENCES FROM THE SEQUENCE GIVEN IN REFERENCE 7 ABOVE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.64 %

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 116031 / % possible obs: 81 % / Rmerge(I) obs: 0.073

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementHighest resolution: 1.8 Å / σ(F): 3 /
RfactorNum. reflection
obs0.177 93120
Refinement stepCycle: LAST / Highest resolution: 1.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10100 0 216 668 10984
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Lowest resolution: 8 Å / σ(F): 3 / Rfactor obs: 0.177
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0190.02
X-RAY DIFFRACTIONp_angle_d0.0390.03
X-RAY DIFFRACTIONp_planar_d0.050.05
X-RAY DIFFRACTIONp_plane_restr0.0180.02
X-RAY DIFFRACTIONp_chiral_restr0.160.15
X-RAY DIFFRACTIONp_mcbond_it2.572
X-RAY DIFFRACTIONp_scbond_it5.13
X-RAY DIFFRACTIONp_mcangle_it3.483
X-RAY DIFFRACTIONp_scangle_it6.994

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