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- PDB-1b7g: GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE -

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Basic information

Entry
Database: PDB / ID: 1b7g
TitleGLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE
ComponentsPROTEIN (GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE)
KeywordsOXIDOREDUCTASE / ARCHAEA / HYPERTHERMOPHILE / GAPDH / HYPERTHERMOPHILIC DEHYDROGENASE
Function / homology
Function and homology information


glyceraldehyde-3-phosphate dehydrogenase (NAD(P)+) (phosphorylating) / 4-hydroxy-tetrahydrodipicolinate reductase / glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) activity / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / lysine biosynthetic process via diaminopimelate / glycolytic process / NAD binding / NADP binding / cytoplasm
Similarity search - Function
Glyceraldehyde-3-phosphate dehydrogenase, type II / Dihydrodipicolinate reductase, N-terminal / Dihydrodipicolinate reductase, N-terminus / Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / 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 ...Glyceraldehyde-3-phosphate dehydrogenase, type II / Dihydrodipicolinate reductase, N-terminal / Dihydrodipicolinate reductase, N-terminus / Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / 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 speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.05 Å
AuthorsIsupov, M.N. / Littlechild, J.A.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: Crystal structure of the glyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic archaeon Sulfolobus solfataricus.
Authors: Isupov, M.N. / Fleming, T.M. / Dalby, A.R. / Crowhurst, G.S. / Bourne, P.C. / Littlechild, J.A.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Characterization, Crystallization and Preliminary X-Ray Investigation of Glyceraldehyde-3-Phosphate Dehydrogenase from the Hyperthermophilic Archaeon Sulfolobus Solfataricus
Authors: Fleming, T.M. / Jones, C.E. / Piper, P.W. / Cowan, D.A. / Isupov, M.N. / Littlechild, J.A.
History
DepositionJan 22, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 3, 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 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
O: PROTEIN (GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE)
Q: PROTEIN (GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,41614
Polymers75,2632
Non-polymers1,15312
Water9,296516
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5590 Å2
ΔGint-171 kcal/mol
Surface area27260 Å2
MethodPISA
2
O: PROTEIN (GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE)
Q: PROTEIN (GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE)
hetero molecules

O: PROTEIN (GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE)
Q: PROTEIN (GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,83228
Polymers150,5264
Non-polymers2,30624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area19180 Å2
ΔGint-418 kcal/mol
Surface area46510 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)101.550, 101.550, 179.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.62399, 0.38067, 0.68244), (0.36973, -0.62556, 0.68701), (0.68843, 0.68101, 0.2496)
Vector: 135.44405, -69.78342, -36.07544)

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Components

#1: Protein PROTEIN (GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE) / E.C.1.2.1.12


Mass: 37631.617 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Cellular location: CYTOPLASM / Production host: Escherichia coli (E. coli)
References: UniProt: P39460, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 516 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsVAL O 2, FOR EASE OF CLONING OF THE GENE IN E.COLI VAL Q 2, FOR EASE OF CLONING OF THE GENE IN E. ...VAL O 2, FOR EASE OF CLONING OF THE GENE IN E.COLI VAL Q 2, FOR EASE OF CLONING OF THE GENE IN E.COLI ILE O 48, CONFLICT BETWEEN THE TWO PUBLISHED SEQUENCES ILE Q 48, CONFLICT BETWEEN THE TWO PUBLISHED SEQUENCES ALA O 51, CONFLICT BETWEEN THE TWO PUBLISHED SEQUENCES ALA Q 51, CONFLICT BETWEEN THE TWO PUBLISHED SEQUENCES GLU O 72, CONFLICT BETWEEN THE TWO PUBLISHED SEQUENCES GLU Q 72, CONFLICT BETWEEN THE TWO PUBLISHED SEQUENCES ASP O 73, CONFLICT BETWEEN THE TWO PUBLISHED SEQUENCES ASP Q 73, CONFLICT BETWEEN THE TWO PUBLISHED SEQUENCES LYS O 159, CONFLICT BETWEEN THE TWO PUBLISHED SEQUENCES LYS Q 159, CONFLICT BETWEEN THE TWO PUBLISHED SEQUENCES

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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: 3.1 Å3/Da / Density % sol: 60 %
Description: THE STRUCTURE WAS SOLVED TO 3. ANGSTROM USING IN- HOUSE DATA
Crystal growpH: 6.5 / Details: pH 6.50
Crystal
*PLUS
Density % sol: 60 %
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
218 %(w/v)ammonium sulfate1drop
310 mMPIPES1drop
45 mMEDTA1drop
510 mMNAD+1drop
635 %ammonium sulfate1reservoir
710 mMPIPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 15, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→22 Å / Num. obs: 59606 / % possible obs: 99.6 % / Redundancy: 5.9 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 27.3
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 2.2 / % possible all: 98.5
Reflection
*PLUS
Highest resolution: 2.05 Å / Lowest resolution: 22 Å / Redundancy: 5.9 % / Biso Wilson estimate: 33 Å2
Reflection shell
*PLUS
% possible obs: 98.5 % / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.2

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXmodel building
MLPHAREphasing
REFMACrefinement
SHELXphasing
RefinementMethod to determine structure: MIR / Resolution: 2.05→22 Å / SU B: 5.4 / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.19 / ESU R Free: 0.19
RfactorNum. reflection% reflectionSelection details
Rfree0.293 1214 2 %RANDOM
Rwork0.226 ---
obs-59606 99.6 %-
Displacement parametersBiso mean: 38 Å2
Baniso -1Baniso -2Baniso -3
1-2.4 Å20 Å20 Å2
2--2.4 Å20 Å2
3----4.8 Å2
Refinement stepCycle: LAST / Resolution: 2.05→22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5268 0 60 516 5844
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.02
X-RAY DIFFRACTIONp_angle_d0.0250.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0370.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it3.74
X-RAY DIFFRACTIONp_mcangle_it4.56
X-RAY DIFFRACTIONp_scbond_it6.88
X-RAY DIFFRACTIONp_scangle_it810
X-RAY DIFFRACTIONp_plane_restr0.0250.03
X-RAY DIFFRACTIONp_chiral_restr0.1260.15
X-RAY DIFFRACTIONp_singtor_nbd0.190.3
X-RAY DIFFRACTIONp_multtor_nbd0.250.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1540.3
X-RAY DIFFRACTIONp_planar_tor4.15
X-RAY DIFFRACTIONp_staggered_tor1515
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor25.520
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.229
Solvent computation
*PLUS
Displacement parameters
*PLUS

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