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- PDB-1cf2: THREE-DIMENSIONAL STRUCTURE OF D-GLYCERALDEHYDE-3-PHOSPHATE DEHYD... -

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Basic information

Entry
Database: PDB / ID: 1cf2
TitleTHREE-DIMENSIONAL STRUCTURE OF D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE FROM THE HYPERTHERMOPHILIC ARCHAEON METHANOTHERMUS FERVIDUS
ComponentsPROTEIN (GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE)
KeywordsOXIDOREDUCTASE / OXYDOREDUCTASE
Function / homology
Function and homology information


glyceraldehyde-3-phosphate dehydrogenase (NAD(P)+) (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) activity / 4-hydroxy-tetrahydrodipicolinate reductase / 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesMethanothermus fervidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsCharron, C. / Talfournier, F. / Isuppov, M.N. / Branlant, G. / Littlechild, J.A. / Vitoux, B. / Aubry, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Crystallization and preliminary X-ray diffraction studies of D-glyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic archaeon Methanothermus fervidus.
Authors: Charron, C. / Talfournier, F. / Isupov, M.N. / Branlant, G. / Littlechild, J.A. / Vitoux, B. / Aubry, A.
History
DepositionMar 24, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Mar 29, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Apr 11, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_beamline
Revision 1.5Dec 27, 2023Group: 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
P: PROTEIN (GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE)
R: PROTEIN (GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE)
O: PROTEIN (GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE)
Q: PROTEIN (GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,17712
Polymers149,8194
Non-polymers3,3588
Water17,294960
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19100 Å2
ΔGint-182 kcal/mol
Surface area43470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.660, 153.280, 74.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.99936, 0.00904, -0.03459), (-0.00659, -0.99751, -0.07028), (-0.03514, -0.07001, 0.99693)73.85568, 77.07173, 4.1492
2given(-0.42904, 0.90153, 0.05626), (0.90298, 0.42646, 0.05247), (0.02332, 0.07331, -0.99704)17.86558, -11.76918, 10.72348
3given(0.43776, -0.89909, -0.00296), (-0.89908, -0.43777, 0.00371), (-0.00463, 0.00103, -0.99999)55.16506, 88.05237, 14.67648

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Components

#1: Protein
PROTEIN (GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE)


Mass: 37454.793 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermus fervidus (archaea) / Production host: Escherichia coli (E. coli) / Strain (production host): HB101
References: UniProt: P10618, 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-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 960 / 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: 2.62 Å3/Da / Density % sol: 53.01 %
Crystal growpH: 6.5 / Details: pH 6.50
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: Jancarik, J., (1991) J. Appl. Crystallogr., 24, 409.
Components of the solutions
*PLUS
Conc.: 10 mg/ml / Common name: protein

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM02 / Wavelength: 0.987
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.11→10 Å / Num. obs: 82965 / % possible obs: 91.7 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Rsym value: 5.6 / Net I/σ(I): 9.1
Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 10 Å / % possible obs: 91.7 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Num. measured all: 415252 / Rmerge(I) obs: 0.056
Reflection shell
*PLUS
Highest resolution: 2.11 Å / Lowest resolution: 2.17 Å / % possible obs: 69.3 % / Rmerge(I) obs: 0.151 / Mean I/σ(I) obs: 4

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Processing

SoftwareName: REFMAC / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→10 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.257 -2 %
Rwork0.194 --
obs-82965 91.7 %
Refinement stepCycle: LAST / Resolution: 2.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10448 0 212 960 11620
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.014
X-RAY DIFFRACTIONp_angle_d2.643
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 10 Å / Rfactor obs: 0.194
Solvent computation
*PLUS
Displacement parameters
*PLUS

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