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- PDB-1ky8: Crystal Structure of the Non-phosphorylating glyceraldehyde-3-pho... -

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Basic information

Entry
Database: PDB / ID: 1ky8
TitleCrystal Structure of the Non-phosphorylating glyceraldehyde-3-phosphate Dehydrogenase
Componentsglyceraldehyde-3-phosphate dehydrogenaseGlyceraldehyde 3-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / GAPN / ALDH
Function / homology
Function and homology information


glyceraldehyde-3-phosphate dehydrogenase [NAD(P)+] / glyceraldehyde-3-phosphate dehydrogenase (NADP+) (non-phosphorylating) activity / metabolic process / NAD binding / NADP binding
Similarity search - Function
Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / NAD(P)-dependent glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesThermoproteus tenax (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsPohl, E. / Brunner, N. / Wilmanns, M. / Hensel, R.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: The Crystal Structure of the Allosteric Non-phosphorylating glyceraldehyde-3-phosphate Dehydrogenase from the Hyperthermophilic Archaeum Thermoproteus tenax
Authors: Pohl, E. / Brunner, N. / Wilmanns, M. / Hensel, R.
History
DepositionFeb 4, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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
A: glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9253
Polymers54,1581
Non-polymers7662
Water6,954386
1
A: glyceraldehyde-3-phosphate dehydrogenase
hetero molecules

A: glyceraldehyde-3-phosphate dehydrogenase
hetero molecules

A: glyceraldehyde-3-phosphate dehydrogenase
hetero molecules

A: glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,69912
Polymers216,6334
Non-polymers3,0668
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z1
crystal symmetry operation9_555-x,-x+y,-z+1/31
crystal symmetry operation12_565x,x-y+1,-z+1/31
Buried area26370 Å2
ΔGint-141 kcal/mol
Surface area58700 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)185.200, 185.200, 132.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
DetailsThe functional tetramer is generated by the crystallographic symmetry

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Components

#1: Protein glyceraldehyde-3-phosphate dehydrogenase / Glyceraldehyde 3-phosphate dehydrogenase / NADP+


Mass: 54158.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoproteus tenax (archaea) / Production host: Escherichia coli (E. coli)
References: UniProt: O57693, glyceraldehyde-3-phosphate dehydrogenase (NADP+)
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 386 / 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: 2

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Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: sodium formate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 20K
Crystal grow
*PLUS
Components of the solutions
*PLUS
Conc.: 2.0 M / Common name: sodium formate

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
41001
1,2,3,41
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONEMBL/DESY, HAMBURG BW7B10.8469
SYNCHROTRONEMBL/DESY, HAMBURG BW7A20.9796
SYNCHROTRONEMBL/DESY, HAMBURG BW7A30.9792
SYNCHROTRONEMBL/DESY, HAMBURG BW7A40.9724
Detector
TypeIDDetectorDate
MARRESEARCH1IMAGE PLATEApr 4, 1999
MARRESEARCH2IMAGE PLATEJan 1, 1999
MARRESEARCH3IMAGE PLATEJan 1, 1999
MARRESEARCH4IMAGE PLATEJan 1, 1999
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111SINGLE WAVELENGTHMx-ray1
2focusing double crystalMADMx-ray1
3focusing double crystalMADMx-ray1
4focusing double crystalMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.84691
20.97961
30.97921
40.97241
ReflectionResolution: 2.4→30 Å / Num. all: 52004 / Num. obs: 52004 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.4→2.5 Å / % possible all: 100
Reflection
*PLUS
Lowest resolution: 50 Å / Num. obs: 53177 / % possible obs: 99.2 % / Num. measured all: 792801 / Rmerge(I) obs: 0.005
Reflection shell
*PLUS
% possible obs: 99.3 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 4.4

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Processing

Software
NameClassification
MAR345data collection
SCALEPACKdata scaling
SOLVEphasing
SHELXmodel building
X-PLORrefinement
SHELXphasing
RefinementMethod to determine structure: MAD / Resolution: 2.4→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.242 2626 random
Rwork0.208 --
all-52004 -
obs-52004 -
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3772 0 49 386 4207
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.48
Refinement
*PLUS
Lowest resolution: 30 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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