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- PDB-2esd: Crystal Structure of thioacylenzyme intermediate of an Nadp Depen... -

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Basic information

Entry
Database: PDB / ID: 2esd
TitleCrystal Structure of thioacylenzyme intermediate of an Nadp Dependent Aldehyde Dehydrogenase
ComponentsNADP-dependent glyceraldehyde-3-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / ALDH / GAPN / ternary complex
Function / homology
Function and homology information


glyceraldehyde-3-phosphate dehydrogenase (NADP+) / glyceraldehyde-3-phosphate dehydrogenase (NADP+) (non-phosphorylating) activity / glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) activity
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, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, C-terminal ...: / 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, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GLYCERALDEHYDE-3-PHOSPHATE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsD'Ambrosio, K. / Didierjean, C. / Benedetti, E. / Aubry, A. / Corbier, C.
Citation
Journal: Biochemistry / Year: 2006
Title: The first crystal structure of a thioacylenzyme intermediate in the ALDH family: new coenzyme conformation and relevance to catalysis
Authors: D'Ambrosio, K. / Pailot, A. / Talfournier, F. / Didierjean, C. / Benedetti, E. / Aubry, A. / Branlant, G. / Corbier, C.
#1: Journal: J.Mol.Biol. / Year: 2000
Title: Structural and biochemical investigations of the catalytic mechanism of an NADP-dependent aldehyde dehydrogenase from Streptococcus mutans
Authors: Cobessi, D. / Tete-Favier, F. / Marchal, S. / Branlant, G. / Aubry, A.
History
DepositionOct 26, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 2, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
B: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
C: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
D: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,52712
Polymers204,8744
Non-polymers3,6548
Water13,980776
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23050 Å2
ΔGint-100 kcal/mol
Surface area57640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.500, 154.900, 112.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is the tetramer present in the asymmetric unit

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Components

#1: Protein
NADP-dependent glyceraldehyde-3-phosphate dehydrogenase / Nadp-Dependent Nonphosphorylating Glyceraldehyde-3-Phosphate Dehydrogenase


Mass: 51218.402 Da / Num. of mol.: 4 / Mutation: E250A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Plasmid: pBluescript SK / Production host: Escherichia coli (E. coli) / Strain (production host): DH5
References: UniProt: Q59931, glyceraldehyde-3-phosphate dehydrogenase (NADP+)
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-G3H / GLYCERALDEHYDE-3-PHOSPHATE


Mass: 170.058 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H7O6P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 776 / 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: 3.03 Å3/Da / Density % sol: 59.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 7% PEG 8000, 10% PEG 1000, 0.8M sodium formate, 0.05M imidazole , pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.9804 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 16, 2002
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9804 Å / Relative weight: 1
ReflectionResolution: 2.55→20 Å / Num. obs: 79121 / % possible obs: 97.4 % / Rsym value: 0.074 / Net I/σ(I): 16.9

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Processing

Software
NameClassification
MAR345data collection
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2euh

2euh


Resolution: 2.55→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.248 7952 -RANDOM
Rwork0.198 ---
all-79121 --
obs-79083 96.9 %-
Refinement stepCycle: LAST / Resolution: 2.55→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14392 0 424 776 15592
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.33

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