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- PDB-2euh: HOLO FORM OF A NADP DEPENDENT ALDEHYDE DEHYDROGENASE COMPLEX WITH... -

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Basic information

Entry
Database: PDB / ID: 2euh
TitleHOLO FORM OF A NADP DEPENDENT ALDEHYDE DEHYDROGENASE COMPLEX WITH NADP+
ComponentsNADP DEPENDENT NON PHOSPHORYLATING GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / DEHYDROGENASE
Function / homology
Function and homology information


glyceraldehyde-3-phosphate dehydrogenase (NADP+) / glyceraldehyde-3-phosphate dehydrogenase (NADP+) (non-phosphorylating) activity / lactaldehyde dehydrogenase (NAD+) 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsCobessi, D. / Tete-Favier, F. / Marchal, S. / Branlant, G. / Aubry, A.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Apo and holo crystal structures of an NADP-dependent aldehyde dehydrogenase from Streptococcus mutans.
Authors: Cobessi, D. / Tete-Favier, F. / Marchal, S. / Azza, S. / Branlant, G. / Aubry, A.
History
DepositionNov 5, 1998Processing site: BNL
Revision 1.0Jul 22, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NADP DEPENDENT NON PHOSPHORYLATING GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
B: NADP DEPENDENT NON PHOSPHORYLATING GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
C: NADP DEPENDENT NON PHOSPHORYLATING GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
D: NADP DEPENDENT NON PHOSPHORYLATING GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,56013
Polymers205,1064
Non-polymers3,4549
Water7,728429
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22450 Å2
ΔGint-168 kcal/mol
Surface area58710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.800, 154.800, 114.300
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(0.385385, 0.015872, 0.922619), (0.00658, -0.999874, 0.014452), (0.922732, 0.000501, -0.385441)12.24882, 76.29271, -19.62094
2given(-0.999621, -0.026879, 0.005895), (-0.026927, 0.999604, -0.008186), (-0.005673, -0.008341, -0.999949)127.53406, 1.98168, 56.57204
3given(-0.374971, 0.023405, -0.926741), (-0.016308, -0.999693, -0.018649), (-0.926893, 0.00812, 0.375237)113.61524, 75.58877, 76.95013

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Components

#1: Protein
NADP DEPENDENT NON PHOSPHORYLATING GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE / NADP DEPENDENT ALDEHYDE DEHYDROGENASE


Mass: 51276.438 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Production host: Escherichia coli (E. coli)
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 429 / 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: 3.12 Å3/Da / Density % sol: 60.6 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
140 mg/mlprotein1drop
250 mMphosphate1drop
42.0 Mammonium sulfate1reservoir
52 %(w/v)PEG4001reservoir
60.1 MHEPES1reservoir
3NADP1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceWavelength: 1.5418
DetectorDetector: IMAGE PLATE / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→16.6 Å / Num. obs: 65491 / % possible obs: 82.6 % / Redundancy: 1.5 % / Rsym value: 0.087
Reflection
*PLUS
Rmerge(I) obs: 0.087
Reflection shell
*PLUS
Rmerge(I) obs: 0.315

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Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EUH

1euh


Resolution: 2.6→8 Å / Data cutoff high absF: 3500 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.288 --RANDOM
Rwork0.235 ---
obs0.235 61490 77.6 %-
Displacement parametersBiso mean: 4.9 Å2
Refinement stepCycle: LAST / Resolution: 2.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14384 0 217 429 15030
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.439
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.38
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.946
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.38
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.946

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