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- PDB-1qi6: SECOND APO FORM OF AN NADP DEPENDENT ALDEHYDE DEHYDROGENASE WITH ... -

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Basic information

Entry
Database: PDB / ID: 1qi6
TitleSECOND APO FORM OF AN NADP DEPENDENT ALDEHYDE DEHYDROGENASE WITH GLU250 SITUATED 3.7 A FROM CYS284
ComponentsPROTEIN (NADP DEPENDENT NONPHOSPHORYLATING GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE)
KeywordsOXIDOREDUCTASE
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-dependent glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsCobessi, D. / Tete-Favier, F. / Marchal, S. / Branlant, G. / Aubry, A.
CitationJournal: 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
DepositionJun 2, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Jan 10, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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: PROTEIN (NADP DEPENDENT NONPHOSPHORYLATING GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE)
B: PROTEIN (NADP DEPENDENT NONPHOSPHORYLATING GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE)
C: PROTEIN (NADP DEPENDENT NONPHOSPHORYLATING GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE)
D: PROTEIN (NADP DEPENDENT NONPHOSPHORYLATING GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,25916
Polymers205,1064
Non-polymers1,15312
Water10,178565
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19010 Å2
ΔGint-292 kcal/mol
Surface area61540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.800, 157.500, 110.300
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(0.251442, 0.019348, 0.967679), (0.005772, -0.999812, 0.018491), (0.967855, 0.000936, -0.251507)-24.47892, 79.43761, 30.58285
2given(-0.999951, -0.009746, 0.001595), (-0.009755, 0.999934, -0.006064), (-0.001536, -0.006079, -0.99998)6.77464, 0.21914, 55.30391
3given(-0.247824, -0.006181, -0.968785), (0.001637, -0.999981, 0.005961), (-0.968803, -0.000109, 0.24783)30.56247, 79.53691, 23.48991

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Components

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


Mass: 51276.438 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: SO4 / Source: (gene. exp.) Streptococcus mutans (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: Q59931, glyceraldehyde-3-phosphate dehydrogenase (NADP+)
#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.: 565 / 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: 2.98 Å3/Da / Density % sol: 60 %
Crystal growpH: 8.5
Details: 2.0 M AMMONIUM SULPHATE, 2 % PEG 400, HEPES O.1 M PH 7.5, PROTEIN 5MG/ML, pH 8.5
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
22.0 Mammonium sulfate1reservoir
30.1 MHEPES1reservoir
42 %PEG4001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS / Detector: IMAGE PLATE / Date: Jun 15, 1997 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 81791 / % possible obs: 96 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.059 / Rsym value: 0.059
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.188 / Rsym value: 0.188 / % possible all: 68.4

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Processing

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

1euh


Resolution: 2.5→8 Å / Data cutoff high absF: 3500 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.28 --RANDOM
Rwork0.232 ---
obs0.232 81631 95.952 %-
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14384 0 60 565 15009
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.295
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.41
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.169
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
Refinement
*PLUS
Highest resolution: 2.5 Å / σ(F): 0 / Rfactor Rfree: 0.28
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.41
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.169

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