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- PDB-1qi1: Ternary Complex of an NADP Dependent Aldehyde Dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 1qi1
TitleTernary Complex of an NADP Dependent Aldehyde Dehydrogenase
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 / 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, N-terminal / 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, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GLYCERALDEHYDE-3-PHOSPHATE / SN-GLYCEROL-3-PHOSPHATE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 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: BNL / Processing site: RCSB
Revision 1.0Jan 10, 2001Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 3, 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_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 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

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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)208,69712
Polymers205,0424
Non-polymers3,6568
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22810 Å2
ΔGint-113 kcal/mol
Surface area58350 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)158.500, 158.500, 282.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.559341, -0.064615, -0.826415), (-0.072396, -0.98934, 0.126353), (-0.82577, 0.130503, 0.548701)10.10347, 235.20862, -14.12903
2given(0.556323, -0.032506, 0.83033), (-0.028313, -0.999396, -0.020154), (0.830484, -0.012297, -0.556907)-7.89173, 237.98, 23.81401
3given(-0.995788, 0.091587, -0.004196), (0.091344, 0.987141, -0.131186), (-0.007873, -0.131017, -0.991349)-20.71248, 3.30139, 37.75797

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Components

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


Mass: 51260.375 Da / Num. of mol.: 4 / Mutation: C284S
Source method: isolated from a genetically manipulated source
Details: NADP, D-GLYCERALDEHYDE-3-PHOSPHATE / 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 / Nicotinamide adenine dinucleotide phosphate


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


Mass: 170.058 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H7O6P
#4: Chemical ChemComp-G3P / SN-GLYCEROL-3-PHOSPHATE / Glycerol 3-phosphate


Mass: 172.074 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H9O6P
Nonpolymer detailsNAP and G3H ARE ASSIGNED OCCUPANCY 0.5 NADP WAS POSITIONED AS GOOD AS THE DENSITY ALLOWED IT ...NAP and G3H ARE ASSIGNED OCCUPANCY 0.5 NADP WAS POSITIONED AS GOOD AS THE DENSITY ALLOWED IT RESULTING FROM ITS POOR QUALITY IN THE NICOTINAMIDE MONONUCLEOSIDE PART. THE G3H ELECTRONIC DENSITY IS POORLY DEFINED IN THE MONOMERS B AND C.

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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: 5 Å3/Da / Density % sol: 75 %
Crystal growpH: 5.5 / Details: AMMONIUM SULFATE 2.0 M , 40 MG/ML PROTEIN, pH 5.5
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112.5 mMsodium phosphate1drop
20.25 mMdithiothreitol1drop
310 mg/mlprotein1drop
44 mMNADP1drop
51.5 Mammonium sulfate1drop

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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: Jan 15, 1999 / 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: 3→15 Å / Num. obs: 65980 / % possible obs: 80.3 % / Observed criterion σ(I): 2 / Redundancy: 1.5 % / Rmerge(I) obs: 0.097 / Rsym value: 0.097 / Net I/σ(I): 7.3
Reflection shellResolution: 3→3.11 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.315 / Mean I/σ(I) obs: 2 / Rsym value: 0.315 / % possible all: 78.2
Reflection
*PLUS
Highest resolution: 3 Å

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EUH

2euh


Resolution: 3→8 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.283 --RANDOM
Rwork0.242 ---
obs0.242 65864 74.96 %-
Refinement stepCycle: LAST / Resolution: 3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14384 0 232 0 14616
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
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_deg2.403
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.19
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.938
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
Refine LS restraints NCSNCS model details: RESTRAINTS
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.19
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.938

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