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- PDB-5jry: Crystal structure of a NAD-dependent Aldehyde dehydrogenase from ... -

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Basic information

Entry
Database: PDB / ID: 5jry
TitleCrystal structure of a NAD-dependent Aldehyde dehydrogenase from Burkholderia multivorans in covalent complex with NAD
ComponentsNAD-dependent aldehyde dehydrogenase
KeywordsOXIDOREDUCTASE / SSGCID / Burkholderia / NAD-dependent aldehyde dehydrogenase / NAD / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / nucleotide 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, glutamic acid active site / Aldehyde dehydrogenases glutamic acid 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, glutamic acid active site / Aldehyde dehydrogenases glutamic acid 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
ACETATE ION / Chem-NDP / NAD-dependent aldehyde dehydrogenase
Similarity search - Component
Biological speciesBurkholderia multivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of a NAD-dependent Aldehyde dehydrogenase from Burkholderia multivorans
Authors: Abendroth, J. / Dranow, D.M. / Lorimer, D.D. / Edewards, T.E.
History
DepositionMay 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Sep 27, 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 / pdbx_struct_special_symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NAD-dependent aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7795
Polymers52,7901
Non-polymers9894
Water11,872659
1
A: NAD-dependent aldehyde dehydrogenase
hetero molecules

A: NAD-dependent aldehyde dehydrogenase
hetero molecules

A: NAD-dependent aldehyde dehydrogenase
hetero molecules

A: NAD-dependent aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,11520
Polymers211,1604
Non-polymers3,95516
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_657-x+1,y,-z+21
crystal symmetry operation4_567x,-y+1,-z+21
Buried area27450 Å2
ΔGint-56 kcal/mol
Surface area56040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.080, 87.030, 124.590
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-502-

GOL

21A-630-

HOH

31A-847-

HOH

41A-1021-

HOH

51A-1234-

HOH

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Components

#1: Protein NAD-dependent aldehyde dehydrogenase


Mass: 52790.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia multivorans (strain ATCC 17616 / 249) (bacteria)
Strain: ATCC 17616 / 249 / Gene: BMULJ_03565 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A0A0H3KPC8, Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 659 / 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: 2.24 Å3/Da / Density % sol: 45 % / Mosaicity: 0.17 °
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Molecular Dimensions Morpheus screen G7: 10% PEG 4000, 20% Glycerol, 20mM of each: Na-formate, Ammonium-acetate, Trisodium citrate, Na/K tartrate, Na oxamate; 100mM MOPS/NaHEPES pH 7.5; ...Details: Molecular Dimensions Morpheus screen G7: 10% PEG 4000, 20% Glycerol, 20mM of each: Na-formate, Ammonium-acetate, Trisodium citrate, Na/K tartrate, Na oxamate; 100mM MOPS/NaHEPES pH 7.5; BumuA.00020.x.B1.PS37849 at 20mg/ml + 2mM NADP; cryo: direct, puck pfb1-6, tray 271259 g7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 31, 2016
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. obs: 147035 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 8 % / Biso Wilson estimate: 8.27 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.71
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.2-1.230.5513.321100
1.23-1.260.4664.271100
1.26-1.30.4074.871100
1.3-1.340.3395.791100
1.34-1.390.2926.691100
1.39-1.430.2437.991100
1.43-1.490.2019.651100
1.49-1.550.1611.911100
1.55-1.620.13514.061100
1.62-1.70.11416.411100
1.7-1.790.09719.251100
1.79-1.90.08122.371100
1.9-2.030.06926.351100
2.03-2.190.06129.341100
2.19-2.40.05632.061100
2.4-2.680.05333.811100
2.68-3.10.0535.61100
3.1-3.790.04738.111100
3.79-5.370.04539.121100
5.370.04737.2199.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2 Å43.79 Å
Translation2 Å43.79 Å

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Processing

Software
NameClassification
XDSdata scaling
XSCALEdata scaling
PHASERphasing
Cootmodel building
PHENIXmodel building
PHENIXrefinement
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3pqa

3pqa


Resolution: 1.2→50 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 10.47
RfactorNum. reflection% reflectionSelection details
Rfree0.1297 1964 1.34 %RANDOM
Rwork0.1128 ---
obs0.113 147020 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 52.88 Å2 / Biso mean: 11.7957 Å2 / Biso min: 2.71 Å2
Refinement stepCycle: final / Resolution: 1.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3607 0 112 687 4406
Biso mean--9.4 24.42 -
Num. residues----477
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073907
X-RAY DIFFRACTIONf_angle_d1.0645348
X-RAY DIFFRACTIONf_chiral_restr0.082605
X-RAY DIFFRACTIONf_plane_restr0.008724
X-RAY DIFFRACTIONf_dihedral_angle_d17.0351502
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.2-1.230.16781570.15371022610383
1.23-1.26330.16061530.13711024910402
1.2633-1.30050.16571680.12861027410442
1.3005-1.34240.13751240.12211029210416
1.3424-1.39040.1441150.11661037010485
1.3904-1.44610.11991760.10371021810394
1.4461-1.51190.13761320.0961034410476
1.5119-1.59160.12071590.09251030810467
1.5916-1.69140.11591740.09471026110435
1.6914-1.82190.1293820.09851045010532
1.8219-2.00530.12491260.10211036910495
2.0053-2.29550.12891280.10241045810586
2.2955-2.89190.11711090.11161048210591
2.8919-43.81520.12621610.1291075510916

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