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- PDB-2vro: Crystal structure of aldehyde dehydrogenase from Burkholderia xen... -

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Basic information

Entry
Database: PDB / ID: 2vro
TitleCrystal structure of aldehyde dehydrogenase from Burkholderia xenovorans LB400
ComponentsALDEHYDE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / ALDEHYDE DEHYDROGENASE / BURKHOLDERIA XENOVORANS LB400 / BENZOATE OXIDATION PATHWAY
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
Phenylacetic acid degradation protein PaaN / 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 domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase ...Phenylacetic acid degradation protein PaaN / 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 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
Chem-ETE / Chem-NDP / 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase
Similarity search - Component
Biological speciesBURKHOLDERIA XENOVORANS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsBains, J. / Boulanger, M.J.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structural and Biochemical Characterization of a Novel Aldehyde Dehydrogenase Encoded by the Benzoate Oxidation (Box) Pathway in Burkholderia Xenovorans Lb400
Authors: Bains, J. / Boulanger, M.J.
History
DepositionApr 9, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ALDEHYDE DEHYDROGENASE
B: ALDEHYDE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,3696
Polymers111,3882
Non-polymers1,9814
Water13,259736
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6620 Å2
ΔGint-35.3 kcal/mol
Surface area42320 Å2
MethodPQS
Unit cell
Length a, b, c (Å)57.980, 67.690, 77.620
Angle α, β, γ (deg.)111.18, 90.48, 113.27
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.10555, 0.64933, -0.75315), (0.65267, -0.61666, -0.44018), (-0.75025, -0.4451, -0.48889)
Vector: -0.21176, 0.18377, -0.12957)

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Components

#1: Protein ALDEHYDE DEHYDROGENASE


Mass: 55693.879 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BURKHOLDERIA XENOVORANS (bacteria) / Strain: LB400 / Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q13WK4, aldehyde dehydrogenase (NAD+)
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-ETE / 2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL


Mass: 208.252 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H20O5
#4: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 736 / 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: 2.14 Å3/Da / Density % sol: 41.97 % / Description: NONE
Crystal growpH: 6 / Details: pH 6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RAXIS 4 / Detector: IMAGE PLATE / Date: Dec 5, 2007 / Details: MIRRORS
RadiationMonochromator: NI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→46.31 Å / Num. obs: 121689 / % possible obs: 92.6 % / Observed criterion σ(I): 3 / Redundancy: 3.67 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.4
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3.17 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.5 / % possible all: 88.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
d*TREKdata reduction
d*TREKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QI1

1qi1


Resolution: 1.6→37.82 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.101 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.238 6128 5 %RANDOM
Rwork0.207 ---
obs0.209 115520 92.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.32 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.6→37.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7723 0 129 736 8588
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0228002
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4811.97910903
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.39851044
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.77122.994314
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.1151193
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0751564
X-RAY DIFFRACTIONr_chiral_restr0.1410.21282
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026018
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2070.24136
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2960.25533
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2628
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2360.235
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0880.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6571.55314
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.03128264
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.8733016
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9014.52639
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.441 451
Rwork0.375 8063

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