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- PDB-4qyj: Structure of Phenylacetaldehyde Dehydrogenase from Pseudomonas pu... -

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Basic information

Entry
Database: PDB / ID: 4qyj
TitleStructure of Phenylacetaldehyde Dehydrogenase from Pseudomonas putida S12
ComponentsAldehyde dehydrogenase
KeywordsOXIDOREDUCTASE / Aldehyde Dehydrogenase
Function / homology
Function and homology information


oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
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, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family ...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, 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
Phenylacetaldehyde dehydrogenase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 Å
AuthorsCrabo, A.G. / Gassner, G.T. / Sazinsky, M.H.
CitationJournal: Arch.Biochem.Biophys. / Year: 2017
Title: Structure and biochemistry of phenylacetaldehyde dehydrogenase from the Pseudomonas putida S12 styrene catabolic pathway.
Authors: Crabo, A.G. / Singh, B. / Nguyen, T. / Emami, S. / Gassner, G.T. / Sazinsky, M.H.
History
DepositionJul 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2017Group: Database references
Revision 1.2Mar 8, 2017Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aldehyde dehydrogenase
B: Aldehyde dehydrogenase
C: Aldehyde dehydrogenase
D: Aldehyde dehydrogenase
E: Aldehyde dehydrogenase
F: Aldehyde dehydrogenase
G: Aldehyde dehydrogenase
H: Aldehyde dehydrogenase


Theoretical massNumber of molelcules
Total (without water)440,3738
Polymers440,3738
Non-polymers00
Water0
1
A: Aldehyde dehydrogenase
B: Aldehyde dehydrogenase
C: Aldehyde dehydrogenase
D: Aldehyde dehydrogenase


Theoretical massNumber of molelcules
Total (without water)220,1864
Polymers220,1864
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15550 Å2
ΔGint-70 kcal/mol
Surface area60340 Å2
MethodPISA
2
E: Aldehyde dehydrogenase
F: Aldehyde dehydrogenase
G: Aldehyde dehydrogenase
H: Aldehyde dehydrogenase


Theoretical massNumber of molelcules
Total (without water)220,1864
Polymers220,1864
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15410 Å2
ΔGint-70 kcal/mol
Surface area60350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.090, 118.690, 304.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12C
22A
13D
23A
14E
24A
15F
25A
16G
26A
17H
27A

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114B1 - 481
2114A1 - 481
1124C1 - 481
2124A1 - 481
1134D1 - 481
2134A1 - 481
1144E1 - 481
2144A1 - 481
1154F1 - 481
2154A1 - 481
1164G1 - 481
2164A1 - 481
1174H1 - 481
2174A1 - 481

NCS ensembles :
ID
1
2
3
4
5
6
7
DetailsTwo copies of the full tetramer are observed in the asymmetric unit.

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Components

#1: Protein
Aldehyde dehydrogenase /


Mass: 55046.570 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: S12 / Gene: RPPX_12610, RPPX_34495 / Production host: Escherichia coli (E. coli) / References: UniProt: V4GH04

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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: 2.3 Å3/Da / Density % sol: 46.56 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100-200 mM trisodium citrate, pH 8.5 and 12-16% PEG 3350 , VAPOR DIFFUSION, SITTING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 1, 2011
RadiationMonochromator: Liquid nitrogen-cooled double crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.83→50 Å / Num. all: 93501 / Num. obs: 89099 / % possible obs: 95.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.83→2.9 Å / % possible all: 98.3

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.83→49.99 Å / Cor.coef. Fo:Fc: 0.886 / Cor.coef. Fo:Fc free: 0.81 / SU B: 41.769 / SU ML: 0.371 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.462 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2583 4677 5 %RANDOM
Rwork0.254 ---
all0.22654 93501 --
obs0.22386 89099 95.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.017 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.83→49.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27306 0 0 0 27306
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02227846
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5351.95938204
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.56653840
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.04324.644926
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.954153834
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9291596
X-RAY DIFFRACTIONr_chiral_restr0.1010.24648
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02121040
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3861.519064
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.653230226
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.27638782
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.9464.57978
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr0.683327846
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1B3391MEDIUM POSITIONAL0.230.5
1B3391MEDIUM THERMAL0.42
2C3401MEDIUM POSITIONAL0.240.5
2C3401MEDIUM THERMAL0.382
3D3401MEDIUM POSITIONAL0.260.5
3D3401MEDIUM THERMAL0.382
4E3406MEDIUM POSITIONAL0.190.5
4E3406MEDIUM THERMAL0.392
5F3391MEDIUM POSITIONAL0.230.5
5F3391MEDIUM THERMAL0.392
6G3401MEDIUM POSITIONAL0.250.5
6G3401MEDIUM THERMAL0.382
7H3401MEDIUM POSITIONAL0.250.5
7H3401MEDIUM THERMAL0.382
LS refinement shellResolution: 2.827→2.9 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 339 -
Rwork0.281 6614 -
obs--97.81 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.68150.1566-0.55880.443-0.04240.5726-0.04860.03380.0212-0.15730.0421-0.0268-0.05070.07460.00650.1646-0.07750.00760.1218-0.00460.058249.5431.171320.305
20.58580.0837-0.14130.52190.34150.5439-0.023-0.0780.0367-0.0143-0.0118-0.0614-0.07120.05750.03480.0949-0.0660.02750.0976-0.01940.083956.840224.2755.8689
30.94630.1-0.33620.3350.26420.802-0.0086-0.05540.0355-0.0778-0.03480.140.0842-0.13270.04340.1403-0.0857-0.00990.0784-0.02620.106913.378612.520538.1547
40.21510.1507-0.1550.92430.33930.8463-0.08910.018-0.1571-0.11720.0158-0.01570.1204-0.05560.07330.0795-0.06840.05070.1232-0.02230.145440.4417-12.959537.8373
50.69360.050.45470.40050.02720.7285-0.01290.0035-0.04330.09510.018-0.0760.09720.0502-0.00510.15970.09270.01670.09870.01330.063629.0241-0.2452132.7526
60.4142-0.01230.17550.7910.50180.6329-0.04810.0737-0.02840.02210.0453-0.07120.04380.08280.00280.05440.05250.01450.13920.03030.093429.0107-0.034895.8322
70.8330.08670.18360.43120.1940.1529-0.0522-0.00040.04570.125-0.01280.1767-0.0237-0.02070.06490.180.06430.06260.10940.01580.1124-10.401115.2873119.3407
80.43220.10570.19930.85690.34490.2111-0.09820.02340.22340.062100.1066-0.0363-0.03190.09820.10770.056-0.00830.14840.05020.185615.607540.0873109.646
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 496
2X-RAY DIFFRACTION2B16 - 496
3X-RAY DIFFRACTION3C16 - 496
4X-RAY DIFFRACTION4D16 - 496
5X-RAY DIFFRACTION5E16 - 496
6X-RAY DIFFRACTION6F16 - 496
7X-RAY DIFFRACTION7G16 - 496
8X-RAY DIFFRACTION8H16 - 496

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