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- PDB-7jso: P. syringae AldA Indole-3-Acetaldehyde Dehydrogenase C302A mutant... -

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Basic information

Entry
Database: PDB / ID: 7jso
TitleP. syringae AldA Indole-3-Acetaldehyde Dehydrogenase C302A mutant in complex with NAD+ and IAA
ComponentsAldehyde dehydrogenase family protein
KeywordsOXIDOREDUCTASE / aldehyde dehydrogenase / auxin
Function / homology
Function and homology information


fermentation / aldehyde dehydrogenase (NAD+) activity / organic substance metabolic process
Similarity search - Function
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
Similarity search - Domain/homology
1H-INDOL-3-YLACETIC ACID / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Aldehyde dehydrogenase family protein
Similarity search - Component
Biological speciesPseudomonas syringae pv. tomato (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.848 Å
AuthorsJez, J.M.
Funding support United States, 4items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1614539 United States
National Science Foundation (NSF, United States)IOS-1645908 United States
National Science Foundation (NSF, United States)DGE-1143954 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
CitationJournal: Biosci.Rep. / Year: 2020
Title: Investigating the reaction and substrate preference of indole-3-acetaldehyde dehydrogenase from the plant pathogen Pseudomonas syringae PtoDC3000.
Authors: Zhang, K. / Lee, J.S. / Liu, R. / Chan, Z.T. / Dawson, T.J. / De Togni, E.S. / Edwards, C.T. / Eng, I.K. / Gao, A.R. / Goicouria, L.A. / Hall, E.M. / Hu, K.A. / Huang, K. / Kizhner, A. / ...Authors: Zhang, K. / Lee, J.S. / Liu, R. / Chan, Z.T. / Dawson, T.J. / De Togni, E.S. / Edwards, C.T. / Eng, I.K. / Gao, A.R. / Goicouria, L.A. / Hall, E.M. / Hu, K.A. / Huang, K. / Kizhner, A. / Kodama, K.C. / Lin, A.Z. / Liu, J.Y. / Lu, A.Y. / Peng, O.W. / Ryu, E.P. / Shi, S. / Sorkin, M.L. / Walker, P.L. / Wang, G.J. / Xu, M.C. / Yang, R.S. / Cascella, B. / Cruz, W. / Holland, C.K. / McClerkin, S.A. / Kunkel, B.N. / Lee, S.G. / Jez, J.M.
History
DepositionAug 15, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Aldehyde dehydrogenase family protein
B: Aldehyde dehydrogenase family protein
C: Aldehyde dehydrogenase family protein
D: Aldehyde dehydrogenase family protein
E: Aldehyde dehydrogenase family protein
F: Aldehyde dehydrogenase family protein
G: Aldehyde dehydrogenase family protein
H: Aldehyde dehydrogenase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)428,70724
Polymers421,9828
Non-polymers6,72516
Water0
1
A: Aldehyde dehydrogenase family protein
C: Aldehyde dehydrogenase family protein
hetero molecules

A: Aldehyde dehydrogenase family protein
C: Aldehyde dehydrogenase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,35412
Polymers210,9914
Non-polymers3,3638
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_756-x+2,y,-z+11
Buried area23810 Å2
ΔGint-110 kcal/mol
Surface area57970 Å2
MethodPISA
2
B: Aldehyde dehydrogenase family protein
D: Aldehyde dehydrogenase family protein
hetero molecules

B: Aldehyde dehydrogenase family protein
D: Aldehyde dehydrogenase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,35412
Polymers210,9914
Non-polymers3,3638
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_756-x+2,y,-z+11
Buried area23800 Å2
ΔGint-107 kcal/mol
Surface area57940 Å2
MethodPISA
3
E: Aldehyde dehydrogenase family protein
G: Aldehyde dehydrogenase family protein
H: Aldehyde dehydrogenase family protein
hetero molecules

F: Aldehyde dehydrogenase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,35412
Polymers210,9914
Non-polymers3,3638
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_747-x+5/2,y-1/2,-z+21
Buried area23430 Å2
ΔGint-109 kcal/mol
Surface area58110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)333.816, 161.095, 84.999
Angle α, β, γ (deg.)90.000, 90.010, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Aldehyde dehydrogenase family protein


Mass: 52747.762 Da / Num. of mol.: 8 / Mutation: C302A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae pv. tomato (strain ATCC BAA-871 / DC3000) (bacteria)
Strain: ATCC BAA-871 / DC3000 / Gene: PSPTO_0092 / Production host: Escherichia coli (E. coli) / References: UniProt: Q88BC5
#2: Chemical
ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH / Nicotinamide adenine dinucleotide


Mass: 665.441 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Chemical
ChemComp-IAC / 1H-INDOL-3-YLACETIC ACID / INDOLE ACETIC ACID / Indole-3-acetic acid


Mass: 175.184 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H9NO2 / Comment: hormone*YM
Has ligand of interestN

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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: 2.71 Å3/Da / Density % sol: 54.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 24% PEG-1000, 100 mM Tris-HCl (pH 7.0), 2 mM IAA, and 5 mM NAD+

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.848→47.9 Å / Num. obs: 103830 / % possible obs: 98.3 % / Redundancy: 5.4 % / Biso Wilson estimate: 22.23 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 13.9
Reflection shellResolution: 2.848→2.92 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 5.4 / Num. unique obs: 5374 / Rsym value: 0.241 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IUW
Resolution: 2.848→47.888 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 38.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2544 1998 1.94 %
Rwork0.2163 101195 -
obs0.217 103193 98.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 119.14 Å2 / Biso mean: 36.3547 Å2 / Biso min: 1.65 Å2
Refinement stepCycle: final / Resolution: 2.848→47.888 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29536 0 456 0 29992
Biso mean--64.74 --
Num. residues----3960
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.848-2.9190.33971410.2768717298
2.919-2.99790.33041430.2815716297
2.9979-3.08610.30331410.2607721099
3.0861-3.18570.30161420.25877295100
3.1857-3.29950.2591410.2522728299
3.2995-3.43160.30781400.24497322100
3.4316-3.58770.29051450.22237272100
3.5877-3.77680.25271460.20827345100
3.7768-4.01330.21081460.1948726999
4.0133-4.3230.23191460.1837728599
4.323-4.75770.20011420.1629718798
4.7577-5.44530.25871420.18237340100
5.4453-6.85730.21481460.21227357100
6.8573-47.8880.17721370.1772669789
Refinement TLS params.Method: refined / Origin x: 381.0329 Å / Origin y: 81.9742 Å / Origin z: 58.9785 Å
111213212223313233
T-0.3665 Å2-0.1202 Å20.1026 Å2--0.1214 Å20.0045 Å2--0.0401 Å2
L0.4801 °2-0.2049 °20.2418 °2--0.0057 °2-0.1248 °2--0.9329 °2
S-0.2518 Å °0.1344 Å °0.0255 Å °0.2495 Å °0.1161 Å °-0.1391 Å °-0.206 Å °0.0944 Å °0.0219 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 497
2X-RAY DIFFRACTION1allA700
3X-RAY DIFFRACTION1allA701
4X-RAY DIFFRACTION1allB3 - 497
5X-RAY DIFFRACTION1allB700
6X-RAY DIFFRACTION1allB701
7X-RAY DIFFRACTION1allC3 - 497
8X-RAY DIFFRACTION1allC700
9X-RAY DIFFRACTION1allC701
10X-RAY DIFFRACTION1allD3 - 497
11X-RAY DIFFRACTION1allD700
12X-RAY DIFFRACTION1allD701
13X-RAY DIFFRACTION1allE3 - 497
14X-RAY DIFFRACTION1allE700
15X-RAY DIFFRACTION1allE701
16X-RAY DIFFRACTION1allF3 - 497
17X-RAY DIFFRACTION1allF700
18X-RAY DIFFRACTION1allF701
19X-RAY DIFFRACTION1allG3 - 497
20X-RAY DIFFRACTION1allG700
21X-RAY DIFFRACTION1allG701
22X-RAY DIFFRACTION1allH3 - 497
23X-RAY DIFFRACTION1allH700
24X-RAY DIFFRACTION1allH701

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