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- PDB-6x9l: Crystal Structure of Aldehyde Dehydrogenase C (AldC) mutant (C291... -

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Basic information

Entry
Database: PDB / ID: 6x9l
TitleCrystal Structure of Aldehyde Dehydrogenase C (AldC) mutant (C291A) from Pseudomonas syringae in complexed with NAD+ and Octanal
ComponentsAldehyde dehydrogenase family protein
KeywordsOXIDOREDUCTASE / Aldehyde Dehydrogenase C / AldC / Aliphatic aldehyde
Function / homologyoxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / OCTANAL / Aldehyde dehydrogenase family protein
Function and homology information
Biological speciesPseudomonas syringae pv. tomato (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsLee, S.G. / Jez, J.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)NIH-AI-097119 United States
CitationJournal: J.Biol.Chem. / Year: 2020
Title: The plant pathogen enzyme AldC is a long-chain aliphatic aldehyde dehydrogenase.
Authors: Lee, S.G. / Harline, K. / Abar, O. / Akadri, S.O. / Bastian, A.G. / Chen, H.S. / Duan, M. / Focht, C.M. / Groziak, A.R. / Kao, J. / Kottapalli, J.S. / Leong, M.C. / Lin, J.J. / Liu, R. / ...Authors: Lee, S.G. / Harline, K. / Abar, O. / Akadri, S.O. / Bastian, A.G. / Chen, H.S. / Duan, M. / Focht, C.M. / Groziak, A.R. / Kao, J. / Kottapalli, J.S. / Leong, M.C. / Lin, J.J. / Liu, R. / Luo, J.E. / Meyer, C.M. / Mo, A.F. / Pahng, S.H. / Penna, V. / Raciti, C.D. / Srinath, A. / Sudhakar, S. / Tang, J.D. / Cox, B.R. / Holland, C.K. / Cascella, B. / Cruz, W. / McClerkin, S.A. / Kunkel, B.N. / Jez, J.M.
History
DepositionJun 3, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 14, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Oct 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,1496
Polymers103,5652
Non-polymers1,5834
Water3,405189
1
A: Aldehyde dehydrogenase family protein
hetero molecules

A: Aldehyde dehydrogenase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,1496
Polymers103,5652
Non-polymers1,5834
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area7900 Å2
ΔGint-18 kcal/mol
Surface area31950 Å2
MethodPISA
2
B: Aldehyde dehydrogenase family protein
hetero molecules

B: Aldehyde dehydrogenase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,1496
Polymers103,5652
Non-polymers1,5834
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area7850 Å2
ΔGint-14 kcal/mol
Surface area31770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.193, 92.170, 231.357
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11B-890-

HOH

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Components

#1: Protein Aldehyde dehydrogenase family protein


Mass: 51782.715 Da / Num. of mol.: 2 / Mutation: C291A
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_3644 / Production host: Escherichia coli (E. coli) / References: UniProt: Q87YZ5
#2: Chemical ChemComp-OYA / OCTANAL / OCTYL ALDEHYDE / Octanal


Mass: 128.212 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H16O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.37 Å3/Da / Density % sol: 48.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% (w/v) PEG-1000 and 100 mM Tris base/ Hydrochloric acid (pH 7.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 32956 / % possible obs: 97.8 % / Redundancy: 4 % / Biso Wilson estimate: 47.21 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 12.8
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 4 % / Rmerge(I) obs: 0.642 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1647 / CC1/2: 0.788 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-3000data reduction
PHASER1.11.1_2575phasing
Cootmodel building
HKL-3000data scaling
HKL-3000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5iuw

5iuw


Resolution: 2.52→39.56 Å / SU ML: 0.2487 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.3151 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1971 1995 6.06 %
Rwork0.1955 30903 -
obs0.1956 32898 97.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.6 Å2
Refinement stepCycle: LAST / Resolution: 2.52→39.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7180 0 106 189 7475
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01377450
X-RAY DIFFRACTIONf_angle_d1.114310175
X-RAY DIFFRACTIONf_chiral_restr0.4231160
X-RAY DIFFRACTIONf_plane_restr0.0071341
X-RAY DIFFRACTIONf_dihedral_angle_d17.58752649
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.52-2.580.24021320.26172049X-RAY DIFFRACTION91.72
2.58-2.650.26531420.25372206X-RAY DIFFRACTION99.41
2.65-2.730.26541450.2552241X-RAY DIFFRACTION99.05
2.73-2.820.26881460.24112186X-RAY DIFFRACTION98.11
2.82-2.920.22911330.23392153X-RAY DIFFRACTION95.61
2.92-3.030.24441400.23612225X-RAY DIFFRACTION99.45
3.03-3.170.21031500.24872252X-RAY DIFFRACTION99.22
3.17-3.340.2581400.22392208X-RAY DIFFRACTION98.95
3.34-3.550.19921480.21312256X-RAY DIFFRACTION98.44
3.55-3.820.21441410.18772139X-RAY DIFFRACTION94.68
3.82-4.20.16131420.16632235X-RAY DIFFRACTION98.22
4.2-4.810.14911430.15212240X-RAY DIFFRACTION98.43
4.81-6.060.17361400.18022226X-RAY DIFFRACTION95.36
6.06-39.560.16821530.16512287X-RAY DIFFRACTION95.28

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