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- PDB-5jfm: Crystal structure of Rhodopseudomonas palustris propionaldehyde d... -

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Basic information

Entry
Database: PDB / ID: 5jfm
TitleCrystal structure of Rhodopseudomonas palustris propionaldehyde dehydrogenase with bound propionyl-CoA
ComponentsAldehyde dehydrogenase
KeywordsOXIDOREDUCTASE / acylating aldehyde dehydrogenase / propionylcysteine / bacterial microcompartments
Function / homology
Function and homology information


acetaldehyde dehydrogenase (acetylating) activity / nucleotide binding / cytoplasm
Similarity search - Function
Acetaldehyde/propionaldehyde dehydrogenase, EutE/PduP-related / 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 ...Acetaldehyde/propionaldehyde dehydrogenase, EutE/PduP-related / 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
propionyl Coenzyme A / COENZYME A / Aldehyde dehydrogenase
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.516 Å
AuthorsZarzycki, J. / Sutter, M. / Kerfeld, C.A.
CitationJournal: Sci Rep / Year: 2017
Title: In Vitro Characterization and Concerted Function of Three Core Enzymes of a Glycyl Radical Enzyme - Associated Bacterial Microcompartment.
Authors: Zarzycki, J. / Sutter, M. / Cortina, N.S. / Erb, T.J. / Kerfeld, C.A.
History
DepositionApr 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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

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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)450,72116
Polymers444,1888
Non-polymers6,5338
Water19,6541091
1
A: Aldehyde dehydrogenase
B: Aldehyde dehydrogenase
C: Aldehyde dehydrogenase
D: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,3328
Polymers222,0944
Non-polymers3,2384
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18410 Å2
ΔGint-23 kcal/mol
Surface area54600 Å2
MethodPISA
2
E: Aldehyde dehydrogenase
F: Aldehyde dehydrogenase
G: Aldehyde dehydrogenase
H: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,3898
Polymers222,0944
Non-polymers3,2944
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17090 Å2
ΔGint-24 kcal/mol
Surface area54680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.106, 105.775, 126.425
Angle α, β, γ (deg.)89.52, 71.00, 68.92
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Aldehyde dehydrogenase


Mass: 55523.531 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (strain BisB18) (phototrophic)
Strain: BisB18 / Gene: RPC_1174 / Production host: Escherichia coli (E. coli) / References: UniProt: Q21A49
#2: Chemical
ChemComp-1VU / propionyl Coenzyme A


Mass: 823.597 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: C24H40N7O17P3S
#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1091 / 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: 2.39 Å3/Da / Density % sol: 48.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.8
Details: 50 mM sodium citrate, pH 4.8, 4% w/v PEG8000, 5 mM propionyl-CoA

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.00001 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 2.516→39.26 Å / Num. obs: 135429 / % possible obs: 95.5 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 11.3
Reflection shellResolution: 2.52→2.65 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.502 / Mean I/σ(I) obs: 2.3 / % possible all: 91.8

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Processing

Software
NameVersionClassification
PHENIX(1.10_2152: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4C3S

4c3s


Resolution: 2.516→39.259 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 23.25
RfactorNum. reflection% reflection
Rfree0.2237 2000 1.48 %
Rwork0.1718 --
obs0.1726 135317 95.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.516→39.259 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26472 0 412 1091 27975
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00627336
X-RAY DIFFRACTIONf_angle_d0.79737132
X-RAY DIFFRACTIONf_dihedral_angle_d14.50316667
X-RAY DIFFRACTIONf_chiral_restr0.0494439
X-RAY DIFFRACTIONf_plane_restr0.0054768
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5163-2.57920.33161300.25898616X-RAY DIFFRACTION86
2.5792-2.64890.28661440.22399652X-RAY DIFFRACTION97
2.6489-2.72690.28311430.21769499X-RAY DIFFRACTION96
2.7269-2.81480.25631450.19689740X-RAY DIFFRACTION97
2.8148-2.91540.25721450.19529665X-RAY DIFFRACTION97
2.9154-3.03210.24931460.20549723X-RAY DIFFRACTION97
3.0321-3.170.25241460.19299694X-RAY DIFFRACTION97
3.17-3.33710.24481440.18189634X-RAY DIFFRACTION97
3.3371-3.5460.2221430.17919499X-RAY DIFFRACTION95
3.546-3.81960.23751410.1679403X-RAY DIFFRACTION94
3.8196-4.20360.20461420.14819429X-RAY DIFFRACTION94
4.2036-4.8110.19121430.13249534X-RAY DIFFRACTION96
4.811-6.05770.17881420.15389469X-RAY DIFFRACTION95
6.0577-39.26380.17261460.14739760X-RAY DIFFRACTION98

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