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

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Basic information

Entry
Database: PDB / ID: 5jfl
TitleCrystal structure of Rhodopseudomonas palustris propionaldehyde dehydrogenase with bound NAD+
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Aldehyde dehydrogenase
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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)449,49616
Polymers444,1888
Non-polymers5,3078
Water16,538918
1
A: Aldehyde dehydrogenase
B: Aldehyde dehydrogenase
C: Aldehyde dehydrogenase
D: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,7488
Polymers222,0944
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20200 Å2
ΔGint-71 kcal/mol
Surface area54810 Å2
MethodPISA
2
E: Aldehyde dehydrogenase
F: Aldehyde dehydrogenase
G: Aldehyde dehydrogenase
H: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,7488
Polymers222,0944
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20100 Å2
ΔGint-73 kcal/mol
Surface area54580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.393, 154.796, 126.594
Angle α, β, γ (deg.)90.00, 90.13, 90.00
Int Tables number4
Space group name H-MP1211

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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-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 918 / 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: 2.37 Å3/Da / Density % sol: 48.08 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 50 mM sodium citrate, pH 4.8, 4% w/v PEG8000, 5 mM NAD+

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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: 2.3→33.643 Å / Num. obs: 357425 / % possible obs: 98.9 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.132 / Net I/σ(I): 10.9
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.868 / Mean I/σ(I) obs: 2.7 / % possible all: 98

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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: 2.3→33.643 Å / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 36.16 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2282 4003 1.12 %
Rwork0.1885 --
obs0.1896 357425 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→33.643 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26378 0 352 918 27648
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00427148
X-RAY DIFFRACTIONf_angle_d0.61336885
X-RAY DIFFRACTIONf_dihedral_angle_d14.56116520
X-RAY DIFFRACTIONf_chiral_restr0.0444445
X-RAY DIFFRACTIONf_plane_restr0.0044730
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3002-2.33980.32591940.294217427X-RAY DIFFRACTION96
2.3398-2.38240.30191960.276617502X-RAY DIFFRACTION97
2.3824-2.42810.30191890.274917427X-RAY DIFFRACTION97
2.4281-2.47770.30331990.259917542X-RAY DIFFRACTION97
2.4777-2.53150.34271970.25817557X-RAY DIFFRACTION97
2.5315-2.59030.30142000.253217523X-RAY DIFFRACTION97
2.5903-2.65510.29441930.250117607X-RAY DIFFRACTION97
2.6551-2.72680.31281990.245817681X-RAY DIFFRACTION97
2.7268-2.8070.24072040.231317637X-RAY DIFFRACTION98
2.807-2.89750.3071920.232917756X-RAY DIFFRACTION98
2.8975-3.00090.23611980.228517684X-RAY DIFFRACTION98
3.0009-3.12090.3261870.214117728X-RAY DIFFRACTION98
3.1209-3.26270.22452000.200617756X-RAY DIFFRACTION98
3.2627-3.43440.22112000.19217723X-RAY DIFFRACTION98
3.4344-3.6490.23611980.177417725X-RAY DIFFRACTION98
3.649-3.930.18252010.165217798X-RAY DIFFRACTION98
3.93-4.3240.18151920.148317772X-RAY DIFFRACTION98
4.324-4.94640.20111980.132717673X-RAY DIFFRACTION98
4.9464-6.21920.18652020.154817864X-RAY DIFFRACTION99
6.2192-26.91440.14772040.132417915X-RAY DIFFRACTION99

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