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

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Basic information

Entry
Database: PDB / ID: 5jfn
TitleCrystal structure of Rhodopseudomonas palustris propionaldehyde dehydrogenase with bound CoA and acylated Cys330
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: 1.9 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.2Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 ..._chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Dec 25, 2024Group: Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature / struct_conn

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,11315
Polymers222,3184
Non-polymers4,79411
Water32,1391784
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22240 Å2
ΔGint-4 kcal/mol
Surface area54100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.188, 106.452, 125.733
Angle α, β, γ (deg.)90.00, 109.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Aldehyde dehydrogenase


Mass: 55579.598 Da / Num. of mol.: 4
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.: 1 / Source method: obtained synthetically / Formula: C24H40N7O17P3S
#3: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1784 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 48.09 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 100 mM HEPES-NaOH, pH 7.0, 19% w/v PEG4000, 4 mM propionyl-CoA

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.977408 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977408 Å / Relative weight: 1
ReflectionResolution: 1.9→39.2 Å / Num. obs: 162389 / % possible obs: 99.7 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.021 / Net I/σ(I): 12.8
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.839 / Mean I/σ(I) obs: 2.1 / % possible all: 98.3

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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: 1.9→39.198 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1865 1994 1.23 %
Rwork0.1616 --
obs0.1619 162309 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→39.198 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13237 0 308 1784 15329
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00413792
X-RAY DIFFRACTIONf_angle_d0.71718698
X-RAY DIFFRACTIONf_dihedral_angle_d13.0888401
X-RAY DIFFRACTIONf_chiral_restr0.0472220
X-RAY DIFFRACTIONf_plane_restr0.0042394
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8996-1.94720.3011340.261510956X-RAY DIFFRACTION96
1.9472-1.99980.23611430.225611461X-RAY DIFFRACTION100
1.9998-2.05860.23831430.20911451X-RAY DIFFRACTION100
2.0586-2.12510.23321440.193311425X-RAY DIFFRACTION100
2.1251-2.2010.21681390.184111449X-RAY DIFFRACTION100
2.201-2.28910.20021440.171311479X-RAY DIFFRACTION100
2.2891-2.39330.21390.164811428X-RAY DIFFRACTION100
2.3933-2.51950.20081450.160611476X-RAY DIFFRACTION100
2.5195-2.67730.19371390.156111480X-RAY DIFFRACTION100
2.6773-2.8840.16871450.158311507X-RAY DIFFRACTION100
2.884-3.17410.18371460.158911467X-RAY DIFFRACTION100
3.1741-3.63310.16871460.148111500X-RAY DIFFRACTION100
3.6331-4.57620.15091460.126811550X-RAY DIFFRACTION100
4.5762-39.20620.1571410.143111686X-RAY DIFFRACTION100

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