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- PDB-5zw7: FAD-PigA complex at 1.3 A -

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Basic information

Entry
Database: PDB / ID: 5zw7
TitleFAD-PigA complex at 1.3 A
ComponentsL-prolyl-[peptidyl-carrier protein] dehydrogenase
KeywordsBIOSYNTHETIC PROTEIN / red pigment / pyrrole / acyl-CoA oxidase / FAD / tetramer
Function / homology
Function and homology information


L-prolyl-[peptidyl-carrier protein] dehydrogenase / oxidoreductase activity, acting on the CH-CH group of donors / antibiotic biosynthetic process / flavin adenine dinucleotide binding
Similarity search - Function
Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain / Acyl-CoA dehydrogenase, middle domain / Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily ...Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain / Acyl-CoA dehydrogenase, middle domain / Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily / Butyryl-CoA Dehydrogenase, subunit A, domain 3 / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Up-down Bundle / Beta Barrel / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / 1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE / L-prolyl-[peptidyl-carrier protein] dehydrogenase
Similarity search - Component
Biological speciesSerratia sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsLee, C.-C. / Ko, T.-P. / Wang, A.H.J.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Taiwan
CitationJournal: Chembiochem / Year: 2019
Title: Crystal Structure of PigA: A Prolyl Thioester-Oxidizing Enzyme in Prodigiosin Biosynthesis.
Authors: Lee, C.-C. / Ko, T.-P. / Chen, C.T. / Chan, Y.T. / Lo, S.Y. / Chang, J.Y. / Chen, Y.W. / Chung, T.F. / Hsieh, H.J. / Hsiao, C.D. / Wang, A.H.J.
History
DepositionMay 14, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 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: L-prolyl-[peptidyl-carrier protein] dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4969
Polymers43,9501
Non-polymers1,5468
Water9,350519
1
A: L-prolyl-[peptidyl-carrier protein] dehydrogenase
hetero molecules

A: L-prolyl-[peptidyl-carrier protein] dehydrogenase
hetero molecules

A: L-prolyl-[peptidyl-carrier protein] dehydrogenase
hetero molecules

A: L-prolyl-[peptidyl-carrier protein] dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,98436
Polymers175,8004
Non-polymers6,18332
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area28000 Å2
ΔGint-170 kcal/mol
Surface area47140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.228, 85.624, 145.928
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-508-

CL

21A-654-

HOH

31A-886-

HOH

41A-1033-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein L-prolyl-[peptidyl-carrier protein] dehydrogenase / proline oxidase / Flavoprotein desaturase PigA / L-prolyl-PCP dehydrogenase


Mass: 43950.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia sp. (strain ATCC 39006) (bacteria)
Strain: ATCC 39006 / Gene: pigA / Production host: Escherichia coli (E. coli)
References: UniProt: Q5W271, L-prolyl-[peptidyl-carrier protein] dehydrogenase

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Non-polymers , 5 types, 527 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-O4B / 1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE / 18-Crown-6


Mass: 264.315 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H24O6
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 519 / 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: 3.03 Å3/Da / Density % sol: 59.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 1.7M (NH4)2SO4, 0.2M NaCl, 0.1M Na-cacodylate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: BRUKER SMART 6500 / Detector: CCD / Date: Feb 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.3→25 Å / Num. obs: 130943 / % possible obs: 100 % / Redundancy: 7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 42.8
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 12927 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZW2

5zw2


Resolution: 1.3→25 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 11.81
RfactorNum. reflection% reflection
Rfree0.1274 2003 1.53 %
Rwork0.1137 --
obs0.1139 130934 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2931 0 102 519 3552
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0183397
X-RAY DIFFRACTIONf_angle_d1.6864575
X-RAY DIFFRACTIONf_dihedral_angle_d22.211289
X-RAY DIFFRACTIONf_chiral_restr0.125488
X-RAY DIFFRACTIONf_plane_restr0.01577
LS refinement shellResolution: 1.3→1.4 Å
RfactorNum. reflection% reflection
Rfree0.195 --
Rwork0.169 12776 -
obs--98.4 %

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