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- PDB-5zw8: PigA with FAD and proline -

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Basic information

Entry
Database: PDB / ID: 5zw8
TitlePigA with FAD and proline
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 / MALONIC ACID / 1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE / PROLINE / L-prolyl-[peptidyl-carrier protein] dehydrogenase
Similarity search - Component
Biological speciesSerratia sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.689 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)45,5197
Polymers43,9501
Non-polymers1,5696
Water8,287460
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)182,07628
Polymers175,8004
Non-polymers6,27524
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 area23860 Å2
ΔGint-200 kcal/mol
Surface area48650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.585, 85.558, 146.144
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-505-

CL

21A-875-

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 , 6 types, 466 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.: 2 / Source method: obtained synthetically / Formula: C12H24O6
#4: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID / Malonic acid


Mass: 104.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O4
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-PRO / PROLINE / Proline


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 460 / 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 Å3/Da / Density % sol: 59.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 7mM L-proline, 1.9M sodium malonate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Apr 30, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.68→40 Å / Num. obs: 59573 / % possible obs: 99.8 % / Redundancy: 8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 22.6
Reflection shellResolution: 1.68→1.74 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.741 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 5885 / % possible all: 99.4

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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: 1.689→31.277 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.21
RfactorNum. reflection% reflection
Rfree0.1798 2008 3.41 %
Rwork0.154 --
obs0.1549 58857 97.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.689→31.277 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2939 0 97 460 3496
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0193192
X-RAY DIFFRACTIONf_angle_d1.6724301
X-RAY DIFFRACTIONf_dihedral_angle_d18.1961895
X-RAY DIFFRACTIONf_chiral_restr0.121466
X-RAY DIFFRACTIONf_plane_restr0.009546
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6891-1.73130.31471090.23973008X-RAY DIFFRACTION73
1.7313-1.77810.24561380.22773911X-RAY DIFFRACTION95
1.7781-1.83040.26081470.21864050X-RAY DIFFRACTION98
1.8304-1.88950.26131400.20664073X-RAY DIFFRACTION100
1.8895-1.9570.20451460.18314122X-RAY DIFFRACTION100
1.957-2.03540.18811440.16554121X-RAY DIFFRACTION100
2.0354-2.1280.20931460.15934134X-RAY DIFFRACTION100
2.128-2.24020.19431490.154135X-RAY DIFFRACTION100
2.2402-2.38050.19091460.14794165X-RAY DIFFRACTION100
2.3805-2.56420.16831440.15164172X-RAY DIFFRACTION100
2.5642-2.82210.19791460.15624144X-RAY DIFFRACTION100
2.8221-3.23010.1841450.15514193X-RAY DIFFRACTION100
3.2301-4.06820.12041520.12334243X-RAY DIFFRACTION100
4.0682-31.28190.14071560.12854378X-RAY DIFFRACTION100

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