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- PDB-5zw2: FAD complex of PigA -

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Basic information

Entry
Database: PDB / ID: 5zw2
TitleFAD complex of PigA
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
Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase, C-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 ...Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase, C-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 oxidase/dehydrogenase, middle domain superfamily / 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
ACETATE ION / 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: 1.803 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)45,85214
Polymers43,9501
Non-polymers1,90213
Water7,710428
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)183,40956
Polymers175,8004
Non-polymers7,60952
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 area30920 Å2
ΔGint-78 kcal/mol
Surface area47430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.014, 85.820, 145.744
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-513-

CL

21A-697-

HOH

31A-818-

HOH

41A-1028-

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, 441 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-O4B / 1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE


Mass: 264.315 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H24O6
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 428 / 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: 3.02 Å3/Da / Density % sol: 59.33 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 40% ethylene glycol, 0.1M Na-acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Apr 24, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 46074 / % possible obs: 93.5 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 23.2
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 5 % / Rmerge(I) obs: 0.294 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 4630 / % possible all: 95

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZW0

5zw0


Resolution: 1.803→19.405 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 16.49
RfactorNum. reflection% reflection
Rfree0.1735 2026 4.44 %
Rwork0.1428 --
obs0.1442 45613 92.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.803→19.405 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2931 0 126 428 3485
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0193363
X-RAY DIFFRACTIONf_angle_d1.5884553
X-RAY DIFFRACTIONf_dihedral_angle_d18.2012029
X-RAY DIFFRACTIONf_chiral_restr0.106493
X-RAY DIFFRACTIONf_plane_restr0.009580
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8026-1.84760.25651300.18182838X-RAY DIFFRACTION85
1.8476-1.89750.20681380.17463053X-RAY DIFFRACTION91
1.8975-1.95330.251490.16913121X-RAY DIFFRACTION94
1.9533-2.01630.17791480.15643199X-RAY DIFFRACTION95
2.0163-2.08830.20381460.15363168X-RAY DIFFRACTION95
2.0883-2.17180.19111430.14683174X-RAY DIFFRACTION95
2.1718-2.27050.15741460.14353158X-RAY DIFFRACTION94
2.2705-2.390.16911470.14393161X-RAY DIFFRACTION94
2.39-2.53940.1911440.14343135X-RAY DIFFRACTION93
2.5394-2.7350.16611520.14623142X-RAY DIFFRACTION93
2.735-3.00930.19871430.1433121X-RAY DIFFRACTION92
3.0093-3.44270.16991400.14033118X-RAY DIFFRACTION91
3.4427-4.32950.13441470.123105X-RAY DIFFRACTION90
4.3295-19.40650.15871530.13953094X-RAY DIFFRACTION87

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