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- PDB-4irn: Crystal Structure of the Prolyl Acyl Carrier Protein Oxidase AnaB -

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Basic information

Entry
Database: PDB / ID: 4irn
TitleCrystal Structure of the Prolyl Acyl Carrier Protein Oxidase AnaB
ComponentsProlyl-ACP dehydrogenase
KeywordsOXIDOREDUCTASE / Acyl CoA Dehydrogenase fold / Acyl-ACP Oxidase
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-CH group of donors; With unknown physiological acceptors / oxidoreductase activity, acting on the CH-CH group of donors / flavin adenine dinucleotide binding
Similarity search - Function
Butyryl-Coa Dehydrogenase, subunit A; domain 1 / Acyl-CoA dehydrogenase/oxidase, N-terminal domain / 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 ...Butyryl-Coa Dehydrogenase, subunit A; domain 1 / Acyl-CoA dehydrogenase/oxidase, N-terminal domain / 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 / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / AnaB
Similarity search - Component
Biological speciesOscillatoria sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMoncoq, K. / Mann, S. / Regad, L. / Mejean, A. / Ploux, O.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structure of the prolyl-acyl carrier protein oxidase involved in the biosynthesis of the cyanotoxin anatoxin-a.
Authors: Moncoq, K. / Regad, L. / Mann, S. / Mejean, A. / Ploux, O.
History
DepositionJan 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2014Group: Database references
Revision 1.2Sep 20, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Prolyl-ACP dehydrogenase
B: Prolyl-ACP dehydrogenase
C: Prolyl-ACP dehydrogenase
D: Prolyl-ACP dehydrogenase
E: Prolyl-ACP dehydrogenase
F: Prolyl-ACP dehydrogenase
G: Prolyl-ACP dehydrogenase
H: Prolyl-ACP dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)379,12616
Polymers372,8428
Non-polymers6,2848
Water8,197455
1
A: Prolyl-ACP dehydrogenase
B: Prolyl-ACP dehydrogenase
C: Prolyl-ACP dehydrogenase
D: Prolyl-ACP dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,5638
Polymers186,4214
Non-polymers3,1424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20070 Å2
ΔGint-139 kcal/mol
Surface area50560 Å2
MethodPISA
2
E: Prolyl-ACP dehydrogenase
F: Prolyl-ACP dehydrogenase
G: Prolyl-ACP dehydrogenase
H: Prolyl-ACP dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,5638
Polymers186,4214
Non-polymers3,1424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20080 Å2
ΔGint-137 kcal/mol
Surface area50450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.442, 191.184, 132.492
Angle α, β, γ (deg.)90.000, 98.940, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Prolyl-ACP dehydrogenase


Mass: 46605.234 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oscillatoria sp. (bacteria) / Strain: PCC 6506 / Gene: anaB, OSCI_4070008 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus
References: UniProt: C4NCB7, Oxidoreductases; Acting on the CH-CH group of donors; With unknown physiological acceptors
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 455 / 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: 2.16 Å3/Da / Density % sol: 43.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 24% PEG 4000, 100mM Tris-HCl pH 8.5 100mM MgCl2 , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 8, 2011
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.8→130.882 Å / Num. all: 76832 / Num. obs: 76832 / % possible obs: 99 % / Redundancy: 3.2 % / Biso Wilson estimate: 49.05 Å2 / Rsym value: 0.118 / Net I/σ(I): 9.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.8-2.953.10.372.134899111670.3798.9
2.95-3.133.20.2742.833400105650.27499
3.13-3.353.20.1983.93184599710.19899.1
3.35-3.613.20.1385.52997693130.13899.1
3.61-3.963.20.0977.82754985350.09799.1
3.96-4.433.20.075102493077310.07599.1
4.43-5.113.20.06710.92204868420.06799
5.11-6.263.20.08491866557970.08499.1
6.26-8.853.20.06211.71431044560.06298.7
8.85-47.7963.20.03318.1777024550.03397.8

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
BUSTER-TNTrefinement
PDB_EXTRACT3.11data extraction
MxCuBEdata collection
XDSdata reduction
PHASERphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JQI
Resolution: 2.8→30 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.8675 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2187 3857 5.03 %RANDOM
Rwork0.1878 ---
obs0.1893 76749 98.82 %-
all-77664 --
Displacement parametersBiso max: 101.17 Å2 / Biso mean: 29.5233 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1-0.8892 Å20 Å20.7658 Å2
2--11.673 Å20 Å2
3----12.5622 Å2
Refine analyzeLuzzati coordinate error obs: 0.314 Å
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23904 0 424 455 24783
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d8792SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes632HARMONIC2
X-RAY DIFFRACTIONt_gen_planes3832HARMONIC5
X-RAY DIFFRACTIONt_it24856HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion3224SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact28003SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d24856HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg33624HARMONIC21.02
X-RAY DIFFRACTIONt_omega_torsion2.13
X-RAY DIFFRACTIONt_other_torsion17.52
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2589 285 5.07 %
Rwork0.2128 5339 -
all0.2152 5624 -
obs-5624 98.82 %

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