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- PDB-9jfn: Arginine decarboxylase in Aspergillus oryzae complexed with agmatine -

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Basic information

Entry
Database: PDB / ID: 9jfn
TitleArginine decarboxylase in Aspergillus oryzae complexed with agmatine
Components(L-tryptophan decarboxylase PsiD-like domain-containing ...) x 2
KeywordsLYASE / arginine decarboxylase / pyruvoyl-dependent decarboxylase / agumatine / Aspergillus oryzae
Function / homology
Function and homology information


phosphatidylserine decarboxylase activity / phosphatidylethanolamine biosynthetic process / mitochondrion
Similarity search - Function
L-tryptophan decarboxylase PsiD-like / Phophatidylserine decarboxylase / Phosphatidylserine decarboxylase-related / Phosphatidylserine decarboxylase
Similarity search - Domain/homology
AGMATINE / DI(HYDROXYETHYL)ETHER / L-tryptophan decarboxylase PsiD-like domain-containing protein
Similarity search - Component
Biological speciesAspergillus oryzae RIB40 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsMikami, B. / Yasukawa, K. / Fujiwara, S. / Takita, T. / Mizutani, K. / Odagaki, Y. / Murakami, Y.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Science and Technology23K24590 Japan
Japan Science and Technology22H03332 Japan
Japan Science and Technology22K05441 Japan
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2024
Title: Unveiling the reaction mechanism of arginine decarboxylase in Aspergillus oryzae: Insights from crystal structure analysis.
Authors: Odagaki, Y. / Murakami, Y. / Takita, T. / Mizutani, K. / Mikami, B. / Fujiwara, S. / Yasukawa, K.
History
DepositionSep 5, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-tryptophan decarboxylase PsiD-like domain-containing protein
E: L-tryptophan decarboxylase PsiD-like domain-containing protein
B: L-tryptophan decarboxylase PsiD-like domain-containing protein
F: L-tryptophan decarboxylase PsiD-like domain-containing protein
C: L-tryptophan decarboxylase PsiD-like domain-containing protein
G: L-tryptophan decarboxylase PsiD-like domain-containing protein
D: L-tryptophan decarboxylase PsiD-like domain-containing protein
H: L-tryptophan decarboxylase PsiD-like domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,476144
Polymers223,4108
Non-polymers9,066136
Water23,7261317
1
A: L-tryptophan decarboxylase PsiD-like domain-containing protein
E: L-tryptophan decarboxylase PsiD-like domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,44742
Polymers55,8522
Non-polymers2,59540
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-23 kcal/mol
Surface area17370 Å2
MethodPISA
2
B: L-tryptophan decarboxylase PsiD-like domain-containing protein
F: L-tryptophan decarboxylase PsiD-like domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,06533
Polymers55,8522
Non-polymers2,21231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5480 Å2
ΔGint-16 kcal/mol
Surface area17180 Å2
MethodPISA
3
C: L-tryptophan decarboxylase PsiD-like domain-containing protein
G: L-tryptophan decarboxylase PsiD-like domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,24338
Polymers55,8522
Non-polymers2,39136
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-15 kcal/mol
Surface area17240 Å2
MethodPISA
4
D: L-tryptophan decarboxylase PsiD-like domain-containing protein
H: L-tryptophan decarboxylase PsiD-like domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,72131
Polymers55,8522
Non-polymers1,86829
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-25 kcal/mol
Surface area17240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.749, 197.286, 196.412
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11B-862-

HOH

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Components

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L-tryptophan decarboxylase PsiD-like domain-containing ... , 2 types, 8 molecules ABCDEFGH

#1: Protein
L-tryptophan decarboxylase PsiD-like domain-containing protein


Mass: 51174.055 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus oryzae RIB40 (mold) / Gene: AO090102000327 / Plasmid: pET-28a(+)-Ao-ADC1 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q2UAM5, arginine decarboxylase
#2: Protein/peptide
L-tryptophan decarboxylase PsiD-like domain-containing protein


Mass: 4678.405 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus oryzae RIB40 (mold) / Gene: AO090102000327 / Plasmid: pET-28a(+)-Ao-ADC1 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q2UAM5, arginine decarboxylase

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Non-polymers , 4 types, 1453 molecules

#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 124 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-AG2 / AGMATINE / (4-AMINOBUTYL)GUANIDINE


Mass: 130.191 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H14N4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1317 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 3.47 Å3/Da / Density % sol: 64.61 % / Description: rectangle plate
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M sodium acetate buffer (pH 7.0), 12% w/v PEG 3350 The crystal was soaked in the reservoir solution with 10 mM L-agmatine for 10 min. followed by brief soaking to the same solution ...Details: 0.1 M sodium acetate buffer (pH 7.0), 12% w/v PEG 3350 The crystal was soaked in the reservoir solution with 10 mM L-agmatine for 10 min. followed by brief soaking to the same solution containing 30% ethylene glycol before flash-cooling.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: May 12, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 140013 / % possible obs: 99.7 % / Redundancy: 9.19 % / Biso Wilson estimate: 37.79 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.009 / Rrim(I) all: 0.0096 / Net I/σ(I): 17.86
Reflection shellResolution: 2.15→2.28 Å / Redundancy: 9.53 % / Rmerge(I) obs: 0.968 / Mean I/σ(I) obs: 2.47 / Num. unique obs: 22183 / CC1/2: 0.884 / Rrim(I) all: 1.022 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 2.15→43.49 Å / SU ML: 0.2573 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.8923
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2135 6998 5 %
Rwork0.1758 132906 -
obs0.1777 139904 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.82 Å2
Refinement stepCycle: LAST / Resolution: 2.15→43.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13192 0 604 1317 15113
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006114330
X-RAY DIFFRACTIONf_angle_d0.794719239
X-RAY DIFFRACTIONf_chiral_restr0.04912050
X-RAY DIFFRACTIONf_plane_restr0.00662506
X-RAY DIFFRACTIONf_dihedral_angle_d14.32415242
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.170.34572170.32864107X-RAY DIFFRACTION93.25
2.17-2.20.34622310.29344387X-RAY DIFFRACTION99.85
2.2-2.230.28472320.27974398X-RAY DIFFRACTION99.74
2.23-2.260.36962330.29774421X-RAY DIFFRACTION99.76
2.26-2.280.30452310.24864389X-RAY DIFFRACTION99.89
2.28-2.320.26162320.23684394X-RAY DIFFRACTION99.91
2.32-2.350.28162320.23274404X-RAY DIFFRACTION99.85
2.35-2.380.28992330.22424419X-RAY DIFFRACTION99.85
2.38-2.420.29232320.23684402X-RAY DIFFRACTION99.94
2.42-2.460.26892300.21234391X-RAY DIFFRACTION99.94
2.46-2.50.25782340.20874434X-RAY DIFFRACTION99.89
2.5-2.550.27282320.2064416X-RAY DIFFRACTION99.98
2.55-2.60.24312340.20264431X-RAY DIFFRACTION99.89
2.6-2.650.28392320.19734424X-RAY DIFFRACTION99.98
2.65-2.710.23742320.19364416X-RAY DIFFRACTION99.91
2.71-2.770.23952330.18554431X-RAY DIFFRACTION99.96
2.77-2.840.24912330.18974422X-RAY DIFFRACTION99.96
2.84-2.920.22422330.19474425X-RAY DIFFRACTION99.96
2.92-30.25692320.19874406X-RAY DIFFRACTION100
3-3.10.24852340.19764450X-RAY DIFFRACTION100
3.1-3.210.24312340.19124441X-RAY DIFFRACTION100
3.21-3.340.22982350.17784457X-RAY DIFFRACTION99.94
3.34-3.490.20752340.17244446X-RAY DIFFRACTION100
3.49-3.680.19952340.16934457X-RAY DIFFRACTION99.98
3.68-3.910.16692350.14734459X-RAY DIFFRACTION100
3.91-4.210.1882350.14094474X-RAY DIFFRACTION100
4.21-4.630.15492360.12994486X-RAY DIFFRACTION100
4.63-5.30.16162380.12914519X-RAY DIFFRACTION100
5.3-6.670.19622400.15114554X-RAY DIFFRACTION99.96
6.67-43.490.15582450.15484646X-RAY DIFFRACTION99.13

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