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- PDB-9jf5: Arginine decarboxylase in Aspergillus oryzae complexed with arginine -

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Basic information

Entry
Database: PDB / ID: 9jf5
TitleArginine decarboxylase in Aspergillus oryzae complexed with arginine
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: 1.9 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 4, 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)234,072169
Polymers223,4108
Non-polymers10,662161
Water30,4271689
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)58,49142
Polymers55,8522
Non-polymers2,63940
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-19 kcal/mol
Surface area17270 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)58,72245
Polymers55,8522
Non-polymers2,86943
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint-16 kcal/mol
Surface area17130 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)58,53542
Polymers55,8522
Non-polymers2,68340
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5270 Å2
ΔGint-16 kcal/mol
Surface area16960 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)58,32340
Polymers55,8522
Non-polymers2,47138
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-26 kcal/mol
Surface area17320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.020, 195.575, 196.124
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-917-

HOH

21D-958-

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, 1850 molecules

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


Mass: 106.120 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 148 / 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.: 1689 / 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: 3.45 Å3/Da / Density % sol: 64.36 % / Description: rectagle plate
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging 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 1 mM L-arginine for 10 min 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: 1.9→50 Å / Num. obs: 200882 / % possible obs: 99.8 % / Redundancy: 7.66 % / Biso Wilson estimate: 27.23 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.082 / Rrim(I) all: 0.088 / Net I/σ(I): 18.02
Reflection shellResolution: 1.9→2.02 Å / Redundancy: 7.26 % / Rmerge(I) obs: 0.847 / Mean I/σ(I) obs: 2.26 / Num. unique obs: 32042 / CC1/2: 0.808 / Rrim(I) all: 0.911 / % possible all: 99.2

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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: 1.9→47.44 Å / SU ML: 0.2029 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.3586
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1889 10043 5 %
Rwork0.1603 190729 -
obs0.1617 200772 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.27 Å2
Refinement stepCycle: LAST / Resolution: 1.9→47.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13181 0 707 1689 15577
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006414486
X-RAY DIFFRACTIONf_angle_d0.801819413
X-RAY DIFFRACTIONf_chiral_restr0.05222058
X-RAY DIFFRACTIONf_plane_restr0.00682531
X-RAY DIFFRACTIONf_dihedral_angle_d14.5365324
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.34583220.30746114X-RAY DIFFRACTION96.39
1.92-1.940.31513350.26916361X-RAY DIFFRACTION99.91
1.94-1.970.26983290.2376246X-RAY DIFFRACTION99.91
1.97-1.990.23083330.22216328X-RAY DIFFRACTION99.97
1.99-2.020.27973320.21236314X-RAY DIFFRACTION99.97
2.02-2.050.24363340.26327X-RAY DIFFRACTION99.9
2.05-2.080.23943320.19446310X-RAY DIFFRACTION99.92
2.08-2.110.23453340.18876344X-RAY DIFFRACTION99.99
2.11-2.140.22583330.18686330X-RAY DIFFRACTION99.97
2.14-2.170.20753330.17836323X-RAY DIFFRACTION99.98
2.17-2.210.22883330.17856325X-RAY DIFFRACTION99.89
2.21-2.250.21463330.1726323X-RAY DIFFRACTION99.89
2.25-2.30.20633330.16756327X-RAY DIFFRACTION100
2.3-2.340.2053340.16016348X-RAY DIFFRACTION99.96
2.34-2.390.20773350.15926358X-RAY DIFFRACTION99.94
2.39-2.450.19173320.16276323X-RAY DIFFRACTION99.92
2.45-2.510.21173350.15586350X-RAY DIFFRACTION99.96
2.51-2.580.19943360.15796389X-RAY DIFFRACTION99.93
2.58-2.650.19393330.16036316X-RAY DIFFRACTION99.98
2.65-2.740.21313350.15746364X-RAY DIFFRACTION99.91
2.74-2.840.18073350.15496376X-RAY DIFFRACTION99.99
2.84-2.950.21893350.16536349X-RAY DIFFRACTION100
2.95-3.090.19433350.16026366X-RAY DIFFRACTION100
3.09-3.250.19673360.15196395X-RAY DIFFRACTION100
3.25-3.450.16493380.15366411X-RAY DIFFRACTION99.99
3.45-3.720.16273370.14556401X-RAY DIFFRACTION99.7
3.72-4.090.14593380.13376419X-RAY DIFFRACTION99.91
4.09-4.680.14813390.12826435X-RAY DIFFRACTION99.99
4.68-5.90.16233420.14216511X-RAY DIFFRACTION99.99
5.9-47.440.17243520.16516646X-RAY DIFFRACTION99.46

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