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- PDB-9fsc: The structure of ornithine decarboxylase from Leishmania infantum -

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Basic information

Entry
Database: PDB / ID: 9fsc
TitleThe structure of ornithine decarboxylase from Leishmania infantum
Componentsornithine decarboxylase
KeywordsLYASE / decarboxylase pyridoxal 5'-phosphate polyamine biosynthesis Orn/Lys/Arg decarboxylase class-II family
Function / homology
Function and homology information


ornithine decarboxylase / putrescine biosynthetic process from arginine, via ornithine / ornithine decarboxylase activity / cytoplasm
Similarity search - Function
Ornithine decarboxylase / Orn/DAP/Arg decarboxylase 2, conserved site / Orn/DAP/Arg decarboxylase 2, pyridoxal-phosphate binding site / Orn/DAP/Arg decarboxylases family 2 pyridoxal-P attachment site. / Orn/DAP/Arg decarboxylases family 2 signature 2. / Ornithine/DAP/Arg decarboxylase / Orn/DAP/Arg decarboxylase 2, C-terminal / Pyridoxal-dependent decarboxylase, C-terminal sheet domain / Orn/DAP/Arg decarboxylase 2, N-terminal / Pyridoxal-dependent decarboxylase, pyridoxal binding domain ...Ornithine decarboxylase / Orn/DAP/Arg decarboxylase 2, conserved site / Orn/DAP/Arg decarboxylase 2, pyridoxal-phosphate binding site / Orn/DAP/Arg decarboxylases family 2 pyridoxal-P attachment site. / Orn/DAP/Arg decarboxylases family 2 signature 2. / Ornithine/DAP/Arg decarboxylase / Orn/DAP/Arg decarboxylase 2, C-terminal / Pyridoxal-dependent decarboxylase, C-terminal sheet domain / Orn/DAP/Arg decarboxylase 2, N-terminal / Pyridoxal-dependent decarboxylase, pyridoxal binding domain / Alanine racemase/group IV decarboxylase, C-terminal / PLP-binding barrel
Similarity search - Domain/homology
PHOSPHATE ION / ornithine decarboxylase
Similarity search - Component
Biological speciesLeishmania infantum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsFiorillo, A. / Ilari, A. / Antonelli, L.
Funding support Italy, 1items
OrganizationGrant numberCountry
Other government Italy
CitationJournal: To Be Published
Title: The structure of ornithine decarboxylase from Leishmania infantum
Authors: Fiorillo, A. / Ilari, A. / Antonelli, L.
History
DepositionJun 20, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ornithine decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,6672
Polymers79,5721
Non-polymers951
Water1,874104
1
A: ornithine decarboxylase
hetero molecules

A: ornithine decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,3344
Polymers159,1442
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area6020 Å2
ΔGint-45 kcal/mol
Surface area32350 Å2
Unit cell
Length a, b, c (Å)119.22, 119.22, 85.47
Angle α, β, γ (deg.)90, 90, 120
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein ornithine decarboxylase


Mass: 79572.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal HIS-tag / Source: (gene. exp.) Leishmania infantum (eukaryote) / Gene: LINJ.12.0100 / Production host: Escherichia coli (E. coli) / References: UniProt: E9AGB5, ornithine decarboxylase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.55 Å3/Da / Density % sol: 65.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES monohydrate pH 6.5, 8% w/v Polyethylene glycol 20,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.27→65.84 Å / Num. obs: 23012 / % possible obs: 93.6 % / Redundancy: 18.92 % / CC1/2: 0.999 / Rmerge(I) obs: 0.0873 / Rpim(I) all: 0.0208 / Rrim(I) all: 0.0898 / Net I/σ(I): 20.44
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. measured obsNum. unique allNum. unique obsCC1/2CC1/2 anomalousRpim(I) allRrim(I) allAbsDiff over sigma anomalous% possible anomalous% possible ellipsoidal% possible ellipsoidal anomalous% possible spherical% possible spherical anomalousRedundancy anomalous% possible all
7.122-65.83815.880.038952.871828018280115111510.999-0.0690.00970.04010.59399.899.899.899.899.89.0399.8
5.607-7.12217.310.051848.881989319893114911490.999-0.1070.01250.05330.681001001001001009.34100
4.875-5.60717.10.056846.851966719667115011500.999-0.3430.01390.05850.6741001001001001009.12100
4.42-4.87517.270.058644.71987619876115111510.999-0.3150.01440.06040.6631001001001001009.15100
4.095-4.4218.210.065940.882095620956115111510.999-0.3640.01580.06780.67899.999.999.999.999.99.5599.9
3.845-4.09517.720.081133.532044420444115411540.998-0.1550.01980.08350.7571001001001001009.28100
3.652-3.84518.430.102728.272119321193115011500.999-0.1490.02460.10560.7710099.910099.91009.6599.9
3.49-3.65218.280.122823.42100921009114911490.998-0.1310.02960.12640.7691001001001001009.57100
3.353-3.4919.50.167119.272239122391114811480.998-0.0610.0390.17170.79199.999.999.999.999.910.1599.9
3.234-3.353200.213715.452304323043115211520.996-0.0250.0490.21930.80310010010010010010.45100
3.132-3.23419.720.276512.492272122721115211520.994-0.0840.06360.28380.77110010010010010010.24100
3.039-3.13219.430.37889.332230822308114811480.989-0.0470.08790.3890.78499.398.799.398.799.310.0798.7
2.951-3.03920.190.4537.922323623236115111510.987-0.0050.10290.46460.80194.393.694.391.292.210.493.6
2.863-2.95119.520.5236.892248222482115211520.979-0.0790.1210.5370.7639291.59282.584.310.0291.5
2.78-2.86319.930.77384.732295422954115211520.951-0.0030.17730.79410.79192.592.292.576.47810.2492.2
2.699-2.7820.210.93533.882319723197114811480.940.0310.21290.95940.78192929269.871.110.3692
2.618-2.69920.331.02943.532337923379115011500.913-0.0260.23351.05580.77393.79393.762.964.710.3993
2.536-2.61819.991.46482.432304523045115311530.795-0.030.33511.50290.77890.890.190.854.65610.1890.1
2.443-2.53620.181.80321.972320523205115011500.702-0.0210.41081.84980.7468382.68341.742.710.2882.6
2.274-2.44319.242.08411.622214922149115111510.611-0.0130.48552.14030.78660.860.560.818.418.89.7860.5

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
XDSdata reduction
STARANISOdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.27→65.84 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.915 / SU R Cruickshank DPI: 0.385 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.383 / SU Rfree Blow DPI: 0.27 / SU Rfree Cruickshank DPI: 0.274
RfactorNum. reflection% reflectionSelection details
Rfree0.2726 1119 -RANDOM
Rwork0.2353 ---
obs0.2372 23012 70.6 %-
Displacement parametersBiso mean: 70.26 Å2
Baniso -1Baniso -2Baniso -3
1--0.9102 Å20 Å20 Å2
2---0.9102 Å20 Å2
3---1.8205 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å
Refinement stepCycle: LAST / Resolution: 2.27→65.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3472 0 5 104 3581
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0083557HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.94830HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1194SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes605HARMONIC5
X-RAY DIFFRACTIONt_it3557HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion458SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2765SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.92
X-RAY DIFFRACTIONt_other_torsion16.96
LS refinement shellResolution: 2.27→2.38 Å
RfactorNum. reflection% reflection
Rfree0.4463 26 -
Rwork0.3307 --
obs0.3378 461 11.51 %

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