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- PDB-2plk: Crystal structure of lysine/ornithine decarboxylase complexed wit... -

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Basic information

Entry
Database: PDB / ID: 2plk
TitleCrystal structure of lysine/ornithine decarboxylase complexed with cadaverine from Vibrio vulnificus
Componentslysine/ornithine decarboxylase
KeywordsLYASE / TYPE IV DECARBOXYLASE / BETA/ALPHA BARREL / BETA BARREL
Function / homology
Function and homology information


ornithine decarboxylase / putrescine biosynthetic process from ornithine / ornithine decarboxylase activity / polyamine biosynthetic process / cytoplasm
Similarity search - Function
Ornithine decarboxylase / Orn/DAP/Arg decarboxylase 2, conserved site / Orn/DAP/Arg decarboxylases family 2 signature 2. / Orn/DAP/Arg decarboxylase 2, C-terminal / Pyridoxal-dependent decarboxylase, C-terminal sheet domain / Ornithine/DAP/Arg decarboxylase / Orn/DAP/Arg decarboxylase 2, N-terminal / Pyridoxal-dependent decarboxylase, pyridoxal binding domain / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Lyase, Ornithine Decarboxylase; Chain A, domain 1 ...Ornithine decarboxylase / Orn/DAP/Arg decarboxylase 2, conserved site / Orn/DAP/Arg decarboxylases family 2 signature 2. / Orn/DAP/Arg decarboxylase 2, C-terminal / Pyridoxal-dependent decarboxylase, C-terminal sheet domain / Ornithine/DAP/Arg decarboxylase / Orn/DAP/Arg decarboxylase 2, N-terminal / Pyridoxal-dependent decarboxylase, pyridoxal binding domain / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Alanine racemase / Alanine racemase/group IV decarboxylase, C-terminal / PLP-binding barrel / TIM Barrel / Alpha-Beta Barrel / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-P3D / Ornithine decarboxylase / Ornithine decarboxylase
Similarity search - Component
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsLee, J. / Goldsmith, E.J. / Phillips, M.A.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Phylogenetic diversity and the structural basis of substrate specificity in the beta/alpha-barrel fold basic amino acid decarboxylases.
Authors: Lee, J. / Michael, A.J. / Martynowski, D. / Goldsmith, E.J. / Phillips, M.A.
History
DepositionApr 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Aug 30, 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: lysine/ornithine decarboxylase
B: lysine/ornithine decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,5014
Polymers91,8382
Non-polymers6632
Water6,305350
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6730 Å2
ΔGint-24 kcal/mol
Surface area27670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.245, 88.027, 99.272
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein lysine/ornithine decarboxylase


Mass: 45919.051 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus (bacteria) / Strain: CMCP6 / Gene: LysA / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q8D594, UniProt: A0A3Q0KZG4*PLUS, lysine decarboxylase, ornithine decarboxylase
#2: Chemical ChemComp-P3D / (4-{(E)-[(5-AMINOPENTYL)IMINO]METHYL}-5-HYDROXY-6-METHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE / PHOSPHORIC ACID MONO-{4-[(5-AMINO-PENTYLIMINO)-METHYL]-5-HYDROXY-6-METHYL-PYRIDIN-3-YLMETHYL} ESTER


Mass: 331.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H22N3O5P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / 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: 2.1 Å3/Da / Density % sol: 41.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: 30% PEG-4000, 0.1M Tris HCl pH8.4, 0.2M Magnesium chloride, 0.5% w/v n-octyl-b-D-glucoside , VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.979269 Å
DetectorType: SBC-3 / Detector: CCD / Date: Dec 15, 2006
RadiationMonochromator: Double-Crystal Monochromator Si-111, Si-220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979269 Å / Relative weight: 1
ReflectionResolution: 2.14→50 Å / Num. obs: 37184 / % possible obs: 90.6 % / Observed criterion σ(F): 1.4 / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Rmerge(I) obs: 0.107 / Rsym value: 0.107 / Net I/σ(I): 14.6
Reflection shellResolution: 2.14→2.19 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.429 / Mean I/σ(I) obs: 2 / Rsym value: 0.429 / % possible all: 87.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-3000data collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1F3T

1f3t


Resolution: 2.14→24.81 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.926 / SU B: 11.744 / SU ML: 0.157 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.292 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24003 1882 5.1 %RANDOM
Rwork0.17451 ---
obs0.17791 35254 89.91 %-
all-35254 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.185 Å2
Baniso -1Baniso -2Baniso -3
1-2.51 Å20 Å20 Å2
2--0.08 Å20 Å2
3----2.59 Å2
Refinement stepCycle: LAST / Resolution: 2.14→24.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5666 0 44 350 6060
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0225829
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5171.9777935
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4515729
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.08924.667255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.00515947
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.61530
X-RAY DIFFRACTIONr_chiral_restr0.0950.2925
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024398
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2080.22780
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.23947
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2377
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.250
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2850.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6991.53758
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.17125923
X-RAY DIFFRACTIONr_scbond_it1.88632317
X-RAY DIFFRACTIONr_scangle_it2.994.52012
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.14→2.196 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 117 -
Rwork0.215 2176 -
obs--77.02 %

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