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- PDB-5gjn: Crystal structure of Lysine decarboxylase from Selenomonas rumina... -

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Basic information

Entry
Database: PDB / ID: 5gjn
TitleCrystal structure of Lysine decarboxylase from Selenomonas ruminantium in P43212 space group
ComponentsLysine/ornithine decarboxylase
KeywordsLYASE / barrel domain
Function / homology
Function and homology information


ornithine decarboxylase / putrescine biosynthetic process from ornithine / lysine decarboxylase / lysine decarboxylase activity / ornithine decarboxylase activity / spermidine biosynthetic process / 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. / 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 ...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. / 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
TRIETHYLENE GLYCOL / Lysine/ornithine decarboxylase
Similarity search - Component
Biological speciesSelenomonas ruminantium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsSagong, H.-Y. / Kim, K.-J.
CitationJournal: PLoS ONE / Year: 2016
Title: Crystal Structure and Pyridoxal 5-Phosphate Binding Property of Lysine Decarboxylase from Selenomonas ruminantium
Authors: Sagong, H.-Y. / Son, H.F. / Kim, S. / Kim, Y.-H. / Kim, I.-K. / Kim, K.-J.
History
DepositionJul 1, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2017Group: Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 9, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysine/ornithine decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8857
Polymers43,2631
Non-polymers6216
Water3,837213
1
A: Lysine/ornithine decarboxylase
hetero molecules

A: Lysine/ornithine decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,76914
Polymers86,5272
Non-polymers1,24212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area7710 Å2
ΔGint-56 kcal/mol
Surface area27710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.966, 105.966, 73.634
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Lysine/ornithine decarboxylase / LDC / PLP binding barrel domain


Mass: 43263.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Selenomonas ruminantium (bacteria) / Strain: ATCC12561 / Gene: ldc / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21T1R / References: UniProt: O50657, lysine decarboxylase

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Non-polymers , 5 types, 219 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.39 Å3/Da / Density % sol: 48.51 % / Mosaicity: 0.54 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: PEG 400, Sodium citrate, MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 10, 2015
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 28705 / % possible obs: 99 % / Redundancy: 11.1 % / Rmerge(I) obs: 0.073 / Net I/av σ(I): 60.951 / Net I/σ(I): 15.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2-2.0310.80.3040.9771100
2.03-2.07110.2650.9781100
2.07-2.1111.10.2280.983199.9
2.11-2.1511.10.210.9851100
2.15-2.211.10.1880.988199.9
2.2-2.2511.20.1670.992199.9
2.25-2.3111.10.1460.993199.9
2.31-2.3711.30.1350.9941100
2.37-2.4411.20.1260.994199.9
2.44-2.5211.30.1120.995199.9
2.52-2.6111.20.1040.996199.9
2.61-2.7111.20.0960.996199.9
2.71-2.8411.30.0860.997199.8
2.84-2.9911.40.080.997199.9
2.99-3.1711.40.0740.998199.8
3.17-3.4211.30.0710.996199.6
3.42-3.7611.20.0660.996199.4
3.76-4.3110.80.0630.996198.3
4.31-5.4310.40.0590.996197.1
5.43-509.70.0580.995188.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
MOLREPphasing
REFMAC5.8.0151refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PLK

2plk


Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.878 / SU ML: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.162 / ESU R Free: 0.156
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2387 1482 5.2 %RANDOM
Rwork0.1958 ---
obs0.2029 27192 99.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 118.37 Å2 / Biso mean: 44.354 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-1.06 Å2-0 Å2-0 Å2
2--1.06 Å2-0 Å2
3----2.13 Å2
Refinement stepCycle: final / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2854 0 40 213 3107
Biso mean--59.91 48.57 -
Num. residues----369
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192942
X-RAY DIFFRACTIONr_bond_other_d0.0020.022810
X-RAY DIFFRACTIONr_angle_refined_deg1.9211.9783966
X-RAY DIFFRACTIONr_angle_other_deg1.07336480
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6855366
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.94823.889126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.1815479
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7821517
X-RAY DIFFRACTIONr_chiral_restr0.1160.2435
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213277
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02644
X-RAY DIFFRACTIONr_mcbond_it4.0574.1221473
X-RAY DIFFRACTIONr_mcbond_other4.0574.121472
X-RAY DIFFRACTIONr_mcangle_it5.3046.1491836
LS refinement shellResolution: 1.999→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 123 -
Rwork0.209 1969 -
all-2092 -
obs--99.86 %

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