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- PDB-3n75: X-ray Crystal Structure of the Escherichia coli Inducible Lysine ... -

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Basic information

Entry
Database: PDB / ID: 3n75
TitleX-ray Crystal Structure of the Escherichia coli Inducible Lysine Decarboxylase LdcI
ComponentsLysine decarboxylase, inducible
KeywordsLYASE / Pyridoxal-5'-phosphate dependent decarboxylase / acid stress response / stringent response / guanosine tetraphosphate (ppGpp)
Function / homology
Function and homology information


lysine catabolic process / lysine decarboxylase / lysine decarboxylase activity / guanosine tetraphosphate binding / identical protein binding / cytoplasm
Similarity search - Function
Ornithine Decarboxylase; Chain A, domain 4 / Orn/Lys/Arg decarboxylase, C-terminal domain / Orn/Lys/Arg decarboxylase, N-terminal / Ornithine/lysine/arginine decarboxylase / Orn/Lys/Arg decarboxylase, N-terminal domain / Orn/Lys/Arg decarboxylases family 1 pyridoxal-P attachment site. / Orn/Lys/Arg decarboxylase, major domain / Orn/Lys/Arg decarboxylase, C-terminal / Orn/Lys/Arg decarboxylase, C-terminal domain superfamily / Orn/Lys/Arg decarboxylase, major domain ...Ornithine Decarboxylase; Chain A, domain 4 / Orn/Lys/Arg decarboxylase, C-terminal domain / Orn/Lys/Arg decarboxylase, N-terminal / Ornithine/lysine/arginine decarboxylase / Orn/Lys/Arg decarboxylase, N-terminal domain / Orn/Lys/Arg decarboxylases family 1 pyridoxal-P attachment site. / Orn/Lys/Arg decarboxylase, major domain / Orn/Lys/Arg decarboxylase, C-terminal / Orn/Lys/Arg decarboxylase, C-terminal domain superfamily / Orn/Lys/Arg decarboxylase, major domain / Orn/Lys/Arg decarboxylase, C-terminal domain / Response regulator / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5',3'-TETRAPHOSPHATE / Inducible lysine decarboxylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKanjee, U. / Alexopoulos, E. / Pai, E.F. / Houry, W.A.
Citation
Journal: Embo J. / Year: 2011
Title: Linkage between the bacterial acid stress and stringent responses: the structure of the inducible lysine decarboxylase.
Authors: Kanjee, U. / Gutsche, I. / Alexopoulos, E. / Zhao, B. / El Bakkouri, M. / Thibault, G. / Liu, K. / Ramachandran, S. / Snider, J. / Pai, E.F. / Houry, W.A.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2008
Title: Crystallization and preliminary X-ray analysis of the inducible lysine decarboxylase from Escherichia coli.
Authors: Alexopoulos, E. / Kanjee, U. / Snider, J. / Houry, W.A. / Pai, E.F.
History
DepositionMay 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 27, 2011Group: Source and taxonomy
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysine decarboxylase, inducible
B: Lysine decarboxylase, inducible
C: Lysine decarboxylase, inducible
D: Lysine decarboxylase, inducible
E: Lysine decarboxylase, inducible
hetero molecules


Theoretical massNumber of molelcules
Total (without water)412,81420
Polymers407,9265
Non-polymers4,88815
Water59,3053292
1
A: Lysine decarboxylase, inducible
B: Lysine decarboxylase, inducible
C: Lysine decarboxylase, inducible
D: Lysine decarboxylase, inducible
E: Lysine decarboxylase, inducible
hetero molecules

A: Lysine decarboxylase, inducible
B: Lysine decarboxylase, inducible
C: Lysine decarboxylase, inducible
D: Lysine decarboxylase, inducible
E: Lysine decarboxylase, inducible
hetero molecules


Theoretical massNumber of molelcules
Total (without water)825,62740
Polymers815,85110
Non-polymers9,77630
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area91790 Å2
ΔGint-433 kcal/mol
Surface area238900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)271.760, 181.993, 170.902
Angle α, β, γ (deg.)90.00, 125.41, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-3018-

HOH

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Components

#1: Protein
Lysine decarboxylase, inducible / / LDC


Mass: 81585.125 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b4131, cadA, JW4092, ldcI, LdcI/CadA / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold (DE3) pLysS / References: UniProt: P0A9H3, lysine decarboxylase
#2: Chemical
ChemComp-G4P / GUANOSINE-5',3'-TETRAPHOSPHATE / guanosine tetraphosphate;ppGpp / Guanosine pentaphosphate


Type: RNA linking / Mass: 603.160 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H17N5O17P4
#3: Chemical
ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3292 / 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: 2

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Sample preparation

CrystalDensity Matthews: 4.22 Å3/Da / Density % sol: 70.87 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 18-28% (v/v) PEG1000, 0.1 M Sodium Chloride, 0.1 M Tris HCl pH 8.5, 0.005 M Tris[2-carboxyethyl] phosphine, 15% (v/v) glycerol. Once crystals formed, they were soaked in mother liquid that ...Details: 18-28% (v/v) PEG1000, 0.1 M Sodium Chloride, 0.1 M Tris HCl pH 8.5, 0.005 M Tris[2-carboxyethyl] phosphine, 15% (v/v) glycerol. Once crystals formed, they were soaked in mother liquid that had been saturated with hexatantalum dodecabromide for derivatization., VAPOR DIFFUSION, HANGING DROP, temperature 285K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-BM11.254431
SYNCHROTRONAPS 14-BM-C20.9002
Detector
TypeIDDetectorDate
SBC-31CCDMar 22, 2006
ADSC QUANTUM 3152CCDAug 2, 2006
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si-111SINGLE WAVELENGTHMx-ray1
2Bent Ge(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.2544311
20.90021
ReflectionResolution: 2→140.3 Å / Num. all: 454474 / Num. obs: 454474 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.44 % / Rmerge(I) obs: 0.161 / Net I/σ(I): 12.6
Reflection shellResolution: 2→2.1 Å / Redundancy: 3.39 % / Rmerge(I) obs: 0.3266 / Mean I/σ(I) obs: 3.82 / Num. unique all: 61407 / % possible all: 99.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ORD

1ord


Resolution: 2→49.89 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.655 / SU ML: 0.075 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19392 22770 5 %RANDOM
Rwork0.16753 ---
obs0.16886 430750 99.76 %-
all-454474 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.734 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20 Å2-0.84 Å2
2--0.32 Å20 Å2
3----1.72 Å2
Refinement stepCycle: LAST / Resolution: 2→49.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28485 0 293 3292 32070
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02229699
X-RAY DIFFRACTIONr_angle_refined_deg1.6331.97740319
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.17753564
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.01224.0241347
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.802155044
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.21215155
X-RAY DIFFRACTIONr_chiral_restr0.1130.24378
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0222289
X-RAY DIFFRACTIONr_nbd_refined0.2060.213730
X-RAY DIFFRACTIONr_nbtor_refined0.3090.220319
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.22865
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2190.2473
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1480.2140
X-RAY DIFFRACTIONr_mcbond_it1.3641.518348
X-RAY DIFFRACTIONr_mcangle_it1.562228797
X-RAY DIFFRACTIONr_scbond_it2.865313081
X-RAY DIFFRACTIONr_scangle_it4.2444.511515
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 1634 -
Rwork0.219 31593 -
obs-32101 99.13 %

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