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- PDB-6y3x: Crystal structure of the Francisella novicida lysine decarboxylas... -

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Basic information

Entry
Database: PDB / ID: 6y3x
TitleCrystal structure of the Francisella novicida lysine decarboxylase LdcF
ComponentsLysine decarboxylase
KeywordsLYASE / lysine decarboxylase / Oxidative Stress Resistance
Function / homology
Function and homology information


arginine decarboxylase activity / lysine decarboxylase activity / L-arginine catabolic process / pyridoxal phosphate binding / cytosol
Similarity search - Function
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 / Pyridoxal phosphate-dependent transferase, small 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 / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Lysine decarboxylase
Similarity search - Component
Biological speciesFrancisella tularensis subsp. novicida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsFelix, J. / Siebert, C. / Gutsche, I. / Renesto, P.
Funding support France, 2items
OrganizationGrant numberCountry
European Molecular Biology Organization (EMBO)ALTF441-2017 France
Marie Sklodowska-Curie Actions, FragNET ITNRespViRaLi France
CitationJournal: Sci Rep / Year: 2021
Title: Structural and functional analysis of the Francisella lysine decarboxylase as a key actor in oxidative stress resistance.
Authors: Felix, J. / Siebert, C. / Ducassou, J.N. / Nigou, J. / Garcia, P.S. / Fraudeau, A. / Huard, K. / Mas, C. / Brochier-Armanet, C. / Coute, Y. / Gutsche, I. / Renesto, P.
History
DepositionFeb 19, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysine decarboxylase
B: Lysine decarboxylase
C: Lysine decarboxylase
D: Lysine decarboxylase
E: Lysine decarboxylase


Theoretical massNumber of molelcules
Total (without water)413,2015
Polymers413,2015
Non-polymers00
Water00
1
A: Lysine decarboxylase
B: Lysine decarboxylase
C: Lysine decarboxylase
D: Lysine decarboxylase
E: Lysine decarboxylase

A: Lysine decarboxylase
B: Lysine decarboxylase
C: Lysine decarboxylase
D: Lysine decarboxylase
E: Lysine decarboxylase


Theoretical massNumber of molelcules
Total (without water)826,40210
Polymers826,40210
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area82320 Å2
ΔGint-405 kcal/mol
Surface area227240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.271, 318.247, 184.022
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUCYSCYS(chain 'A' and (resid 24 through 30 or (resid 31...AA24 - 5530 - 61
12VALVALLEULEU(chain 'A' and (resid 24 through 30 or (resid 31...AA58 - 24064 - 246
13ARGARGLYSLYS(chain 'A' and (resid 24 through 30 or (resid 31...AA243 - 282249 - 288
14THRTHRLEULEU(chain 'A' and (resid 24 through 30 or (resid 31...AA285 - 324291 - 330
15LYSLYSTHRTHR(chain 'A' and (resid 24 through 30 or (resid 31...AA328 - 367334 - 373
16LLPLLPASPASP(chain 'A' and (resid 24 through 30 or (resid 31...AA369 - 711375 - 717
27GLUGLUCYSCYS(chain 'B' and (resid 24 through 30 or (resid 31...BB24 - 5530 - 61
28VALVALLEULEU(chain 'B' and (resid 24 through 30 or (resid 31...BB58 - 24064 - 246
29ARGARGLYSLYS(chain 'B' and (resid 24 through 30 or (resid 31...BB243 - 282249 - 288
210THRTHRLEULEU(chain 'B' and (resid 24 through 30 or (resid 31...BB285 - 324291 - 330
211LYSLYSTHRTHR(chain 'B' and (resid 24 through 30 or (resid 31...BB328 - 367334 - 373
212LLPLLPASPASP(chain 'B' and (resid 24 through 30 or (resid 31...BB369 - 711375 - 717
313GLUGLUCYSCYS(chain 'C' and (resid 24 through 30 or (resid 31...CC24 - 5530 - 61
314VALVALLEULEU(chain 'C' and (resid 24 through 30 or (resid 31...CC58 - 24064 - 246
315ARGARGLYSLYS(chain 'C' and (resid 24 through 30 or (resid 31...CC243 - 282249 - 288
316THRTHRLEULEU(chain 'C' and (resid 24 through 30 or (resid 31...CC285 - 324291 - 330
317LYSLYSTHRTHR(chain 'C' and (resid 24 through 30 or (resid 31...CC328 - 367334 - 373
318LLPLLPASPASP(chain 'C' and (resid 24 through 30 or (resid 31...CC369 - 711375 - 717
419GLUGLUCYSCYS(chain 'D' and (resid 24 or (resid 25 and (name...DD24 - 5530 - 61
420VALVALLEULEU(chain 'D' and (resid 24 or (resid 25 and (name...DD58 - 24064 - 246
421ARGARGLYSLYS(chain 'D' and (resid 24 or (resid 25 and (name...DD243 - 282249 - 288
422THRTHRLEULEU(chain 'D' and (resid 24 or (resid 25 and (name...DD285 - 324291 - 330
423LYSLYSTHRTHR(chain 'D' and (resid 24 or (resid 25 and (name...DD328 - 367334 - 373
424LLPLLPASPASP(chain 'D' and (resid 24 or (resid 25 and (name...DD369 - 711375 - 717
525GLUGLUCYSCYS(chain 'E' and (resid 24 through 30 or (resid 31...EE24 - 5530 - 61
526VALVALLEULEU(chain 'E' and (resid 24 through 30 or (resid 31...EE58 - 24064 - 246
527ARGARGLYSLYS(chain 'E' and (resid 24 through 30 or (resid 31...EE243 - 282249 - 288
528THRTHRLEULEU(chain 'E' and (resid 24 through 30 or (resid 31...EE285 - 324291 - 330
529LYSLYSTHRTHR(chain 'E' and (resid 24 through 30 or (resid 31...EE328 - 367334 - 373
530LLPLLPASPASP(chain 'E' and (resid 24 through 30 or (resid 31...EE369 - 711375 - 717

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Components

#1: Protein
Lysine decarboxylase


Mass: 82640.203 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. novicida (bacteria)
Gene: FTN_0504 / Production host: Escherichia coli (E. coli) / References: UniProt: A0Q584
Has ligand of interestY

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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: 2.93 Å3/Da / Density % sol: 57.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Buffer: 50 mM HEPES pH 7, 25 mM NaCl, 0.1 mM PLP, 1 mM DTT Crystallization condition: 25% Ethylene Glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0744 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0744 Å / Relative weight: 1
ReflectionResolution: 3.4→146.7 Å / Num. obs: 66664 / % possible obs: 99 % / Redundancy: 3.8 % / Biso Wilson estimate: 152.29 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.087 / Net I/σ(I): 12.16
Reflection shellResolution: 3.4→3.6 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 0.94 / Num. unique obs: 10429 / CC1/2: 0.449 / Rrim(I) all: 1.709 / % possible all: 96.6

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Processing

Software
NameVersionClassification
PHENIXdev_3689refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3N75

3n75


Resolution: 3.4→89.27 Å / SU ML: 0.6107 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.9385
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2343 6654 10 %
Rwork0.1855 59912 -
obs0.1904 66566 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 165.19 Å2
Refinement stepCycle: LAST / Resolution: 3.4→89.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28440 0 0 0 28440
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002729160
X-RAY DIFFRACTIONf_angle_d0.643939668
X-RAY DIFFRACTIONf_chiral_restr0.04264384
X-RAY DIFFRACTIONf_plane_restr0.0045139
X-RAY DIFFRACTIONf_dihedral_angle_d7.8883872
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.430.59522010.60051826X-RAY DIFFRACTION90.45
3.43-3.470.49812210.48041975X-RAY DIFFRACTION98.79
3.47-3.520.49582150.43021963X-RAY DIFFRACTION99.27
3.52-3.560.36352180.35721976X-RAY DIFFRACTION99.64
3.56-3.610.38382210.31611990X-RAY DIFFRACTION99.1
3.61-3.660.36392200.31211989X-RAY DIFFRACTION99.5
3.66-3.710.32562200.27421968X-RAY DIFFRACTION99.64
3.71-3.770.27512230.25942008X-RAY DIFFRACTION99.64
3.77-3.820.29872220.24091989X-RAY DIFFRACTION99.68
3.82-3.890.30622190.23331975X-RAY DIFFRACTION99.55
3.89-3.950.28662220.22251999X-RAY DIFFRACTION99.69
3.95-4.030.29222210.22491990X-RAY DIFFRACTION99.73
4.03-4.10.27822190.22151980X-RAY DIFFRACTION99.59
4.1-4.190.28712230.20091998X-RAY DIFFRACTION99.64
4.19-4.280.25252220.18661999X-RAY DIFFRACTION99.37
4.28-4.380.22632210.17271992X-RAY DIFFRACTION99.55
4.38-4.490.21782230.15591999X-RAY DIFFRACTION99.42
4.49-4.610.22272230.14991999X-RAY DIFFRACTION99.46
4.61-4.740.20412230.1481995X-RAY DIFFRACTION99.51
4.74-4.90.1852220.14761989X-RAY DIFFRACTION99.73
4.9-5.070.21562210.15061992X-RAY DIFFRACTION99.77
5.07-5.270.20172250.15622039X-RAY DIFFRACTION99.69
5.28-5.520.23372220.15631997X-RAY DIFFRACTION99.46
5.52-5.810.2192220.16192000X-RAY DIFFRACTION99.24
5.81-6.170.22342260.17282024X-RAY DIFFRACTION99.69
6.17-6.650.24552260.1812028X-RAY DIFFRACTION99.65
6.65-7.310.24682240.18222015X-RAY DIFFRACTION99.25
7.31-8.370.19852260.16022046X-RAY DIFFRACTION99.21
8.37-10.540.16262280.13352063X-RAY DIFFRACTION99.22
10.55-89.270.22452350.19622109X-RAY DIFFRACTION97.54
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.65606034987-0.166517878107-0.04835363419342.338652745940.6120495339011.917351193540.2514446957350.1841395463240.805752083916-0.4150863975310.05831930872480.470033252413-0.611003390464-0.579049153221-1.14543056039E-51.251117971510.1709059237020.3589844558221.242768304840.4036406453021.90789873755-13.7695927801-28.726650095735.5080629069
22.70403637392-0.0763252219613-0.6540753127081.365244093250.208359040872.52694982411-0.1700864037630.864127277156-1.10986581394-0.5591374412010.124404360013-0.2808469745210.712755818403-0.00518821230734-0.004276199934721.718854451830.01165190211080.08871066363011.22553846221-0.5017589710011.5486867923615.7349718328-125.66713400710.0355246033
31.56127375303-0.00135469785139-0.5399569129711.08042675014-0.6226024443612.407188804250.02714158055770.007203339874330.008029100418920.3231364727510.4477344453170.646620014142-0.437211151269-1.037503677150.01086112312151.202927998050.3886976074230.3519683828891.770057985970.3919134731721.4663385923-51.6156094476-70.372240763267.3115575606
42.279338796540.696048308115-0.1844934432241.80813715351-0.03313828860471.804758556690.03356836100070.8075411854720.46893709948-0.9299736129060.290866759553-0.115048821992-0.8219951581460.2045157923560.005229437103591.85141767566-0.1845499990.3754956026341.614301898130.06841315042260.94564248187327.8304910975-63.32959290230.161883101487
51.674468496690.1412167892440.09662214445542.67704073449-0.3148447437431.53629063884-0.007404804216970.425655761166-1.18063234957-0.225483103270.1099554758070.5317232721060.876076959024-0.4921058666641.11523448619E-51.50536743457-0.4085076787940.0123040261981.48187494364-0.1116341939421.95055611109-33.28161245-130.16529827452.2338144596
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'D' and resid 24 through 741)
2X-RAY DIFFRACTION2(chain 'E' and resid 24 through 741)
3X-RAY DIFFRACTION3(chain 'A' and resid 24 through 741)
4X-RAY DIFFRACTION4(chain 'B' and resid 24 through 741)
5X-RAY DIFFRACTION5(chain 'C' and resid 24 through 741)

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