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- PDB-3q16: Linkage between the Bacterial Acid Stress and Stringent Responses... -

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Basic information

Entry
Database: PDB / ID: 3q16
TitleLinkage between the Bacterial Acid Stress and Stringent Responses: The Structure of the Inducible Lysine Decarboxylase
ComponentsLysine decarboxylase, inducible
KeywordsLYASE / Aspartate aminotranferase / CheY / PLP / pyridoxal-5-phosphate / inducible lysine decarboxylase
Function / homology
Function and homology information


lysine decarboxylase / lysine catabolic process / lysine decarboxylase activity / arginine decarboxylase activity / guanosine tetraphosphate binding / arginine catabolic process / pyridoxal phosphate binding / identical protein 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
Inducible lysine decarboxylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.1 Å
AuthorsEl Bakkouri, M. / Pai, E.F. / Houry, W.A.
CitationJournal: 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.
History
DepositionDec 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 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_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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
Revision 1.3Dec 6, 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


Theoretical massNumber of molelcules
Total (without water)407,9265
Polymers407,9265
Non-polymers00
Water00
1
A: Lysine decarboxylase, inducible
B: Lysine decarboxylase, inducible
C: Lysine decarboxylase, inducible
D: Lysine decarboxylase, inducible
E: Lysine decarboxylase, inducible

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


Theoretical massNumber of molelcules
Total (without water)815,85110
Polymers815,85110
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area80710 Å2
ΔGint-400 kcal/mol
Surface area238610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)270.290, 181.290, 169.930
Angle α, β, γ (deg.)90.00, 125.06, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 4 / Auth seq-ID: 10 - 700 / Label seq-ID: 10 - 700

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE

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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: K12 / Gene: cadA, ldcI / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21GOLD(DE3)pLysS / References: UniProt: P0A9H3, lysine decarboxylase

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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: 4.18 Å3/Da / Density % sol: 70.55 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris, 0.1 M ammonium bromide, 25-35% PEG1000, 0-10% glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Dec 12, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 4.1→140.227 Å / Num. all: 52673 / Num. obs: 40852 / % possible obs: 77.4 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.219 / Rsym value: 0.219 / Net I/σ(I): 6.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym value% possible all
4.1-4.322.60.4211.70.42179.3
4.32-4.582.70.3262.10.32679
4.58-4.92.70.2842.40.28478.6
4.9-5.292.70.2852.40.28578.1
5.29-5.82.70.2652.60.26577.3
5.8-6.482.80.252.70.2576.9
6.48-7.492.80.2023.20.20276
7.49-9.172.80.1374.40.13774.8
9.17-12.972.70.11650.11674.1
12.97-68.3592.60.1084.80.10871.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MxDCdata collection
MOSFLMdata reduction
SCALAdata scaling
REFMAC5.2.0019phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3N75

3n75


Resolution: 4.1→68 Å / Cor.coef. Fo:Fc: 0.845 / Cor.coef. Fo:Fc free: 0.809 / SU B: 62.579 / SU ML: 0.799 / Cross valid method: THROUGHOUT / ESU R Free: 1.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30432 2077 5.1 %RANDOM
Rwork0.27629 ---
obs0.27771 38774 77.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 100.395 Å2
Baniso -1Baniso -2Baniso -3
1-3.45 Å20 Å2-2.94 Å2
2---0.01 Å20 Å2
3----6.82 Å2
Refinement stepCycle: LAST / Resolution: 4.1→68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28485 0 0 0 28485
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.02229254
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.7661.96139672
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.42953564
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.80924.0241347
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.396155044
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.44615155
X-RAY DIFFRACTIONr_chiral_restr0.0460.24342
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02122181
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1520.212505
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2930.219924
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0960.2645
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1260.2548
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1180.228
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1071.517751
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.191228797
X-RAY DIFFRACTIONr_scbond_it0.069311503
X-RAY DIFFRACTIONr_scangle_it0.1314.510868
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 5538 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.210.5
Bmedium positional0.180.5
Cmedium positional0.170.5
Dmedium positional0.180.5
Emedium positional0.190.5
Amedium thermal0.022
Bmedium thermal0.042
Cmedium thermal0.022
Dmedium thermal0.032
Emedium thermal0.032
LS refinement shellResolution: 4.1→4.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 144 -
Rwork0.317 2941 -
obs--79.55 %

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