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- PDB-5xoy: Crystal structure of LysK from Thermus thermophilus in complex wi... -

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Basic information

Entry
Database: PDB / ID: 5xoy
TitleCrystal structure of LysK from Thermus thermophilus in complex with Lysine
Components[LysW]-lysine hydrolase
KeywordsHYDROLASE
Function / homology
Function and homology information


[amino group carrier protein]-lysine hydrolase / lysine biosynthetic process via aminoadipic acid / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / cobalt ion binding / zinc ion binding / cytoplasm
Similarity search - Function
[LysW]-lysine/[LysW]-ornithine hydrolase / Alpha-Beta Plaits - #360 / Peptidase M20 / Peptidase family M20/M25/M40 / Zn peptidases / Aminopeptidase / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
LYSINE / [LysW]-lysine hydrolase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsTomita, T. / Fujita, S. / Hasebe, F. / Cho, S.-H. / Yoshida, A. / Kuzuyama, T. / Nishiyama, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
JSPS24228001 Japan
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: Crystal structure of LysK, an enzyme catalyzing the last step of lysine biosynthesis in Thermus thermophilus, in complex with lysine: Insight into the mechanism for recognition of the amino- ...Title: Crystal structure of LysK, an enzyme catalyzing the last step of lysine biosynthesis in Thermus thermophilus, in complex with lysine: Insight into the mechanism for recognition of the amino-group carrier protein, LysW
Authors: Fujita, S. / Cho, S.-H. / Yoshida, A. / Hasebe, F. / Tomita, T. / Kuzuyama, T. / Nishiyama, M.
History
DepositionMay 31, 2017Deposition site: PDBJ / Processing site: PDBJ
SupersessionSep 13, 2017ID: 3X3E
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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

Downloads & links

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Assembly

Deposited unit
A: [LysW]-lysine hydrolase
B: [LysW]-lysine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,3956
Polymers81,9592
Non-polymers4354
Water2,990166
1
A: [LysW]-lysine hydrolase
B: [LysW]-lysine hydrolase
hetero molecules

A: [LysW]-lysine hydrolase
B: [LysW]-lysine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,79012
Polymers163,9194
Non-polymers8718
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area8600 Å2
ΔGint-120 kcal/mol
Surface area51370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.778, 69.927, 118.094
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein [LysW]-lysine hydrolase


Mass: 40979.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / Gene: lysK, TT_C1396 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 RIL Codon-plus (DE3)
References: UniProt: Q8VUS5, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Chemical ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N2O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 3.34 Å3/Da / Density % sol: 63.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris-HCl (pH 8.5), 1.5M Ammonium sulfate, 12 % Glycerol

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.39→50 Å / Num. obs: 44181 / % possible obs: 99.8 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 29.9
Reflection shellResolution: 2.39→2.44 Å / Rmerge(I) obs: 0.517 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 2180 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Q7A

4q7a


Resolution: 2.39→35.65 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.94 / SU B: 6.723 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.246 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2286 2224 5 %RANDOM
Rwork0.18845 ---
obs0.19047 41817 99.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.518 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å2-0 Å2
2---0.02 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.39→35.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5366 0 25 166 5557
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0195557
X-RAY DIFFRACTIONr_bond_other_d0.0010.025378
X-RAY DIFFRACTIONr_angle_refined_deg1.6031.9797540
X-RAY DIFFRACTIONr_angle_other_deg0.856312380
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6585691
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.58322.709251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.17415901
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9211551
X-RAY DIFFRACTIONr_chiral_restr0.10.2808
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216257
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021264
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.4874.7852767
X-RAY DIFFRACTIONr_mcbond_other3.4824.7842766
X-RAY DIFFRACTIONr_mcangle_it5.0467.1623451
X-RAY DIFFRACTIONr_mcangle_other5.0457.1643452
X-RAY DIFFRACTIONr_scbond_it4.355.4082790
X-RAY DIFFRACTIONr_scbond_other4.3325.4062783
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.6847.8814076
X-RAY DIFFRACTIONr_long_range_B_refined8.69838.3416130
X-RAY DIFFRACTIONr_long_range_B_other8.69538.3366123
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.389→2.451 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 142 -
Rwork0.263 2848 -
obs--93.2 %

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