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- PDB-3ljc: Crystal structure of Lon N-terminal domain. -

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Basic information

Entry
Database: PDB / ID: 3ljc
TitleCrystal structure of Lon N-terminal domain.
ComponentsATP-dependent protease LaEndopeptidase La
KeywordsHYDROLASE / Lon N-domain / Allosteric enzyme / ATP-binding / DNA-binding / Nucleotide-binding / Protease / Serine protease / Stress response
Function / homology
Function and homology information


endopeptidase La / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / response to X-ray / cellular response to heat / peptidase activity / response to heat / sequence-specific DNA binding / serine-type endopeptidase activity / ATP hydrolysis activity ...endopeptidase La / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / response to X-ray / cellular response to heat / peptidase activity / response to heat / sequence-specific DNA binding / serine-type endopeptidase activity / ATP hydrolysis activity / proteolysis / DNA binding / ATP binding / cytosol / cytoplasm
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1480 / LON domain-like / Lon protease, bacterial / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / Lon protease, bacterial/eukaryotic-type / Peptidase S16, active site / ATP-dependent serine proteases, lon family, serine active site. / Lon proteolytic domain profile. / Peptidase S16, Lon proteolytic domain / Lon protease ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1480 / LON domain-like / Lon protease, bacterial / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / Lon protease, bacterial/eukaryotic-type / Peptidase S16, active site / ATP-dependent serine proteases, lon family, serine active site. / Lon proteolytic domain profile. / Peptidase S16, Lon proteolytic domain / Lon protease / Lon protease (S16) C-terminal proteolytic domain / Lon protease, N-terminal domain superfamily / Lon N-terminal domain profile. / Lon protease, N-terminal domain / ATP-dependent protease La (LON) substrate-binding domain / Found in ATP-dependent protease La (LON) / PUA-like superfamily / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Roll / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsLi, M. / Gustchina, A. / Dauter, Z. / Wlodawer, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2010
Title: Structure of the N-terminal fragment of Escherichia coli Lon protease
Authors: Li, M. / Gustchina, A. / Rasulova, F.S. / Melnikov, E.E. / Maurizi, M.R. / Rotanova, T.V. / Dauter, Z. / Wlodawer, A.
History
DepositionJan 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-dependent protease La


Theoretical massNumber of molelcules
Total (without water)29,5751
Polymers29,5751
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.568, 91.568, 81.862
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein ATP-dependent protease La / Endopeptidase La


Mass: 29574.955 Da / Num. of mol.: 1 / Fragment: Lon N-domain (UNP residues 1-245)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: lon, capR, deg, lopA, muc, b0439, JW0429 / Plasmid: pBAD33 / Production host: Escherichia coli (E. coli) / Strain (production host): MG1655 / References: UniProt: P0A9M0, endopeptidase La

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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: 3.47 Å3/Da / Density % sol: 64.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 06M MgFormate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: marccd 300 / Detector: CCD / Date: Jan 1, 2006
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 12507 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 8.6 % / Rsym value: 0.053 / Net I/σ(I): 33.5
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.051 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1184 / Rsym value: 0.533 / % possible all: 96.3

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Processing

Software
NameVersionClassification
MAR345data collection
SHELXSphasing
REFMAC5.5.0104refinement
HKL-3000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.929 / SU B: 26.508 / SU ML: 0.275 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.407 / ESU R Free: 0.298 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28239 606 4.9 %RANDOM
Rwork0.23292 ---
obs0.23522 11878 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 96.309 Å2
Baniso -1Baniso -2Baniso -3
1-3.21 Å21.6 Å20 Å2
2--3.21 Å20 Å2
3----4.81 Å2
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1897 0 0 0 1897
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221908
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3132.0012569
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5685238
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.9592584
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.51315377
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9221514
X-RAY DIFFRACTIONr_chiral_restr0.090.2299
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211394
X-RAY DIFFRACTIONr_gen_planes_other
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_it11.96521194
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it16.26831933
X-RAY DIFFRACTIONr_scbond_it15.8062714
X-RAY DIFFRACTIONr_scangle_it20.5343636
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.601→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.432 47 -
Rwork0.334 807 -
obs--94.47 %
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)
11.4207-0.5144-2.76531.69190.38787.4020.1194-0.30950.1901-0.1911-0.0819-0.6458-1.1151.0809-0.03750.6517-0.2384-0.03340.43540.17220.5392-27.539956.0861-0.3582
21.06910.36140.46920.65581.22292.7345-0.0128-0.0692-0.01160.0430.0399-0.05650.27620.399-0.02710.25230.0865-0.03270.28330.03470.1118-38.993132.96027.4056
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 117
2X-RAY DIFFRACTION2A123 - 224

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