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- PDB-1rre: Crystal structure of E.coli Lon proteolytic domain -

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Basic information

Entry
Database: PDB / ID: 1rre
TitleCrystal structure of E.coli Lon proteolytic domain
ComponentsATP-dependent protease LaEndopeptidase La
KeywordsHYDROLASE / ATP-dependent protease / catalytic Ser-Lys dyad
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
Lon protease, bacterial / 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, bacterial / 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) / Ribosomal Protein S5; domain 2 - #10 / PUA-like superfamily / Ribosomal Protein S5; domain 2 / 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 / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsBotos, I. / Melnikov, E.E. / Cherry, S. / Tropea, J.E. / Khalatova, A.G. / Rasulova, F. / Dauter, Z. / Maurizi, M.R. / Rotanova, T.V. / Wlodawer, A. / Gustchina, A.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: The catalytic domain of Escherichia coli Lon protease has a unique fold and a Ser-Lys dyad in the active site
Authors: Botos, I. / Melnikov, E.E. / Cherry, S. / Tropea, J.E. / Khalatova, A.G. / Rasulova, F. / Dauter, Z. / Maurizi, M.R. / Rotanova, T.V. / Wlodawer, A. / Gustchina, A.
History
DepositionDec 8, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-dependent protease La
B: ATP-dependent protease La
C: ATP-dependent protease La
D: ATP-dependent protease La
E: ATP-dependent protease La
F: ATP-dependent protease La
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,80511
Polymers129,3246
Non-polymers4805
Water14,268792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9750 Å2
ΔGint-123 kcal/mol
Surface area44360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.370, 86.370, 124.160
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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


Mass: 21554.080 Da / Num. of mol.: 6 / Fragment: proteolytic domain / Mutation: S679A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: LON, CAPR, DEG, MUC, LOPA, B0439, C0555 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A9M0, endopeptidase La
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 792 / 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: 2.07 Å3/Da / Density % sol: 40.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: ammonium sulfate, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 1, 2003
RadiationMonochromator: SAGITALLY FOCUSED Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.75→20 Å / Num. obs: 105429 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.075 / Net I/σ(I): 19.2
Reflection shellResolution: 1.75→1.81 Å / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.75→19.96 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.926 / SU B: 3.777 / SU ML: 0.117 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.158 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26269 9386 9.6 %RANDOM
Rwork0.20475 ---
obs0.21025 88329 93.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.21 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0.02 Å20 Å2
2---0.04 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.75→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8203 0 25 792 9020
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0218365
X-RAY DIFFRACTIONr_bond_other_d0.0020.028017
X-RAY DIFFRACTIONr_angle_refined_deg1.751.99211372
X-RAY DIFFRACTIONr_angle_other_deg1.404318681
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.99451095
X-RAY DIFFRACTIONr_chiral_restr0.110.21370
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029197
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021420
X-RAY DIFFRACTIONr_nbd_refined0.2350.22065
X-RAY DIFFRACTIONr_nbd_other0.2470.210012
X-RAY DIFFRACTIONr_nbtor_other0.0880.25372
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1990.2579
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2010.238
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2790.2113
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.226
X-RAY DIFFRACTIONr_mcbond_it1.0091.55447
X-RAY DIFFRACTIONr_mcangle_it1.78728800
X-RAY DIFFRACTIONr_scbond_it2.80732913
X-RAY DIFFRACTIONr_scangle_it4.6734.52559
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.344 663
Rwork0.308 6165
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)
10.4001-0.2170.03060.5165-0.14840.5990.0137-0.013-0.054-0.0779-0.02830.01480.0073-0.01620.01460.11850.00610.01410.0562-0.00070.0017-1.388111.994234.1355
20.53750.2016-0.15021.2953-0.26020.48790.0038-0.01680.063-0.1771-0.02040.18070.05830.00350.01660.10520.0071-0.04460.0226-0.00440.0546-23.347431.784731.0778
30.8689-0.1093-0.30620.5585-0.0740.2596-0.00830.0514-0.052-0.02960.00510.0078-0.045-0.02830.00320.09710.0119-0.01790.0544-0.00290.014-16.613460.717428.0686
40.58870.1135-0.21111.17130.34530.3055-0.00470.03190.0342-0.015-0.0485-0.063-0.0296-0.01560.05330.07660.0036-0.01090.03580.02340.047611.642769.035327.2798
50.34250.2804-0.1846-0.03580.11740.43930.00970.02590.01680.0239-0.0186-0.05740.012300.00890.05970.0115-0.00650.02510.03980.125534.075249.31629.1776
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA594 - 77510 - 191
2X-RAY DIFFRACTION2BB594 - 77510 - 191
3X-RAY DIFFRACTION3CC594 - 77510 - 191
4X-RAY DIFFRACTION4DD594 - 77510 - 191
5X-RAY DIFFRACTION5EE594 - 78410 - 200

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