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- PDB-1z0g: Crystal Structure of A. fulgidus Lon proteolytic domain -

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Basic information

Entry
Database: PDB / ID: 1z0g
TitleCrystal Structure of A. fulgidus Lon proteolytic domain
ComponentsPutative protease La homolog type
KeywordsHYDROLASE / 'ATP-DEPENDENT PROTEASE / CATALYTIC SER-LYS DYAD / B-type Lon'
Function / homology
Function and homology information


ATP-dependent peptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / protein catabolic process / serine-type endopeptidase activity / regulation of DNA-templated transcription / ATP hydrolysis activity / proteolysis / ATP binding / plasma membrane
Similarity search - Function
Lon protease, archaeal / LonB, AAA+ ATPase LID domain, archaeal-type / Archaeal LonB, AAA+ ATPase LID domain / Magnesium chelatase ChlI-like, catalytic domain / Magnesium chelatase, subunit ChlI / Sigma-54 interaction domain / RNA polymerase sigma factor 54 interaction domain / Lon proteolytic domain profile. / Peptidase S16, Lon proteolytic domain / Lon protease ...Lon protease, archaeal / LonB, AAA+ ATPase LID domain, archaeal-type / Archaeal LonB, AAA+ ATPase LID domain / Magnesium chelatase ChlI-like, catalytic domain / Magnesium chelatase, subunit ChlI / Sigma-54 interaction domain / RNA polymerase sigma factor 54 interaction domain / Lon proteolytic domain profile. / Peptidase S16, Lon proteolytic domain / Lon protease / Lon protease (S16) C-terminal proteolytic domain / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 / 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
Archaeal Lon protease
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsBotos, I. / Melnikov, E.E. / Cherry, S. / Kozlov, S. / Makhovskaya, O.V. / Tropea, J.E. / Gustchina, A. / Rotanova, T.V. / Wlodawer, A.
Citation
Journal: J.Mol.Biol. / Year: 2005
Title: Atomic-resolution Crystal Structure of the Proteolytic Domain of Archaeoglobus fulgidus Lon Reveals the Conformational Variability in the Active Sites of Lon Proteases
Authors: Botos, I. / Melnikov, E.E. / Cherry, S. / Kozlov, S. / Makhovskaya, O.V. / Tropea, J.E. / Gustchina, A. / Rotanova, T.V. / Wlodawer, A.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Pathological crystallography: case studies of several unusual macromolecular crystals
Authors: Dauter, Z. / Botos, I. / LaRonde-LeBlanc, N. / Wlodawer, A.
History
DepositionMar 1, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative protease La homolog type
B: Putative protease La homolog type
C: Putative protease La homolog type
D: Putative protease La homolog type
E: Putative protease La homolog type
F: Putative protease La homolog type


Theoretical massNumber of molelcules
Total (without water)131,0416
Polymers131,0416
Non-polymers00
Water19,7261095
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9920 Å2
ΔGint-35 kcal/mol
Surface area47740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.650, 88.690, 147.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Putative protease La homolog type


Mass: 21840.221 Da / Num. of mol.: 6 / Fragment: proteolytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: O29883, endopeptidase La
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1095 / 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: 2.13 Å3/Da / Density % sol: 42.36 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 400, calcium acetate, sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 28, 2004 / Details: mirrors
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.27→20 Å / Num. all: 50449 / Num. obs: 50449 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2.27→2.328 Å / % possible all: 95.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.27→15 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.881 / SU B: 18.261 / SU ML: 0.248 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.449 / ESU R Free: 0.336 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32876 1038 2.1 %RANDOM
Rwork0.19545 ---
obs0.1983 49274 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.024 Å2
Baniso -1Baniso -2Baniso -3
1--2.93 Å20 Å20 Å2
2--2.98 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.27→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8778 0 0 1095 9873
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0450.0228856
X-RAY DIFFRACTIONr_angle_refined_deg3.2431.98411946
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.84251162
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.85625.793328
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.641151682
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.9961542
X-RAY DIFFRACTIONr_chiral_restr0.2460.21468
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.026308
X-RAY DIFFRACTIONr_nbd_refined0.310.25003
X-RAY DIFFRACTIONr_nbtor_refined0.3250.25938
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2440.2976
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2730.2119
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2950.243
X-RAY DIFFRACTIONr_mcbond_it1.8131.56131
X-RAY DIFFRACTIONr_mcangle_it2.64729362
X-RAY DIFFRACTIONr_scbond_it4.42533213
X-RAY DIFFRACTIONr_scangle_it6.5944.52584
LS refinement shellResolution: 2.27→2.328 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 67 -
Rwork0.213 2960 -
obs--100 %

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