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- PDB-3l18: Ton1285, an Intracellular Protease from Thermococcus onnurineus NA1 -

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Basic information

Entry
Database: PDB / ID: 3l18
TitleTon1285, an Intracellular Protease from Thermococcus onnurineus NA1
ComponentsIntracellular protease I
KeywordsHYDROLASE / GATase1_PfpI_like / Protease
Function / homology
Function and homology information


peptidase activity / proteolysis
Similarity search - Function
: / Deglycase PfpI / PfpI endopeptidase domain profile. / DJ-1/PfpI / DJ-1/PfpI family / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Intracellular protease I
Similarity search - Component
Biological speciesThermococcus onnurineus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsJung, H.J. / Cha, S.S.
CitationJournal: To be Published
Title: Structure Based Classification of the DJ-1 Superfamily: The Relationship between Homologous Structures and Various Functions
Authors: Jung, H.J. / Cha, S.S.
History
DepositionDec 11, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Intracellular protease I
B: Intracellular protease I


Theoretical massNumber of molelcules
Total (without water)37,7772
Polymers37,7772
Non-polymers00
Water4,738263
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-7 kcal/mol
Surface area13380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.114, 87.114, 80.119
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 4 / Auth seq-ID: 2 - 165 / Label seq-ID: 4 - 167

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Intracellular protease I


Mass: 18888.574 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus onnurineus (archaea) / Strain: NA1 / Gene: intracellular protease I / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: B6YXG0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 2.32 Å3/Da / Density % sol: 47.05 %
Crystal growTemperature: 295 K / Method: evaporation / pH: 8
Details: 20% PEG 8000, 0.1M HEPES pH7.5, 0.2M Ammonium sulfate, pH 8.0, EVAPORATION, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 22, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 31234 / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Net I/σ(I): 5.9
Reflection shellResolution: 1.78→50 Å / Redundancy: 16.1 % / Mean I/σ(I) obs: 4.23 / Num. unique all: 32912 / % possible all: 99.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
CCP4model building
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1G2I

1g2i


Resolution: 1.78→29.49 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.942 / Occupancy max: 1 / Occupancy min: 1 / SU B: 5.155 / SU ML: 0.074 / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / ESU R: 0.222 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21451 1669 5.1 %RANDOM
Rwork0.16006 ---
obs0.1628 31234 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 48.9 Å2 / Biso mean: 19.725 Å2 / Biso min: 12.12 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.78→29.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2653 0 0 263 2916
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222711
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3121.9553669
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3595333
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.79523.651126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.17215472
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0761520
X-RAY DIFFRACTIONr_chiral_restr0.0940.2407
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022046
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2090.21275
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.21834
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2212
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1470.237
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.210.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8921.51713
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.26522685
X-RAY DIFFRACTIONr_scbond_it2.01731134
X-RAY DIFFRACTIONr_scangle_it3.0124.5984
X-RAY DIFFRACTIONr_rigid_bond_restr1.29132847
X-RAY DIFFRACTIONr_sphericity_free4.6083263
X-RAY DIFFRACTIONr_sphericity_bonded2.09332653
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1300 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.280.5
medium thermal0.742
LS refinement shellResolution: 1.784→1.83 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 102 -
Rwork0.172 2300 -
obs--99.05 %

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