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- PDB-5txw: Structure of Pfp1 protease from Thermococcus thioreducens: large ... -

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Basic information

Entry
Database: PDB / ID: 5txw
TitleStructure of Pfp1 protease from Thermococcus thioreducens: large cell H3 crystal form
ComponentsPeptidaseProtease
KeywordsHYDROLASE / protease / hexamer / thermophile / noncrystallographic symmetry
Function / homology
Function and homology information


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
Biological speciesThermococcus thioreducens (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsLarson, S.B. / McPherson, A.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2017
Title: The structure of the Pfp1 protease from the hyperthermophilic archaeon Thermococcus thioreducens in two crystal forms.
Authors: Larson, S.B. / McPherson, A.
History
DepositionNov 17, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_id
Revision 1.2Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Oct 4, 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
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidase
B: Peptidase
C: Peptidase
D: Peptidase


Theoretical massNumber of molelcules
Total (without water)73,8444
Polymers73,8444
Non-polymers00
Water11,512639
1
A: Peptidase
B: Peptidase


Theoretical massNumber of molelcules
Total (without water)36,9222
Polymers36,9222
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-9 kcal/mol
Surface area13110 Å2
MethodPISA
2
C: Peptidase
D: Peptidase


Theoretical massNumber of molelcules
Total (without water)36,9222
Polymers36,9222
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-9 kcal/mol
Surface area13150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.850, 152.850, 82.541
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein
Peptidase / Protease / intracellular protease


Mass: 18461.092 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus thioreducens (archaea) / Gene: AMR53_10535 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0Q2XKL6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 639 / 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: 5

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Sample preparation

CrystalDensity Matthews: 2.528 Å3/Da / Density % sol: 51.3 % / Description: large hexagonal prisms
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.4 M Sodium Citrate, pH 6.5, vapor diffusion, sitting drop
Temp details: Room temperature

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Data collection

DiffractionMean temperature: 298 K / Ambient temp details: Room temperature
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54187 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Apr 10, 2013 / Details: Osmic mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 1.86→38.22 Å / Num. obs: 52126 / % possible obs: 86.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.8 % / Biso Wilson estimate: 15.88 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.123 / Net I/σ(I): 11.9
Reflection shellResolution: 1.86→1.9 Å / Redundancy: 1 % / Rmerge(I) obs: 0.583 / Mean I/σ(I) obs: 0.6 / CC1/2: 0.485 / % possible all: 33.5

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Processing

Software
NameVersionClassification
iMOSFLM7.1.3data reduction
Aimless0.5.8data scaling
CNS1.2phasing
REFMAC5.8.0107refinement
Coot0.8.1model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G2I

1g2i


Resolution: 1.86→38.22 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.597 / SU ML: 0.096 / SU R Cruickshank DPI: 0.1236 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.12 / SU Rfree Cruickshank DPI: 0.1203 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.1734 2499 4.8 %RANDOM
Rwork0.1274 ---
obs0.12962 49624 86.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: Babinet bulk solvent modeling
Displacement parametersBiso mean: 20.02 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å2-0.06 Å20 Å2
2---0.11 Å20 Å2
3---0.37 Å2
Refinement stepCycle: 1 / Resolution: 1.86→38.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5196 0 0 639 5835
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0195537
X-RAY DIFFRACTIONr_bond_other_d00.025589
X-RAY DIFFRACTIONr_angle_refined_deg1.231.9767513
X-RAY DIFFRACTIONr_angle_other_deg0.628312828
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8965.067672
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.17624.157255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.169151023
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6431539
X-RAY DIFFRACTIONr_chiral_restr0.0780.2855
X-RAY DIFFRACTIONr_gen_planes_refined0.020.0216111
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021190
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_it2.7181.4272662
X-RAY DIFFRACTIONr_mcbond_other2.7071.4252661
X-RAY DIFFRACTIONr_mcangle_it3.6752.1183326
X-RAY DIFFRACTIONr_mcangle_other3.6752.123327
X-RAY DIFFRACTIONr_scbond_it5.6932.0742875
X-RAY DIFFRACTIONr_scbond_other5.6912.0762875
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.5352.8374185
X-RAY DIFFRACTIONr_long_range_B_refined11.30714.0986537
X-RAY DIFFRACTIONr_long_range_B_other11.1713.0736292
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.86→1.908 Å
RfactorNum. reflection% reflection
Rfree0.307 59 3.75 %
Rwork0.307 1514 -
obs--35.1 %

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