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- PDB-7r66: Structure of Pfp1 protease from Thermococcus thioreducens: large ... -

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Basic information

Entry
Database: PDB / ID: 7r66
TitleStructure of Pfp1 protease from Thermococcus thioreducens: large unit cell at 1.44 A resolution
ComponentsPeptidase
KeywordsHYDROLASE / intracellular / disulfide bonds / catalytic triad / proteasome / bacteria / supersite
Function / homology: / Deglycase PfpI / PfpI endopeptidase domain profile. / DJ-1/PfpI / DJ-1/PfpI family / Class I glutamine amidotransferase-like / PHOSPHATE ION / Peptidase
Function and homology information
Biological speciesThermococcus thioreducens (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
AuthorsMcPherson, A.
CitationJournal: Acta Crystallogr. / Year: 2017
Title: Structure of the Pfp1 protease from a hypothermophilic archer, Thermococcus thioreducens, in two crystal forms
Authors: Larson, S.B. / McPherson, A.
History
DepositionJun 22, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,50710
Polymers73,8444
Non-polymers6636
Water10,773598
1
A: Peptidase
B: Peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2775
Polymers36,9222
Non-polymers3553
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-29 kcal/mol
Surface area12810 Å2
MethodPISA
2
C: Peptidase
D: Peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2305
Polymers36,9222
Non-polymers3083
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-38 kcal/mol
Surface area12840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.030, 151.030, 80.716
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3

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Components

#1: Protein
Peptidase / 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: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 598 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.48 Å3/Da / Density % sol: 50 % / Description: hexagonal prisms
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Sitting drop crystallization using Cryschem plates. Drops were equal amounts of a 25 mg / ml protein stock solution in water and the reservoir solution. The reservoir was 1.4 M sodium ...Details: Sitting drop crystallization using Cryschem plates. Drops were equal amounts of a 25 mg / ml protein stock solution in water and the reservoir solution. The reservoir was 1.4 M sodium citrate at pH 6.5. Crystallization was at room temperature. Drops were 10 ul total starting volume, reservoirs 0.6 ml.
PH range: 6.0 - 7.0

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Data collection

DiffractionMean temperature: 173 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1158 Å
DetectorType: DECTRIS EIGER X 500K / Detector: PIXEL / Date: Jun 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionResolution: 1.38→75 Å / Num. obs: 141230 / % possible obs: 100 % / Redundancy: 47 % / Biso Wilson estimate: 19.95 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.216 / Rpim(I) all: 0.44 / Rrim(I) all: 0.221 / Rsym value: 0.21 / Net I/σ(I): 11.9
Reflection shellResolution: 1.38→1.4 Å / Redundancy: 19.8 % / Mean I/σ(I) obs: 0.3 / Num. unique obs: 7080 / CC1/2: 0.073 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TXW

5txw


Resolution: 1.44→68.69 Å / SU ML: 0.1423 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 18.5948
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1659 6116 4.92 %
Rwork0.1339 118119 -
obs0.1355 124235 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.88 Å2
Refinement stepCycle: LAST / Resolution: 1.44→68.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5196 0 42 598 5836
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01065555
X-RAY DIFFRACTIONf_angle_d1.17367559
X-RAY DIFFRACTIONf_chiral_restr0.0824848
X-RAY DIFFRACTIONf_plane_restr0.0142967
X-RAY DIFFRACTIONf_dihedral_angle_d13.64342111
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.44-1.460.30682060.29223928X-RAY DIFFRACTION99.95
1.46-1.470.29222300.27033937X-RAY DIFFRACTION99.95
1.47-1.490.32181900.2673970X-RAY DIFFRACTION100
1.49-1.510.31112440.24413880X-RAY DIFFRACTION100
1.51-1.530.27271890.22543930X-RAY DIFFRACTION99.95
1.53-1.550.25182000.2083954X-RAY DIFFRACTION99.98
1.55-1.570.25581970.19024018X-RAY DIFFRACTION100
1.57-1.60.23241840.17243846X-RAY DIFFRACTION100
1.6-1.620.18182040.14893988X-RAY DIFFRACTION99.98
1.62-1.650.17552250.1423903X-RAY DIFFRACTION100
1.65-1.680.20031900.143948X-RAY DIFFRACTION99.93
1.68-1.710.18161830.13043966X-RAY DIFFRACTION100
1.71-1.740.18251960.12353936X-RAY DIFFRACTION100
1.74-1.780.16992000.11793940X-RAY DIFFRACTION100
1.78-1.810.16482060.10923920X-RAY DIFFRACTION100
1.81-1.860.15992460.11513951X-RAY DIFFRACTION100
1.86-1.90.17722040.11663920X-RAY DIFFRACTION99.9
1.9-1.950.19382000.13883930X-RAY DIFFRACTION99.85
1.95-2.010.15872000.10813946X-RAY DIFFRACTION100
2.01-2.080.13842370.10523908X-RAY DIFFRACTION100
2.08-2.150.13542010.10543917X-RAY DIFFRACTION100
2.15-2.240.1421910.10953955X-RAY DIFFRACTION99.66
2.24-2.340.16552160.11243915X-RAY DIFFRACTION99.69
2.34-2.460.13481770.11523958X-RAY DIFFRACTION100
2.46-2.620.15292110.11383943X-RAY DIFFRACTION100
2.62-2.820.14672070.11893913X-RAY DIFFRACTION99.98
2.82-3.10.17812050.13683966X-RAY DIFFRACTION100
3.1-3.550.15082100.12743922X-RAY DIFFRACTION100
3.55-4.470.14091930.12013943X-RAY DIFFRACTION99.98
4.47-68.690.17291740.16533968X-RAY DIFFRACTION99.83

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