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- PDB-5tw0: Structure of Pfp1 protease from Thermococcus thioreducens: small ... -

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Basic information

Entry
Database: PDB / ID: 5tw0
TitleStructure of Pfp1 protease from Thermococcus thioreducens: small cell H3 crystal form
ComponentsPeptidase
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 / molecular replacement / Resolution: 1.96 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 10, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 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 1.2Apr 3, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidase
B: Peptidase


Theoretical massNumber of molelcules
Total (without water)36,9222
Polymers36,9222
Non-polymers00
Water3,225179
1


  • Idetical with deposited unit
  • defined by software
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)91.576, 91.576, 118.705
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Peptidase / intracellular protease 1


Mass: 18461.092 Da / Num. of mol.: 2
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


Mass: 18.015 Da / Num. of mol.: 179 / 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: 4

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.59 % / Description: rhomboidal
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 20% PEG 3350, 0.2 M sodium citrate / 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 19, 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: 1.96→32.97 Å / Num. obs: 23283 / % possible obs: 87.2 % / Redundancy: 9.5 % / Biso Wilson estimate: 30.498 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.135 / Net I/σ(I): 10.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
1.96-2.011.20.4241.40.537128
8.98-32.9721.10.07533.30.997197.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.71 Å29.95 Å
Translation6.71 Å29.95 Å

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOSFLM7.1.3data reduction
Aimless0.5.8data scaling
PHASER2.5.7phasing
REFMAC5.8.0107refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: partially refined model from a different crystal form

Resolution: 1.96→32.97 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.957 / SU B: 10.377 / SU ML: 0.126 / SU R Cruickshank DPI: 0.1614 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.161 / ESU R Free: 0.146
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED TO B Factors
RfactorNum. reflection% reflectionSelection details
Rfree0.1942 924 4 %RANDOM
Rwork0.1484 ---
obs0.1502 21941 85.78 %-
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 max: 108.91 Å2 / Biso mean: 42.708 Å2 / Biso min: 20.38 Å2
Baniso -1Baniso -2Baniso -3
1-1.04 Å20.52 Å2-0 Å2
2--1.04 Å2-0 Å2
3----3.36 Å2
Refinement stepCycle: final / Resolution: 1.96→32.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2598 0 0 179 2777
Biso mean---56.28 -
Num. residues----332
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192731
X-RAY DIFFRACTIONr_bond_other_d00.022688
X-RAY DIFFRACTIONr_angle_refined_deg1.121.9663707
X-RAY DIFFRACTIONr_angle_other_deg0.57436151
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2765336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.5823.75128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.37115480
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7961521
X-RAY DIFFRACTIONr_chiral_restr0.0740.2412
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.0213061
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02598
X-RAY DIFFRACTIONr_mcbond_it2.2872.2061341
X-RAY DIFFRACTIONr_mcbond_other2.2882.2041340
X-RAY DIFFRACTIONr_mcangle_it3.123.2921678
LS refinement shellResolution: 1.961→2.012 Å
RfactorNum. reflection% reflection
Rfree0.427 27 4.9 %
Rwork0.396 545 -
obs--28.69 %
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)
11.57040.11990.2472.78150.15051.80710.0095-0.0218-0.1293-0.1432-0.0160.54860.0997-0.39360.00650.0181-0.031-0.03970.154-0.02970.191617.571322.87953.0546
22.6397-0.88170.43612.5486-0.31711.3482-0.096-0.2606-0.42710.08710.11670.37570.2654-0.216-0.02070.1189-0.04380.0120.06120.05960.14434.20210.433364.426
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 166
2X-RAY DIFFRACTION2B1 - 166

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