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- PDB-6ltq: Crystal structure of pyrrolidone carboxyl peptidase from thermoph... -

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Basic information

Entry
Database: PDB / ID: 6ltq
TitleCrystal structure of pyrrolidone carboxyl peptidase from thermophilic keratin degrading bacterium Fervidobacterium islandicum AW-1 (FiPcp)
ComponentsPyroglutamyl-peptidase I
KeywordsHYDROLASE / Thermophilic / peptidase / chemical modidification / pyrrolidone
Function / homologyPyroglutamyl peptidase I, Cys active site / Pyrrolidone-carboxylate peptidase cysteine active site. / pyroglutamyl-peptidase activity / Peptidase C15, pyroglutamyl peptidase I / Peptidase C15, pyroglutamyl peptidase I-like / Peptidase C15, pyroglutamyl peptidase I-like superfamily / Pyroglutamyl peptidase / cytosol / 5-oxoprolyl-peptidase
Function and homology information
Biological speciesFervidobacterium islandicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsDhanasingh, I. / Jin, H.S. / Lee, D.W. / Lee, S.H.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: Structure of oxidized pyrrolidone carboxypeptidase from Fervidobacterium islandicum AW-1 reveals unique structural features for thermostability and keratinolysis.
Authors: Dhanasingh, I. / Sung, J.Y. / La, J.W. / Kang, E. / Lee, D.W. / Lee, S.H.
History
DepositionJan 23, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyroglutamyl-peptidase I
B: Pyroglutamyl-peptidase I
C: Pyroglutamyl-peptidase I
D: Pyroglutamyl-peptidase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,12723
Polymers99,2314
Non-polymers1,89619
Water13,493749
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Size exclusion chromatography yielded a elution peak corresponding to a molecular weight of 110kDa which refers to a tetramer in solution.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10600 Å2
ΔGint-45 kcal/mol
Surface area34080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.035, 86.610, 93.529
Angle α, β, γ (deg.)90.000, 105.180, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 14 through 73 or resid 75...
21(chain B and (resid 14 through 73 or resid 75...
31(chain C and (resid 14 through 73 or resid 75...
41(chain D and (resid 14 through 73 or resid 75...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSASNASN(chain A and (resid 14 through 73 or resid 75...AA14 - 7314 - 73
12ILEILELYSLYS(chain A and (resid 14 through 73 or resid 75...AA75 - 11275 - 112
13ASPASPLYSLYS(chain A and (resid 14 through 73 or resid 75...AA114 - 218114 - 218
14PHEPHEILEILE(chain A and (resid 14 through 73 or resid 75...AA220 - 221220 - 221
21LYSLYSASNASN(chain B and (resid 14 through 73 or resid 75...BB14 - 7314 - 73
22ILEILELYSLYS(chain B and (resid 14 through 73 or resid 75...BB75 - 11275 - 112
23ASPASPLYSLYS(chain B and (resid 14 through 73 or resid 75...BB114 - 218114 - 218
24PHEPHEILEILE(chain B and (resid 14 through 73 or resid 75...BB220 - 221220 - 221
31LYSLYSASNASN(chain C and (resid 14 through 73 or resid 75...CC14 - 7314 - 73
32ILEILELYSLYS(chain C and (resid 14 through 73 or resid 75...CC75 - 11275 - 112
33ASPASPLYSLYS(chain C and (resid 14 through 73 or resid 75...CC114 - 218114 - 218
34PHEPHEILEILE(chain C and (resid 14 through 73 or resid 75...CC220 - 221220 - 221
41LYSLYSASNASN(chain D and (resid 14 through 73 or resid 75...DD14 - 7314 - 73
42ILEILELYSLYS(chain D and (resid 14 through 73 or resid 75...DD75 - 11275 - 112
43ASPASPLYSLYS(chain D and (resid 14 through 73 or resid 75...DD114 - 218114 - 218
44PHEPHEILEILE(chain D and (resid 14 through 73 or resid 75...DD220 - 221220 - 221

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Components

#1: Protein
Pyroglutamyl-peptidase I


Mass: 24807.740 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fervidobacterium islandicum (bacteria) / Gene: NA23_05565 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1B0VKK9, pyroglutamyl-peptidase I
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 749 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.4 Å3/Da / Density % sol: 48.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100mM Bis Tris Hydrochloric acid pH 5.5, 200mM Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Sep 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.845→50 Å / Num. obs: 80445 / % possible obs: 99.7 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.022 / Rrim(I) all: 0.059 / Χ2: 0.958 / Net I/σ(I): 10.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.85-1.887.50.61439820.9050.2390.6590.906100
1.88-1.927.50.52740520.9240.2050.5660.915100
1.92-1.957.50.41740050.9510.1620.4480.928100
1.95-1.997.50.34840290.9650.1350.3730.929100
1.99-2.047.50.28940110.9750.1130.3110.951100
2.04-2.087.50.23640230.9820.0920.2530.967100
2.08-2.147.50.240000.9860.0780.2150.996100
2.14-2.197.50.1640190.9910.0620.1711.008100
2.19-2.267.50.1340440.9930.050.1391.041100
2.26-2.337.50.11340070.9950.0440.1211.061100
2.33-2.417.50.09740670.9960.0380.1041.041100
2.41-2.517.50.08939950.9960.0350.0961.053100
2.51-2.637.50.07740290.9970.030.0821.041100
2.63-2.767.50.06840280.9970.0270.0741.004100
2.76-2.947.50.05840610.9980.0230.0620.965100
2.94-3.167.50.0540190.9980.0190.0530.931100
3.16-3.487.40.04240580.9980.0170.0450.874100
3.48-3.997.30.03840460.9980.0150.0410.84999.9
3.99-5.0270.03640470.9980.0150.040.82199.1
5.02-506.60.03939230.9980.0170.0420.84494.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DF5

2df5


Resolution: 1.85→28.288 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.76
RfactorNum. reflection% reflection
Rfree0.2235 3956 5.03 %
Rwork0.1738 --
obs0.1763 78613 97.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 111.32 Å2 / Biso mean: 25.9983 Å2 / Biso min: 3.77 Å2
Refinement stepCycle: final / Resolution: 1.85→28.288 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6655 0 124 749 7528
Biso mean--53.74 37.5 -
Num. residues----842
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2432X-RAY DIFFRACTION8.828TORSIONAL
12B2432X-RAY DIFFRACTION8.828TORSIONAL
13C2432X-RAY DIFFRACTION8.828TORSIONAL
14D2432X-RAY DIFFRACTION8.828TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.85-1.86740.27911010.2297209977
1.8674-1.8910.29061220.235232184
1.891-1.91590.27031150.2211239088
1.9159-1.94210.27611300.2154248692
1.9421-1.96980.24661370.2187260894
1.9698-1.99920.27381560.2135263398
1.9992-2.03050.26471300.21342746100
2.0305-2.06370.25831370.20922715100
2.0637-2.09930.23091570.20362724100
2.0993-2.13750.27841430.20142741100
2.1375-2.17860.25121550.19942746100
2.1786-2.2230.26731440.18742707100
2.223-2.27130.22771450.18532746100
2.2713-2.32420.23611600.18142700100
2.3242-2.38230.23911450.17842714100
2.3823-2.44660.26081460.18052771100
2.4466-2.51860.24851360.1972738100
2.5186-2.59980.2551610.17342730100
2.5998-2.69270.24891510.17762710100
2.6927-2.80040.26661500.17582739100
2.8004-2.92770.21591550.17912737100
2.9277-3.08190.24521420.1762742100
3.0819-3.27470.21151250.1682764100
3.2747-3.52710.20391540.15492754100
3.5271-3.88130.1761320.13942772100
3.8813-4.4410.15011410.1313275199
4.441-5.58820.1721520.1374274999
5.5882-28.2880.22231340.1894262493

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