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- PDB-6r5b: Crystal structure of PPEP-1(W103H/E143A/Y178F) in complex with su... -

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Basic information

Entry
Database: PDB / ID: 6r5b
TitleCrystal structure of PPEP-1(W103H/E143A/Y178F) in complex with substrate peptide Ac-EVNPPVP-CONH2
Components
  • ACE-GLU-VAL-ASN-PRO-PRO-VAL-LPD
  • Pro-Pro endopeptidase
KeywordsHYDROLASE / Pro-Pro endopeptidase 1 / zinc metallopeptidase / Clostridium difficile / virulence factor
Function / homology
Function and homology information


Pro-Pro endopeptidase / metallopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
Anthrax toxin, lethal/endema factor, N-/C-terminal / : / Anthrax toxin lethal factor, N- and C-terminal domain / Anthrax toxin lethal factor (ATLF)-like domain profile. / Metallopeptidase, catalytic domain superfamily
Similarity search - Domain/homology
Pro-Pro endopeptidase
Similarity search - Component
Biological speciesPeptoclostridium difficile (bacteria)
Clostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsPichlo, C. / Wojtalla, F. / Baumann, U.
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Molecular determinants of the mechanism and substrate specificity ofClostridium difficileproline-proline endopeptidase-1.
Authors: Pichlo, C. / Juetten, L. / Wojtalla, F. / Schacherl, M. / Diaz, D. / Baumann, U.
History
DepositionMar 24, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 7, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 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

Downloads & links

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Assembly

Deposited unit
A: Pro-Pro endopeptidase
B: Pro-Pro endopeptidase
C: ACE-GLU-VAL-ASN-PRO-PRO-VAL-LPD
E: ACE-GLU-VAL-ASN-PRO-PRO-VAL-LPD


Theoretical massNumber of molelcules
Total (without water)45,2754
Polymers45,2754
Non-polymers00
Water4,143230
1
A: Pro-Pro endopeptidase
E: ACE-GLU-VAL-ASN-PRO-PRO-VAL-LPD


Theoretical massNumber of molelcules
Total (without water)22,6372
Polymers22,6372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-10 kcal/mol
Surface area8750 Å2
MethodPISA
2
B: Pro-Pro endopeptidase
C: ACE-GLU-VAL-ASN-PRO-PRO-VAL-LPD


Theoretical massNumber of molelcules
Total (without water)22,6372
Polymers22,6372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-11 kcal/mol
Surface area8810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.358, 43.008, 123.214
Angle α, β, γ (deg.)90.00, 95.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Pro-Pro endopeptidase / PPEP-1 / Zinc metalloprotease Zmp1


Mass: 21861.584 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Peptoclostridium difficile (bacteria) / Gene: zmp1, ppep-1, CD630_28300 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: Q183R7, Pro-Pro endopeptidase
#2: Protein/peptide ACE-GLU-VAL-ASN-PRO-PRO-VAL-LPD


Mass: 775.892 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Clostridioides difficile (bacteria)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.17 Å3/Da / Density % sol: 43.43 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 1.5 microl 12 mg per ml rPPEP-1 W103H E143A Y178F with 6 mM substrate peptide in 20 mM Tris pH 7.5, 200 mM NaCl was mixed with 1.5 microl precipitant solution containing: 100 mM Tris pH 7.5, ...Details: 1.5 microl 12 mg per ml rPPEP-1 W103H E143A Y178F with 6 mM substrate peptide in 20 mM Tris pH 7.5, 200 mM NaCl was mixed with 1.5 microl precipitant solution containing: 100 mM Tris pH 7.5, 2.1 M ammonium phosphate dibasic. Reservoir volume: 200 microl

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.06→40.847 Å / Num. obs: 24292 / % possible obs: 99.39 % / Redundancy: 3.3 % / Net I/σ(I): 5.04
Reflection shellResolution: 2.06→2.134 Å

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Processing

Software
NameVersionClassification
PHENIX(dev_3395: ???)refinement
XDS20180126data reduction
XDS20180126data scaling
PHENIX20180126phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5A0P

5a0p


Resolution: 2.06→40.847 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 23.21
RfactorNum. reflection% reflection
Rfree0.2251 1216 5.01 %
Rwork0.1896 --
obs0.1914 24289 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.06→40.847 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3098 0 0 230 3328
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023244
X-RAY DIFFRACTIONf_angle_d0.5514408
X-RAY DIFFRACTIONf_dihedral_angle_d10.5561948
X-RAY DIFFRACTIONf_chiral_restr0.037483
X-RAY DIFFRACTIONf_plane_restr0.002587
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.14250.31471270.27162498X-RAY DIFFRACTION98
2.1425-2.240.31761370.26442535X-RAY DIFFRACTION99
2.24-2.35810.28821300.24022584X-RAY DIFFRACTION100
2.3581-2.50580.27251400.22712532X-RAY DIFFRACTION100
2.5058-2.69930.29471310.22492571X-RAY DIFFRACTION100
2.6993-2.97080.23921290.21252533X-RAY DIFFRACTION100
2.9708-3.40050.21621390.17962584X-RAY DIFFRACTION100
3.4005-4.28360.18991370.14582600X-RAY DIFFRACTION100
4.2836-40.85530.17111460.1552636X-RAY DIFFRACTION99
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)
11.39690.38470.24241.95910.30321.51680.0531-0.02570.04790.0275-0.00150.16660.09010.0334-0.00010.21630.00480.02390.26640.01070.257411.183110.562746.2792
21.37840.28460.54481.41340.51241.89470.1778-0.009-0.11430.1501-0.0673-0.07270.2592-0.09770.00030.3475-0.0131-0.04180.2777-0.01430.2951-5.80616.928713.5934
30.3005-0.25680.20880.2642-0.08080.35850.18710.0689-0.2878-0.5099-0.08480.07370.1149-0.05140.02660.5454-0.15930.10620.4179-0.04830.3645-14.82056.924414.7699
40.04260.0342-0.02170.0485-0.00370.01990.0029-0.071-0.4083-0.0192-0.0371-0.1040.17630.12980.00090.254-0.03960.02350.40960.03510.264118.557510.055140.9317
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 28 through 220)
2X-RAY DIFFRACTION2(chain 'B' and resid 30 through 220)
3X-RAY DIFFRACTION3chain 'C'
4X-RAY DIFFRACTION4chain 'E'

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