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- PDB-6r58: Crystal structure of PPEP-1(E143A/Y178F/E184A) in complex with su... -

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Basic information

Entry
Database: PDB / ID: 6r58
TitleCrystal structure of PPEP-1(E143A/Y178F/E184A) in complex with substrate peptide Ac-EVNAPVP-CONH2
Components
  • ACE-GLU-VAL-ASN-ALA-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 factor (ATLF)-like domain profile. / Anthrax toxin, lethal/endema factor, N-/C-terminal / Anthrax toxin lethal factor, N- and C-terminal domain / Metallopeptidase, catalytic domain superfamily
Similarity search - Domain/homology
NICKEL (II) ION / PHOSPHATE ION / Pro-Pro endopeptidase
Similarity search - Component
Biological speciesPeptoclostridium difficile (bacteria)
Clostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPichlo, C. / 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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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: Pro-Pro endopeptidase
D: Pro-Pro endopeptidase
E: ACE-GLU-VAL-ASN-ALA-PRO-VAL-LPD
F: ACE-GLU-VAL-ASN-ALA-PRO-VAL-LPD
I: ACE-GLU-VAL-ASN-ALA-PRO-VAL-LPD
G: ACE-GLU-VAL-ASN-ALA-PRO-VAL-LPD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,75613
Polymers90,4068
Non-polymers3505
Water8,071448
1
A: Pro-Pro endopeptidase
E: ACE-GLU-VAL-ASN-ALA-PRO-VAL-LPD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6673
Polymers22,6012
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-49 kcal/mol
Surface area9200 Å2
MethodPISA
2
B: Pro-Pro endopeptidase
F: ACE-GLU-VAL-ASN-ALA-PRO-VAL-LPD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6963
Polymers22,6012
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-17 kcal/mol
Surface area9150 Å2
MethodPISA
3
C: Pro-Pro endopeptidase
I: ACE-GLU-VAL-ASN-ALA-PRO-VAL-LPD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6673
Polymers22,6012
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-50 kcal/mol
Surface area9040 Å2
MethodPISA
4
D: Pro-Pro endopeptidase
G: ACE-GLU-VAL-ASN-ALA-PRO-VAL-LPD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7264
Polymers22,6012
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-61 kcal/mol
Surface area9270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.995, 73.322, 237.348
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 8 molecules ABCDEFIG

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


Mass: 21851.611 Da / Num. of mol.: 4
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-ALA-PRO-VAL-LPD


Mass: 749.855 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Clostridioides difficile (bacteria)

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Non-polymers , 4 types, 453 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 448 / 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: 2.07 Å3/Da / Density % sol: 40.55 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 1 microl 12 mg per ml rPPEP-1 E143A Y178F E184A with 6 mM substrate peptide in 20 mM Tris pH 7.5, 200 mM NaCl was mixed with 2 microl precipitant solution containing: 100 mM Tris pH 9.0, 2 M ...Details: 1 microl 12 mg per ml rPPEP-1 E143A Y178F E184A with 6 mM substrate peptide in 20 mM Tris pH 7.5, 200 mM NaCl was mixed with 2 microl precipitant solution containing: 100 mM Tris pH 9.0, 2 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: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→46.125 Å / Num. obs: 60403 / % possible obs: 99.91 % / Redundancy: 6.6 % / Net I/σ(I): 15.64
Reflection shellResolution: 1.9→1.968 Å

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Processing

Software
NameVersionClassification
PHENIX(dev_3409: ???)refinement
XDS20161205data reduction
XDS20161205data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5A0P

5a0p


Resolution: 1.9→46.125 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 21.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2137 1990 3.3 %
Rwork0.1897 --
obs0.1905 60380 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→46.125 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6238 0 9 448 6695
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036425
X-RAY DIFFRACTIONf_angle_d0.628699
X-RAY DIFFRACTIONf_dihedral_angle_d14.5123833
X-RAY DIFFRACTIONf_chiral_restr0.04955
X-RAY DIFFRACTIONf_plane_restr0.0041134
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.94750.35241380.31314127X-RAY DIFFRACTION100
1.9475-2.00020.30921390.26144062X-RAY DIFFRACTION100
2.0002-2.0590.23841420.24134142X-RAY DIFFRACTION100
2.059-2.12550.2391390.21974080X-RAY DIFFRACTION100
2.1255-2.20150.24171390.214096X-RAY DIFFRACTION100
2.2015-2.28960.25631430.21324164X-RAY DIFFRACTION100
2.2896-2.39380.23261410.20034141X-RAY DIFFRACTION100
2.3938-2.520.2571410.19644141X-RAY DIFFRACTION100
2.52-2.67790.22611420.19794150X-RAY DIFFRACTION100
2.6779-2.88460.2211410.19744147X-RAY DIFFRACTION100
2.8846-3.17480.20851430.1974183X-RAY DIFFRACTION100
3.1748-3.63410.19451440.17394217X-RAY DIFFRACTION100
3.6341-4.57790.1631460.14934261X-RAY DIFFRACTION100
4.5779-46.13880.18711520.17144479X-RAY DIFFRACTION100
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)
11.7611-0.14520.03541.72850.40392.1296-0.0233-0.01380.0493-0.02140.0288-0.0697-0.09840.10250.00070.16750.0043-0.01640.10090.01730.15729.2456.978510.1399
22.61960.1940.53162.21990.27583.7413-0.0866-0.16260.00190.01330.1089-0.06710.03590.2144-0.0190.1647-0.0093-0.00580.18660.0250.174112.990623.700248.6999
32.61390.12930.24541.74270.07132.4654-0.0809-0.12170.07010.04480.0993-0.0173-0.24290.0155-0.01940.18260.0087-0.00730.10750.00810.16369.347543.401210.3669
43.134-0.0445-0.04641.7120.00554.1888-0.0891-0.259-0.07720.08610.03880.01560.0375-0.37850.03380.165-0.0054-0.01450.1983-0.01630.18798.813-11.538745.8626
54.2483-0.86110.30972.9872-0.93813.3447-0.134-0.55760.14770.19250.19790.3032-0.0201-0.4605-0.04710.1906-0.0043-0.00460.28030.00470.2003-7.40784.057119.213
62.8143-0.23360.11331.70650.38173.34-0.08960.13350.1741-0.0560.00740.15860.0126-0.29110.0940.207-0.0192-0.00150.25360.05270.2519-3.214130.412941.6792
73.7564-0.5360.1772.3594-0.83793.6602-0.1738-0.63170.00210.26190.18940.2339-0.2392-0.63370.00330.20110.0487-0.00330.39240.02620.2069-7.157242.356319.8665
84.68730.00750.09223.82130.36693.74480.05350.6234-0.1551-0.20120.0136-0.13230.08420.5317-0.05530.1910.0117-0.00720.2865-0.02130.228424.7751-17.693838.9146
94.25690.6103-1.90186.6386-2.619.73750.41270.16960.4992-0.4774-0.07570.6671-0.2528-0.4801-0.38590.37710.0328-0.05010.2091-0.01450.34383.45314.729715.0464
103.9775-0.86451.29782.476-4.36397.75620.1162-0.1247-0.4476-0.15770.07310.65630.2407-0.6442-0.13380.444-0.0930.0190.3092-0.02590.31057.034918.919540.7886
111.478-2.0179-3.16593.84666.16219.87390.12130.15170.38360.07820.6048-0.90210.05050.4227-0.56140.40450.0208-0.02520.232-0.00730.325414.2991-5.757837.6673
121.64740.4258-1.05112.8555-0.67434.05030.45310.44720.6567-0.04160.12840.2272-0.1303-0.545-0.5971.04850.2884-0.13770.69550.06290.5313.919752.102314.7339
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 30 through 151)
2X-RAY DIFFRACTION2(chain 'B' and resid 29 through 151)
3X-RAY DIFFRACTION3(chain 'C' and resid 29 through 151)
4X-RAY DIFFRACTION4(chain 'D' and resid 23 through 151)
5X-RAY DIFFRACTION5(chain 'A' and resid 152 through 220)
6X-RAY DIFFRACTION6(chain 'B' and resid 152 through 220)
7X-RAY DIFFRACTION7(chain 'C' and resid 152 through 220)
8X-RAY DIFFRACTION8(chain 'D' and resid 152 through 220)
9X-RAY DIFFRACTION9(chain 'E' )
10X-RAY DIFFRACTION10(chain 'F' )
11X-RAY DIFFRACTION11(chain 'G' )
12X-RAY DIFFRACTION12(chain 'I' )

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