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- PDB-6r50: Crystal structure of holo PPEP-1(E143A/Y178F) in complex with sub... -

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Basic information

Entry
Database: PDB / ID: 6r50
TitleCrystal structure of holo PPEP-1(E143A/Y178F) 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/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: 1.807 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 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: ACE-GLU-VAL-ASN-ALA-PRO-VAL-LPD
D: ACE-GLU-VAL-ASN-ALA-PRO-VAL-LPD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4506
Polymers45,3194
Non-polymers1312
Water6,972387
1
A: Pro-Pro endopeptidase
D: ACE-GLU-VAL-ASN-ALA-PRO-VAL-LPD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7253
Polymers22,6602
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-48 kcal/mol
Surface area9030 Å2
MethodPISA
2
B: Pro-Pro endopeptidase
C: ACE-GLU-VAL-ASN-ALA-PRO-VAL-LPD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7253
Polymers22,6602
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-47 kcal/mol
Surface area9000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.540, 42.927, 123.450
Angle α, β, γ (deg.)90.00, 95.98, 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: 21909.646 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Peptoclostridium difficile / 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.: 2 / Source method: obtained synthetically / Source: (synth.) Clostridioides difficile (bacteria)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 387 / 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: 2.21 Å3/Da / Density % sol: 44.42 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 1 microl 12 mg per ml rPPEP-1 E143A Y178F with 6 mM substrate peptide in 20 mM Tris pH 7.5, 200 mM NaCl, 0.1 mM ZnCl2 was mixed with 2 microl precipitant solution containing: 100 mM Tris pH ...Details: 1 microl 12 mg per ml rPPEP-1 E143A Y178F with 6 mM substrate peptide in 20 mM Tris pH 7.5, 200 mM NaCl, 0.1 mM ZnCl2 was mixed with 2 microl precipitant solution containing: 100 mM Tris pH 7.5, 2.25 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: 1.807→40.93 Å / Num. obs: 35979 / % possible obs: 99 % / Redundancy: 3.4 % / Net I/σ(I): 13.5
Reflection shellResolution: 1.81→1.87 Å

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Processing

Software
NameVersionClassification
PHENIX(dev_3395: ???)refinement
XDS20160617data reduction
XDS20160617data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5A0P

5a0p


Resolution: 1.807→40.926 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.48 / Phase error: 16.28
RfactorNum. reflection% reflection
Rfree0.1757 1785 4.96 %
Rwork0.1453 --
obs0.1468 35978 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.807→40.926 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3135 0 2 387 3524
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093289
X-RAY DIFFRACTIONf_angle_d0.8534468
X-RAY DIFFRACTIONf_dihedral_angle_d9.7371974
X-RAY DIFFRACTIONf_chiral_restr0.052489
X-RAY DIFFRACTIONf_plane_restr0.006590
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8074-1.85630.26521270.21082476X-RAY DIFFRACTION95
1.8563-1.91090.23481380.18522633X-RAY DIFFRACTION100
1.9109-1.97250.24271390.17552628X-RAY DIFFRACTION100
1.9725-2.0430.1981380.15972618X-RAY DIFFRACTION100
2.043-2.12480.18031370.14172600X-RAY DIFFRACTION100
2.1248-2.22150.16991400.14352639X-RAY DIFFRACTION100
2.2215-2.33870.17951330.13422628X-RAY DIFFRACTION100
2.3387-2.48520.1671370.13692641X-RAY DIFFRACTION100
2.4852-2.6770.16181440.1412649X-RAY DIFFRACTION100
2.677-2.94630.16711340.14422607X-RAY DIFFRACTION100
2.9463-3.37250.16671380.14822662X-RAY DIFFRACTION100
3.3725-4.24830.17491350.12362668X-RAY DIFFRACTION100
4.2483-40.93630.14591450.14312744X-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)
10.7786-0.17860.01421.30250.12521.23780.03650.0132-0.02190.053-0.037-0.0020.0746-0.0847-00.1233-0.0195-0.00270.1387-0.01380.1271-18.1395.9833-47.6536
20.6016-0.36270.1750.2503-0.14280.0950.09770.3561-0.2656-0.39810.07920.23570.1303-0.18190.0190.2772-0.04410.01060.2416-0.06220.1961-26.99536.2181-46.3136
30.99190.16210.2540.15360.03860.06520.0276-0.2388-0.2698-0.008-0.1077-0.21230.04140.2737-0.03620.10780.0168-0.01450.18450.01250.14985.83359.5847-20.5055
40.50680.088-0.00031.2940.19521.30680.0067-0.00510.00580.00270.00080.06170.065-0.0347-00.09630.0031-0.00940.12410.00270.1296-1.491710.048-14.9364
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'B' and resid 30 through 220)
2X-RAY DIFFRACTION2chain 'C'
3X-RAY DIFFRACTION3chain 'D'
4X-RAY DIFFRACTION4(chain 'A' and resid 27 through 220)

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