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- PDB-6r4z: Crystal structure of holo PPEP-1(E143A/Y178F) in complex with pro... -

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Basic information

Entry
Database: PDB / ID: 6r4z
TitleCrystal structure of holo PPEP-1(E143A/Y178F) in complex with product peptide Ac-EVNP-CO2 (substrate peptide: Ac-EVNPPVP-CONH2)
Components
  • ACE-GLU-VAL-ASN-PRO
  • 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
NICKEL (II) ION / Pro-Pro endopeptidase
Similarity search - Component
Biological speciesPeptoclostridium difficile (bacteria)
Clostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.052 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.pdbx_ptnr2_label_alt_id / _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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pro-Pro endopeptidase
B: Pro-Pro endopeptidase
D: ACE-GLU-VAL-ASN-PRO
E: ACE-GLU-VAL-ASN-PRO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9767
Polymers44,7864
Non-polymers1903
Water11,367631
1
A: Pro-Pro endopeptidase
E: ACE-GLU-VAL-ASN-PRO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5174
Polymers22,3932
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-52 kcal/mol
Surface area9600 Å2
MethodPISA
2
B: Pro-Pro endopeptidase
D: ACE-GLU-VAL-ASN-PRO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4593
Polymers22,3932
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-42 kcal/mol
Surface area9200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.039, 42.806, 119.048
Angle α, β, γ (deg.)90.00, 92.41, 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 (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


Mass: 483.515 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: Chemical ChemComp-NI / NICKEL (II) ION


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


Mass: 18.015 Da / Num. of mol.: 631 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.11 Å3/Da / Density % sol: 41.58 %
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 (Ac-EVNPPVP-CONH2) in 20 mM Tris pH 7.5, 200 mM NaCl, 0.1 mM ZnCl2 was mixed with 2 microL precipitant solution ...Details: 1 microl 12 mg per ml rPPEP-1 E143A Y178F with 6 mM substrate peptide (Ac-EVNPPVP-CONH2) 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 8.5, 2.55 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: X06SA / Wavelength: 0.73 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.73 Å / Relative weight: 1
ReflectionResolution: 1.052→34.922 Å / Num. all: 1163245 / Num. obs: 170479 / % possible obs: 98.68 % / Redundancy: 6.8 % / Net I/σ(I): 22.22
Reflection shellResolution: 1.052→1.09 Å / Num. unique obs: 16593

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Processing

Software
NameVersionClassification
PHENIX(1.15rc3_3435: ???)refinement
XDS20160617data reduction
XDS20160617data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5A0P

5a0p


Resolution: 1.052→34.922 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.5 / Phase error: 13.78
RfactorNum. reflection% reflection
Rfree0.1513 2004 1.18 %
Rwork0.1328 --
obs0.133 170477 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.052→34.922 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3119 0 3 631 3753
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093311
X-RAY DIFFRACTIONf_angle_d1.0064502
X-RAY DIFFRACTIONf_dihedral_angle_d12.3841227
X-RAY DIFFRACTIONf_chiral_restr0.077488
X-RAY DIFFRACTIONf_plane_restr0.008599
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0517-1.0780.21041370.211411391X-RAY DIFFRACTION94
1.078-1.10710.16011450.17511967X-RAY DIFFRACTION99
1.1071-1.13970.14841390.153111900X-RAY DIFFRACTION98
1.1397-1.17650.1811400.143511918X-RAY DIFFRACTION98
1.1765-1.21850.14521530.134112148X-RAY DIFFRACTION100
1.2185-1.26730.14631420.127512095X-RAY DIFFRACTION100
1.2673-1.3250.15971410.123412151X-RAY DIFFRACTION99
1.325-1.39490.13791480.117711992X-RAY DIFFRACTION99
1.3949-1.48230.14191370.11212141X-RAY DIFFRACTION99
1.4823-1.59670.11861450.107911809X-RAY DIFFRACTION97
1.5967-1.75740.14181430.116512205X-RAY DIFFRACTION99
1.7574-2.01170.14771450.127912169X-RAY DIFFRACTION100
2.0117-2.53440.14871470.127712268X-RAY DIFFRACTION100
2.5344-34.94090.16011420.143212319X-RAY DIFFRACTION98

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