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- PDB-6r4w: Crystal structure of apo PPEP-1(E143A/Y178F) in complex with subs... -

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Basic information

Entry
Database: PDB / ID: 6r4w
TitleCrystal structure of apo 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 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
Pro-Pro endopeptidase
Similarity search - Component
Biological speciesPeptoclostridium difficile (bacteria)
Clostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.391 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
Water8,035446
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 area1880 Å2
ΔGint-49 kcal/mol
Surface area9090 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 area1800 Å2
ΔGint-49 kcal/mol
Surface area9050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.364, 42.923, 123.354
Angle α, β, γ (deg.)90.00, 96.28, 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-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 / Water


Mass: 18.015 Da / Num. of mol.: 446 / 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: 2.2 Å3/Da / Density % sol: 44.08 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 1.5 microl 12 mg per ml rPPEP-1 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 8.0, 2.25 ...Details: 1.5 microl 12 mg per ml rPPEP-1 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 8.0, 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: Aug 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.39→40.871 Å / Num. obs: 77720 / % possible obs: 99 % / Redundancy: 4.2 % / Net I/σ(I): 14.7
Reflection shellResolution: 1.39→1.44 Å / Num. unique obs: 7542 / CC1/2: 0.606 / Rrim(I) all: 0.887

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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: 1.391→40.871 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 20.74
RfactorNum. reflection% reflection
Rfree0.188 2023 2.6 %
Rwork0.1668 --
obs0.1674 77691 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.391→40.871 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3135 0 2 446 3583
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083306
X-RAY DIFFRACTIONf_angle_d0.9194497
X-RAY DIFFRACTIONf_dihedral_angle_d11.8821223
X-RAY DIFFRACTIONf_chiral_restr0.071494
X-RAY DIFFRACTIONf_plane_restr0.007594
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3913-1.42610.3131440.29055203X-RAY DIFFRACTION97
1.4261-1.46460.27031380.28125356X-RAY DIFFRACTION99
1.4646-1.50770.2641500.25955372X-RAY DIFFRACTION100
1.5077-1.55640.22891410.21465433X-RAY DIFFRACTION100
1.5564-1.6120.21321380.20365361X-RAY DIFFRACTION99
1.612-1.67660.26681480.23175372X-RAY DIFFRACTION99
1.6766-1.75290.281430.23515337X-RAY DIFFRACTION99
1.7529-1.84530.21781400.17275464X-RAY DIFFRACTION100
1.8453-1.96090.20461470.16045435X-RAY DIFFRACTION100
1.9609-2.11230.1631510.14935406X-RAY DIFFRACTION100
2.1123-2.32480.17621370.14265446X-RAY DIFFRACTION100
2.3248-2.66120.171490.15295479X-RAY DIFFRACTION100
2.6612-3.35260.16891460.15385442X-RAY DIFFRACTION99
3.3526-40.8890.15471510.14075562X-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)
10.9665-0.06320.00151.42920.20461.5950.0494-0.00120.01890.105-0.02780.0072-0.00790.0323-0.00220.09760.00440.00340.1119-0.00010.10121.364114.9805-12.2274
20.9545-0.13060.09451.32470.2180.93340.01620.0589-0.1058-0.1714-0.02120.22180.3263-0.0746-0.00110.1974-0.0049-0.03410.1319-0.00030.1374-6.68570.2989-20.2363
31.40690.0325-0.01131.02030.16061.3280.0716-0.01390.04080.0285-0.0097-0.0324-0.0418-0.0889-0.00030.09690.00150.00750.123-0.00460.1073-18.61712.8844-52.117
41.3960.13120.62031.4825-0.22591.20020.1803-0.0633-0.18020.2924-0.0630.06090.2863-0.05320.00510.2181-0.0152-0.02210.1176-0.00910.1296-17.2158-2.0275-42.7848
51.0912-0.80540.60421.9086-1.16930.74120.04950.4774-0.2653-0.33640.22330.11930.165-0.30860.44810.2805-0.07350.07280.308-0.05220.2326-26.9486.315-46.5096
60.08420.0454-0.04310.06490.01430.05740.12420.104-0.3668-0.150.0577-0.13070.09210.25630.00020.16760.0171-0.01190.20650.00390.20626.15669.6845-20.4762
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 26 through 157)
2X-RAY DIFFRACTION2(chain 'A' and resid 158 through 220)
3X-RAY DIFFRACTION3(chain 'B' and resid 29 through 131)
4X-RAY DIFFRACTION4(chain 'B' and resid 132 through 220)
5X-RAY DIFFRACTION5chain 'C'
6X-RAY DIFFRACTION6chain 'D'

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