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- PDB-6r5a: Crystal structure of PPEP-1(W103F) -

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Basic information

Entry
Database: PDB / ID: 6r5a
TitleCrystal structure of PPEP-1(W103F)
ComponentsPro-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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2646
Polymers43,8892
Non-polymers3754
Water7,674426
1
A: Pro-Pro endopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1323
Polymers21,9451
Non-polymers1882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pro-Pro endopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1323
Polymers21,9451
Non-polymers1882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.579, 66.161, 118.399
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 21944.646 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: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 426 / 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: 1.9 Å3/Da / Density % sol: 35.26 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 4 microl 12 mg per ml rPPEP-1 W103F in 20 mM Tris pH 8.5, 200 mM NaCl was mixed with 1 microl precipitant solution containing: 100 mM Tris pH 8.5, 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: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.48→44.12 Å / Num. obs: 56407 / % possible obs: 99.54 % / Redundancy: 8.5 % / Net I/σ(I): 14.14
Reflection shellResolution: 1.48→1.533 Å / Num. unique obs: 5477 / CC1/2: 0.836 / Rrim(I) all: 0.819

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Processing

Software
NameVersionClassification
PHENIX(dev_3409: ???)refinement
XDS20160617data reduction
XDS20160617data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5A0P

5a0p


Resolution: 1.48→44.117 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 20.13
RfactorNum. reflection% reflection
Rfree0.1989 1971 3.5 %
Rwork0.1651 --
obs0.1663 56382 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.48→44.117 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3012 0 18 426 3456
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053154
X-RAY DIFFRACTIONf_angle_d0.7194275
X-RAY DIFFRACTIONf_dihedral_angle_d13.9421165
X-RAY DIFFRACTIONf_chiral_restr0.059466
X-RAY DIFFRACTIONf_plane_restr0.004559
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.5170.27841350.22593770X-RAY DIFFRACTION98
1.517-1.5580.28561380.21393793X-RAY DIFFRACTION99
1.558-1.60390.24981370.19973822X-RAY DIFFRACTION99
1.6039-1.65570.22561400.18923840X-RAY DIFFRACTION99
1.6557-1.71480.22551390.17513845X-RAY DIFFRACTION100
1.7148-1.78350.23261390.16623850X-RAY DIFFRACTION100
1.7835-1.86470.21831400.16053854X-RAY DIFFRACTION100
1.8647-1.9630.20491410.15813870X-RAY DIFFRACTION100
1.963-2.0860.23851410.15123877X-RAY DIFFRACTION100
2.086-2.2470.17391420.14633921X-RAY DIFFRACTION100
2.247-2.47310.17621410.14873908X-RAY DIFFRACTION100
2.4731-2.83090.17391440.15853938X-RAY DIFFRACTION100
2.8309-3.56640.19811440.15953977X-RAY DIFFRACTION100
3.5664-44.13660.17281500.16934146X-RAY DIFFRACTION100

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