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- PDB-6r52: Crystal structure of PPEP-1(K101A) -

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Basic information

Entry
Database: PDB / ID: 6r52
TitleCrystal structure of PPEP-1(K101A)
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/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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.022 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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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_label_asym_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)44,2266
Polymers43,8512
Non-polymers3754
Water5,314295
1
A: Pro-Pro endopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1133
Polymers21,9261
Non-polymers1882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pro-Pro endopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1133
Polymers21,9261
Non-polymers1882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.920, 70.940, 115.670
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: 21925.580 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-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#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.: 295 / 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: 2.01 Å3/Da / Density % sol: 38.74 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 200 nl 12 mg per ml rPPEP-1 K101A in 20 mM Tris pH 7.5, 200 mM NaCl was mixed with 100 nl precipitant solution: 100 mM Tris pH 8.5, 2.25 M ammonium phosphate dibasic. Reservoir volume: 60 microl

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.28 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28 Å / Relative weight: 1
ReflectionResolution: 2.022→44.83 Å / Num. obs: 23791 / % possible obs: 99.78 % / Redundancy: 6.4 % / Net I/σ(I): 10.75
Reflection shellResolution: 2.022→2.094 Å / Num. unique obs: 2298

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Processing

Software
NameVersionClassification
PHENIX(dev_3395: ???)refinement
XDSJun 17, 2015data reduction
XDSJun 17, 2015data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5A0P

5a0p


Resolution: 2.022→44.826 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.45 / Phase error: 20.21
RfactorNum. reflection% reflection
Rfree0.2063 1192 5.01 %
Rwork0.1772 --
obs0.1787 23783 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.022→44.826 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3030 0 18 295 3343
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053164
X-RAY DIFFRACTIONf_angle_d0.7654291
X-RAY DIFFRACTIONf_dihedral_angle_d11.9331885
X-RAY DIFFRACTIONf_chiral_restr0.043465
X-RAY DIFFRACTIONf_plane_restr0.004562
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0216-2.10260.26531280.23452428X-RAY DIFFRACTION99
2.1026-2.19830.26321310.20042474X-RAY DIFFRACTION100
2.1983-2.31420.23051270.20082467X-RAY DIFFRACTION100
2.3142-2.45910.20571340.18642485X-RAY DIFFRACTION100
2.4591-2.6490.24341320.19012494X-RAY DIFFRACTION100
2.649-2.91550.19341320.18172504X-RAY DIFFRACTION100
2.9155-3.33730.21031300.17362531X-RAY DIFFRACTION100
3.3373-4.20420.18361350.14972532X-RAY DIFFRACTION100
4.2042-44.83680.17841430.16432676X-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)
12.131-0.05670.06920.8673-0.59862.1423-0.04390.0922-0.0209-0.03610.0029-0.03030.04340.07210.03360.1306-0.0070.01220.105-0.01910.118-0.5449-5.043815.8791
22.0726-0.06930.67170.9974-0.60073.0029-0.00440.0863-0.03630.04680.0075-0.0154-0.05910.1637-0.00610.1473-0.00050.00720.1408-0.01950.1175-0.8261-39.818111.471
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'B' and not (resname HOH or resname WAT))
2X-RAY DIFFRACTION2(chain 'A' and not (resname HOH or resname WAT))

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