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- PDB-6r55: Crystal structure of PPEP-1(E184K) -

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Basic information

Entry
Database: PDB / ID: 6r55
TitleCrystal structure of PPEP-1(E184K)
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: 1.401 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)44,3436
Polymers43,9682
Non-polymers3754
Water9,386521
1
A: Pro-Pro endopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1713
Polymers21,9841
Non-polymers1882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pro-Pro endopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1713
Polymers21,9841
Non-polymers1882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.970, 71.670, 117.810
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: 21983.750 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


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


Mass: 18.015 Da / Num. of mol.: 521 / 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: 2.06 Å3/Da / Density % sol: 40.38 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 1.5 microl 12 mg per ml rPPEP-1 E184K in 20 mM Tris pH 7.5, 200 mM NaCl was mixed with 1.5 microl precipitant solution containing: 100 mM Tris pH 8.5, 2.1 M ammonium phosphate dibasic. ...Details: 1.5 microl 12 mg per ml rPPEP-1 E184K in 20 mM Tris pH 7.5, 200 mM NaCl was mixed with 1.5 microl precipitant solution containing: 100 mM Tris pH 8.5, 2.1 M ammonium phosphate dibasic. Reservior 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: Feb 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.401→45.507 Å / Num. obs: 71875 / % possible obs: 99.3 % / Redundancy: 4.3 % / Net I/σ(I): 13.12
Reflection shellResolution: 1.401→1.451 Å

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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: 1.401→45.507 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 18.23
RfactorNum. reflection% reflection
Rfree0.1827 2520 3.51 %
Rwork0.1587 --
obs0.1595 71850 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.401→45.507 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3037 0 18 521 3576
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053177
X-RAY DIFFRACTIONf_angle_d0.8284306
X-RAY DIFFRACTIONf_dihedral_angle_d15.7981172
X-RAY DIFFRACTIONf_chiral_restr0.066466
X-RAY DIFFRACTIONf_plane_restr0.005562
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4012-1.42810.31861400.2993716X-RAY DIFFRACTION97
1.4281-1.45730.3141380.26993795X-RAY DIFFRACTION100
1.4573-1.48890.28591380.25533862X-RAY DIFFRACTION100
1.4889-1.52360.23951350.23193802X-RAY DIFFRACTION100
1.5236-1.56170.22531400.21783802X-RAY DIFFRACTION100
1.5617-1.60390.25261380.19873851X-RAY DIFFRACTION100
1.6039-1.65110.24271380.1883801X-RAY DIFFRACTION100
1.6511-1.70440.2111390.17763837X-RAY DIFFRACTION100
1.7044-1.76530.18521390.16673823X-RAY DIFFRACTION99
1.7653-1.8360.2131370.15883834X-RAY DIFFRACTION99
1.836-1.91960.18161400.1533833X-RAY DIFFRACTION100
1.9196-2.02080.17761400.14633857X-RAY DIFFRACTION100
2.0208-2.14740.17941430.13513898X-RAY DIFFRACTION100
2.1474-2.31320.16271380.12953855X-RAY DIFFRACTION100
2.3132-2.54590.15151420.1343903X-RAY DIFFRACTION100
2.5459-2.91430.15881440.14473883X-RAY DIFFRACTION99
2.9143-3.67150.15941390.1453902X-RAY DIFFRACTION98
3.6715-45.53110.16731520.15234076X-RAY DIFFRACTION98
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)
11.4579-0.1184-0.20681.22170.08272.10360.0107-0.0006-0.0769-0.0360.03320.03170.02720.0021-0.03790.0882-0.00640.00580.0923-0.00710.0791-6.212-40.87718.6221
22.4475-0.1109-0.1121.7024-0.14932.3958-0.045-0.08660.0227-0.02760.0533-0.25280.04350.2503-0.00150.0777-0.00350.01210.1045-0.0170.10389.9261-38.340717.7677
31.05810.0321-0.37870.7608-0.35941.74540.01370.0851-0.0198-0.02370.01030.05-0.0083-0.1135-0.02560.07960.00050.00110.0845-0.0140.0878-5.8029-6.180912.7768
42.27880.0947-0.13241.706-0.3122.50170.0133-0.14840.09480.0764-0.0028-0.076-0.05520.2428-0.0070.0742-0.0083-0.0010.0975-0.02010.077210.3992-2.796922.1107
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 26 through 153)
2X-RAY DIFFRACTION2(chain 'A' and resid 154 through 301)
3X-RAY DIFFRACTION3(chain 'B' and resid 29 through 153)
4X-RAY DIFFRACTION4(chain 'B' and resid 154 through 301)

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