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- PDB-5n12: Crystal structure of TCE treated rPPEP-1 -

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Basic information

Entry
Database: PDB / ID: 5n12
TitleCrystal structure of TCE treated rPPEP-1
ComponentsPro-Pro endopeptidase
KeywordsHYDROLASE / Metalloprotease / TCE / Zinc / Clostridium difficle
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
2,2,2-tris-chloroethanol / Pro-Pro endopeptidase
Similarity search - Component
Biological speciesPeptoclostridium difficile 630 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.38 Å
AuthorsPichlo, C. / Schacherl, M. / Baumann, U.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2018
Title: Improved protein-crystal identification by using 2,2,2-trichloroethanol as a fluorescence enhancer.
Authors: Pichlo, C. / Toelzer, C. / Chojnacki, K. / Ocal, S. / Uthoff, M. / Ruegenberg, S. / Hermanns, T. / Schacherl, M. / Denzel, M.S. / Hofmann, K. / Niefind, K. / Baumann, U.
History
DepositionFeb 4, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.2Jan 17, 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_ncs_dom_lim
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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6779
Polymers43,8532
Non-polymers8237
Water8,125451
1
A: Pro-Pro endopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2644
Polymers21,9271
Non-polymers3373
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pro-Pro endopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4135
Polymers21,9271
Non-polymers4864
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.169, 71.769, 117.798
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 28 or resseq 30:31 or resseq...
21(chain B and (resseq 28 or resseq 30:31 or resseq...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERSERSER(chain A and (resseq 28 or resseq 30:31 or resseq...AA285
12THRTHRILEILE(chain A and (resseq 28 or resseq 30:31 or resseq...AA30 - 317 - 8
13GLNGLNPROPRO(chain A and (resseq 28 or resseq 30:31 or resseq...AA33 - 10010 - 77
14GLYGLYGLYGLY(chain A and (resseq 28 or resseq 30:31 or resseq...AA102 - 11879 - 95
15THRTHRGLUGLU(chain A and (resseq 28 or resseq 30:31 or resseq...AA120 - 14097 - 117
16HISHISLEULEU(chain A and (resseq 28 or resseq 30:31 or resseq...AA142 - 153119 - 130
17ASPASPSERSER(chain A and (resseq 28 or resseq 30:31 or resseq...AA155 - 157132 - 134
18SERSERSERSER(chain A and (resseq 28 or resseq 30:31 or resseq...AA159136
19ALAALAALAALA(chain A and (resseq 28 or resseq 30:31 or resseq...AA160137
110SERSERLYSLYS(chain A and (resseq 28 or resseq 30:31 or resseq...AA24 - 2201 - 197
111SERSERLYSLYS(chain A and (resseq 28 or resseq 30:31 or resseq...AA24 - 2201 - 197
112SERSERLYSLYS(chain A and (resseq 28 or resseq 30:31 or resseq...AA24 - 2201 - 197
21SERSERSERSER(chain B and (resseq 28 or resseq 30:31 or resseq...BB285
22THRTHRILEILE(chain B and (resseq 28 or resseq 30:31 or resseq...BB30 - 317 - 8
23GLNGLNPROPRO(chain B and (resseq 28 or resseq 30:31 or resseq...BB33 - 10010 - 77
24GLYGLYGLYGLY(chain B and (resseq 28 or resseq 30:31 or resseq...BB102 - 11879 - 95
25THRTHRGLUGLU(chain B and (resseq 28 or resseq 30:31 or resseq...BB120 - 14097 - 117
26HISHISLEULEU(chain B and (resseq 28 or resseq 30:31 or resseq...BB142 - 153119 - 130
27ASPASPSERSER(chain B and (resseq 28 or resseq 30:31 or resseq...BB155 - 157132 - 134
28SERSERSERSER(chain B and (resseq 28 or resseq 30:31 or resseq...BB159136
29ALAALAALAALA(chain B and (resseq 28 or resseq 30:31 or resseq...BB160137
210ASPASPLYSLYS(chain B and (resseq 28 or resseq 30:31 or resseq...BB27 - 2204 - 197
211ASPASPLYSLYS(chain B and (resseq 28 or resseq 30:31 or resseq...BB27 - 2204 - 197
212ASPASPLYSLYS(chain B and (resseq 28 or resseq 30:31 or resseq...BB27 - 2204 - 197

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Components

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


Mass: 21926.631 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Peptoclostridium difficile 630 (bacteria)
Gene: zmp1, 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-8FH / 2,2,2-tris-chloroethanol


Mass: 149.404 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3Cl3O
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 451 / 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: 2.08 Å3/Da / Density % sol: 40.88 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: Protein to precipitant solution: 1.5 microl:1.5 microl Protein: 12 mg ml 20 mM Tris pH 7.5 200 mM NaCl Precipitant solution: 0.1 M Tris pH 8.5 2.0 M ammonium phosphate dibasic
PH range: 7.5 - 9.0

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.38→45.53 Å / Num. obs: 76075 / % possible obs: 100 % / Redundancy: 6.5 % / Biso Wilson estimate: 15.25 Å2 / Net I/σ(I): 14.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5A0P

5a0p


Resolution: 1.38→45.53 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.32 / Phase error: 18.14
RfactorNum. reflection% reflection
Rfree0.1841 2122 2.79 %
Rwork0.1637 --
obs0.1643 76052 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 70.93 Å2 / Biso mean: 20.85 Å2 / Biso min: 9.32 Å2
Refinement stepCycle: final / Resolution: 1.38→45.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3070 0 67 451 3588
Biso mean--24.99 29.18 -
Num. residues----391
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083227
X-RAY DIFFRACTIONf_angle_d0.9764375
X-RAY DIFFRACTIONf_chiral_restr0.07471
X-RAY DIFFRACTIONf_plane_restr0.006569
X-RAY DIFFRACTIONf_dihedral_angle_d14.5821183
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2112X-RAY DIFFRACTION4.847TORSIONAL
12B2112X-RAY DIFFRACTION4.847TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.38-1.41210.30281380.246348444982
1.4121-1.44740.24651400.220448625002
1.4474-1.48660.22161400.203648745014
1.4866-1.53030.20571400.191248775017
1.5303-1.57970.21941390.18148785017
1.5797-1.63620.20911410.170948574998
1.6362-1.70170.20281410.164749165057
1.7017-1.77910.17241400.159948845024
1.7791-1.87290.1781410.160649335074
1.8729-1.99030.19411400.163848975037
1.9903-2.14390.16211430.154649265069
2.1439-2.35970.17461390.146949355074
2.3597-2.70110.17991450.152149995144
2.7011-3.40290.16711430.16550175160
3.4029-45.55440.18091520.159252315383
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)
11.02360.04140.03970.6023-0.0461.2729-0.0076-0.03090.0392-0.02420.0211-0.0098-0.00180.0316-0.00930.0968-0.0058-0.00510.0766-0.00860.080443.2458219.7055-192.6988
21.32130.0201-0.3360.79510.11211.3394-0.0046-0.01070.0673-0.01760.0309-0.0397-0.01250.0247-0.01740.1021-0.0077-0.01610.0793-0.00560.075942.7393255.2581-188.8264
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 24 through 220)A24 - 220
2X-RAY DIFFRACTION2(chain 'B' and resid 27 through 220)B27 - 220

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