[English] 日本語
Yorodumi
- PDB-6r4x: Crystal structure of PPEP-1(E143A/Y178F) in complex with substrat... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6r4x
TitleCrystal structure of PPEP-1(E143A/Y178F) in complex with substrate peptide Ac-EVNPAVP-CONH2
Components
  • ACE-GLU-VAL-ASN-PRO-ALA-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/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)
Clostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.831 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 / diffrn_source
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _diffrn_source.pdbx_synchrotron_site
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pro-Pro endopeptidase
B: Pro-Pro endopeptidase
C: ACE-GLU-VAL-ASN-PRO-ALA-VAL-LPD
D: ACE-GLU-VAL-ASN-PRO-ALA-VAL-LPD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4506
Polymers45,3194
Non-polymers1312
Water6,954386
1
A: Pro-Pro endopeptidase
D: ACE-GLU-VAL-ASN-PRO-ALA-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 area1890 Å2
ΔGint-49 kcal/mol
Surface area9000 Å2
MethodPISA
2
B: Pro-Pro endopeptidase
C: ACE-GLU-VAL-ASN-PRO-ALA-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 area1840 Å2
ΔGint-49 kcal/mol
Surface area8910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.237, 42.933, 121.227
Angle α, β, γ (deg.)90.00, 96.64, 90.00
Int Tables number4
Space group name H-MP1211

-
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-PRO-ALA-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


Mass: 18.015 Da / Num. of mol.: 386 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.87 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 2 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 microl precipitant solution containing: 100 mM Tris pH 7.5, 2.25 M ...Details: 2 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 microl precipitant solution containing: 100 mM Tris pH 7.5, 2.25 M ammonium phosphate. Reservoir solution: 200 microl

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.831→60.21 Å / Num. obs: 33603 / % possible obs: 99.26 % / Redundancy: 3.3 % / Net I/σ(I): 9.59
Reflection shellResolution: 1.831→1.897 Å

-
Processing

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

5a0p


Resolution: 1.831→60.207 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.45 / Phase error: 21.57
RfactorNum. reflection% reflection
Rfree0.2123 1674 4.98 %
Rwork0.1774 --
obs0.1791 33600 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.831→60.207 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3135 0 2 386 3523
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043280
X-RAY DIFFRACTIONf_angle_d0.5814454
X-RAY DIFFRACTIONf_dihedral_angle_d2.9472667
X-RAY DIFFRACTIONf_chiral_restr0.039488
X-RAY DIFFRACTIONf_plane_restr0.003587
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8314-1.88530.34051370.30482604X-RAY DIFFRACTION99
1.8853-1.94620.30121390.26462665X-RAY DIFFRACTION100
1.9462-2.01570.25731460.24442598X-RAY DIFFRACTION99
2.0157-2.09640.24231320.21992678X-RAY DIFFRACTION99
2.0964-2.19180.24961360.20182639X-RAY DIFFRACTION99
2.1918-2.30740.20171380.18892612X-RAY DIFFRACTION99
2.3074-2.4520.19911400.17332668X-RAY DIFFRACTION100
2.452-2.64130.20961440.17332657X-RAY DIFFRACTION100
2.6413-2.90710.22371330.17122654X-RAY DIFFRACTION99
2.9071-3.32770.21161460.16042706X-RAY DIFFRACTION100
3.3277-4.19240.17061390.13962672X-RAY DIFFRACTION99
4.1924-60.23910.18651440.15412773X-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)
11.26370.0594-0.12922.07540.1631.53050.04980.00810.04830.0061-0.04170.0039-0.06180.0016-0.00080.1950.0128-0.02630.12860.00690.12741.409215.4916-12.1851
21.15230.071-0.4591.2869-0.01611.17330.05030.07770.04490.0791-0.03350.00230.0051-0.0502-0.02080.10210.0051-0.00450.14350.00720.1218-18.202412.7513-50.3735
31.9981-0.1167-0.06262.70410.43852.15260.07140.0714-0.0957-0.2385-0.08730.16160.1856-0.07350.00160.24960.0032-0.06220.1412-0.00110.1479-5.683-0.1215-19.3344
42.23350.13450.1562.7766-0.2012.3185-0.0233-0.0372-0.16910.3103-0.060.03210.20760.05710.07670.23290.00960.01330.14520.00840.195-16.5733-3.8884-41.8379
56.8390.29854.14245.4780.12082.5207-0.09010.2929-0.0969-0.44420.37570.23040.31670.0976-0.22410.2577-0.02550.0390.27430.00910.2675-26.79867.1385-46.342
69.3633-1.96157.17883.2555-1.98899.7822-0.0666-0.3465-0.2559-0.04250.0558-0.08410.04450.16140.03710.29140.04010.05830.29290.07160.20676.53829.406-20.1357
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 26 through 151)
2X-RAY DIFFRACTION2(chain 'B' and resid 29 through 151)
3X-RAY DIFFRACTION3(chain 'A' and resid 152 through 220)
4X-RAY DIFFRACTION4(chain 'B' and resid 152 through 220)
5X-RAY DIFFRACTION5(chain 'C' )
6X-RAY DIFFRACTION6(chain 'D' )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more