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- PDB-4yec: Crystal structure of a clostripain (PARMER_00083) from Parabacter... -

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Basic information

Entry
Database: PDB / ID: 4yec
TitleCrystal structure of a clostripain (PARMER_00083) from Parabacteroides merdae ATCC 43184 in complex with peptide inhibitor Ac-VLTK-AOMK
Components
  • (Clostripain family) x 2
  • Peptide inhibitor Ac-VLTK-AOMK
KeywordsUnknown Function/Inhibitor / clostripain / microbiome / secreted protease / inhibitor / Unknown Function-Inhibitor complex
Function / homologyRossmann fold - #11970 / Peptidase C11, clostripain / Clostripain family / Prokaryotic membrane lipoprotein lipid attachment site profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Peptide inhibitor Ac-VLTK-AOMK / Clostripain family
Function and homology information
Biological speciesParabacteroides merdae ATCC 43184 (bacteria)
unidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 Å
AuthorsWolan, D.W. / Gonzalez-Paez, G.E. / Chatterjee, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)3U54GM094586-03S1 United States
CitationJournal: ACS Chem. Biol. / Year: 2017
Title: Substrate Profiling and High Resolution Co-complex Crystal Structure of a Secreted C11 Protease Conserved across Commensal Bacteria.
Authors: Roncase, E.J. / Moon, C. / Chatterjee, S. / Gonzalez-Paez, G.E. / Craik, C.S. / O'Donoghue, A.J. / Wolan, D.W.
History
DepositionFeb 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2017Group: Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / pdbx_validate_close_contact / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _pdbx_validate_close_contact.auth_atom_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Clostripain family
B: Clostripain family
C: Peptide inhibitor Ac-VLTK-AOMK


Theoretical massNumber of molelcules
Total (without water)42,0673
Polymers42,0673
Non-polymers00
Water5,116284
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6160 Å2
ΔGint-43 kcal/mol
Surface area14170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.886, 107.344, 40.937
Angle α, β, γ (deg.)90.00, 116.59, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Clostripain family


Mass: 14048.896 Da / Num. of mol.: 1 / Fragment: UNP residues 23-146
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parabacteroides merdae ATCC 43184 (bacteria)
Gene: PARMER_00083
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A7A9N3
#2: Protein Clostripain family


Mass: 27534.025 Da / Num. of mol.: 1 / Fragment: UNP residues 148-375
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parabacteroides merdae ATCC 43184 (bacteria)
Gene: PARMER_00083
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A7A9N3
#3: Protein/peptide Peptide inhibitor Ac-VLTK-AOMK


Type: Peptide-like / Class: Inhibitor / Mass: 483.645 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) unidentified (others) / References: Peptide inhibitor Ac-VLTK-AOMK
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.82 Å3/Da / Density % sol: 32.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.3 / Details: 0.05M NH4CL, 20.0% PEG-3350, NO BUFFER

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.0332 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 14, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.12→36.61 Å / Num. obs: 90762 / % possible obs: 78.9 % / Redundancy: 3 % / Biso Wilson estimate: 14.66 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 9.32
Reflection shellResolution: 1.12→1.14 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.327 / Mean I/σ(I) obs: 2.1 / % possible all: 14.6

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
Cootmodel building
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UWS

3uws


Resolution: 1.12→36.61 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1911 1998 2.2 %random
Rwork0.1583 ---
obs0.159 90707 78.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.03 Å2
Refinement stepCycle: LAST / Resolution: 1.12→36.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2863 0 0 284 3147
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113010
X-RAY DIFFRACTIONf_angle_d1.394111
X-RAY DIFFRACTIONf_dihedral_angle_d12.7171125
X-RAY DIFFRACTIONf_chiral_restr0.062446
X-RAY DIFFRACTIONf_plane_restr0.009529
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.12-1.14760.3964320.25241310X-RAY DIFFRACTION16
1.1476-1.17860.254530.23562276X-RAY DIFFRACTION29
1.1786-1.21330.2583840.20463827X-RAY DIFFRACTION48
1.2133-1.25250.20621410.18715548X-RAY DIFFRACTION70
1.2525-1.29720.23191410.17596888X-RAY DIFFRACTION86
1.2972-1.34920.20721650.16137399X-RAY DIFFRACTION92
1.3492-1.41060.19161620.15817469X-RAY DIFFRACTION93
1.4106-1.48490.20121750.14797679X-RAY DIFFRACTION96
1.4849-1.5780.18811700.13987584X-RAY DIFFRACTION94
1.578-1.69980.18461720.14687662X-RAY DIFFRACTION95
1.6998-1.87090.17331790.15697783X-RAY DIFFRACTION97
1.8709-2.14160.20861710.15067688X-RAY DIFFRACTION96
2.1416-2.6980.17661800.16877853X-RAY DIFFRACTION98
2.698-36.62770.18961730.15577743X-RAY DIFFRACTION95

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