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- PDB-2n6j: Solution structure of Zmp1, a zinc-dependent metalloprotease secr... -

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Basic information

Entry
Database: PDB / ID: 2n6j
TitleSolution structure of Zmp1, a zinc-dependent metalloprotease secreted by Clostridium difficile
ComponentsZinc metalloprotease Zmp1
KeywordsHYDROLASE / metalloprotease / vaccine
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 630 (bacteria)
MethodSOLUTION NMR / torsion angle dynamics, molecular dynamics
Model detailsfewest violations, model1
AuthorsBanci, L. / Cantini, F. / Scarselli, M. / Rubino, J.T. / Martinelli, M.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2016
Title: Structural characterization of zinc-bound Zmp1, a zinc-dependent metalloprotease secreted by Clostridium difficile.
Authors: Rubino, J.T. / Martinelli, M. / Cantini, F. / Castagnetti, A. / Leuzzi, R. / Banci, L. / Scarselli, M.
History
DepositionAug 24, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2016Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Zinc metalloprotease Zmp1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6932
Polymers21,6271
Non-polymers651
Water181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 400target function
RepresentativeModel #1fewest violations

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Components

#1: Protein Zinc metalloprotease Zmp1


Mass: 21627.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Peptoclostridium difficile 630 (bacteria)
Strain: 630 / Gene: zmp1, CD630_28300 / Production host: Escherichia coli (E. coli) / Strain (production host): T7
References: UniProt: Q183R7, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-1H NOESY
1313D HNCA
1413D HNCO
1513D CBCA(CO)NH
1613D HN(CA)CB
1713D HN(CO)CA
1813D HNHA
1913D 1H-15N NOESY
11013D 1H-13C NOESY
11113D (H)CCH-TOCSY

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Sample preparation

DetailsContents: 0.6 mM [U-100% 15N] Zmp1, 0.5 mM [U-99% 13C; U-99% 15N] Zmp1, 1 mM Zmp1, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMZmp1-1[U-100% 15N]1
0.5 mMZmp1-2[U-99% 13C; U-99% 15N]1
1 mMZmp1-31
Sample conditionsIonic strength: hepes 20 / pH: 7.2 / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9501
Bruker AvanceBrukerAVANCE9002
Bruker AvanceBrukerAVANCE5003
Bruker AvanceBrukerAVANCE7004

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert P.structure solution
CYANA2.1Guntert P.validation
CYANA2.1Guntert P.refinement
PSVSBhattacharya and Montelionestructure solution
PSVSBhattacharya and Montelionevalidation
PSVSBhattacharya and Montelionerefinement
Amber10Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CARA2Keller and Wuthrichdata analysis
CARA2Keller and Wuthrichrefinement
TopSpin3Bruker Biospincollection
RefinementMethod: torsion angle dynamics, molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 2617 / NOE intraresidue total count: 469 / NOE long range total count: 592 / NOE medium range total count: 808 / NOE sequential total count: 748 / Protein phi angle constraints total count: 137 / Protein psi angle constraints total count: 138
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 400 / Conformers submitted total number: 20

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