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- PDB-6sqx: Insights into a novel NlpC/P60 Endopeptidase from Photobacterium ... -

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Basic information

Entry
Database: PDB / ID: 6sqx
TitleInsights into a novel NlpC/P60 Endopeptidase from Photobacterium damselae subsp. piscicida
ComponentsPeptide-binding protein
KeywordsHYDROLASE / NlpC/P60 / cell wall hydrolases / Crystallography X-Ray / D / L-endopeptidase
Function / homology
Function and homology information


NLPC/P60, N-terminal domain / Uncharacterised peptidase with NlpC/P60 domain, YkfC type / SH3b1 domain / NLPC_P60 stabilising domain, N term / SH3 domain (SH3b1 type) / Endopeptidase, NLPC/P60 domain / NlpC/P60 family / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
BICARBONATE ION / DI(HYDROXYETHYL)ETHER / Peptide-binding protein
Similarity search - Component
Biological speciesPhotobacterium damsela subsp. piscicida (causative agent of fish pasteurellosis)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsLisboa, J. / Pereira, P.J.B. / dos Santos, N.M.S.
Funding support Portugal, 1items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a TecnologiaPTDC/CVT-CVT/30018/2017 Portugal
CitationJournal: Msphere / Year: 2021
Title: A Secreted NlpC/P60 Endopeptidase from Photobacterium damselae subsp. piscicida Cleaves the Peptidoglycan of Potentially Competing Bacteria.
Authors: Lisboa, J. / Pereira, C. / Rifflet, A. / Ayala, J. / Terceti, M.S. / Barca, A.V. / Rodrigues, I. / Pereira, P.J.B. / Osorio, C.R. / Garcia-Del Portillo, F. / Gomperts Boneca, I. / do Vale, A. ...Authors: Lisboa, J. / Pereira, C. / Rifflet, A. / Ayala, J. / Terceti, M.S. / Barca, A.V. / Rodrigues, I. / Pereira, P.J.B. / Osorio, C.R. / Garcia-Del Portillo, F. / Gomperts Boneca, I. / do Vale, A. / Dos Santos, N.M.S.
History
DepositionSep 4, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Feb 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Jan 24, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptide-binding protein
B: Peptide-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,52548
Polymers114,7872
Non-polymers2,73846
Water18,9881054
1
A: Peptide-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,66122
Polymers57,3931
Non-polymers1,26821
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peptide-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,86426
Polymers57,3931
Non-polymers1,47125
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.578, 109.966, 130.936
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Peptide-binding protein / SH3 domain of the SH3b1 type


Mass: 57393.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Signal Peptide: M1-A19 LEHHHHHH: His Tag
Source: (gene. exp.) Photobacterium damsela subsp. piscicida (causative agent of fish pasteurellosis)
Gene: E4T26_07800, FA893_15790, PDPJ_2_00460 / Cell line (production host): Codon + / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1V1VDL8

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Non-polymers , 5 types, 1100 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 38 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: CHO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1054 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.51 Å3/Da / Density % sol: 50.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 100 mM Imidazole pH 8.0 + 15 % PEG 8K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 12, 2016
RadiationMonochromator: Silicon Si crystal (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.4→38.3 Å / Num. obs: 216685 / % possible obs: 99.85 % / Redundancy: 5.5 % / CC1/2: 1 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.022 / Rrim(I) all: 0.051 / Net I/σ(I): 18.86
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 5.4 % / Rmerge(I) obs: 1.47 / Num. unique obs: 21426 / CC1/2: 0.616 / Rpim(I) all: 0.69 / Rrim(I) all: 1.626 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3m1u

3m1u


Resolution: 1.4→38.29 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 19.61
RfactorNum. reflection% reflection
Rfree0.1754 10695 4.94 %
Rwork0.1467 --
obs0.1481 216667 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 105.92 Å2 / Biso mean: 28.36 Å2 / Biso min: 12.61 Å2
Refinement stepCycle: final / Resolution: 1.4→38.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7391 0 169 1055 8615
Biso mean--43.42 38.51 -
Num. residues----914
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.420.33493610.31416467682895
1.42-1.430.33793570.294168017158100
1.43-1.450.31783540.278468067160100
1.45-1.470.30733480.254967927140100
1.47-1.490.28493620.24968517213100
1.49-1.510.2723470.252567867133100
1.51-1.530.31743490.25568387187100
1.53-1.550.28333530.239468217174100
1.55-1.580.24633540.21668027156100
1.58-1.60.23563420.204868417183100
1.6-1.630.24193790.191768327211100
1.63-1.660.19613490.159968207169100
1.66-1.690.20623360.150268627198100
1.69-1.730.18883690.148768347203100
1.73-1.760.19193690.139768467215100
1.76-1.80.19893730.139868017174100
1.8-1.850.1783600.135268427202100
1.85-1.90.16733460.123268827228100
1.9-1.950.16983430.118268527195100
1.95-2.020.14813680.122868867254100
2.02-2.090.16773570.125968547211100
2.09-2.170.16223270.130969037230100
2.17-2.270.14693250.1369517276100
2.27-2.390.17173520.140669237275100
2.39-2.540.17483630.133369067269100
2.54-2.740.173550.14469467301100
2.74-3.010.17933690.14569297298100
3.01-3.450.15273540.143770097363100
3.45-4.350.15233670.133270367403100
4.35-38.290.15724070.143172537660100

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