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- PDB-8b2q: Matrix-metallopeptidase inhibitor Potempin A (PotA) from Tannerel... -

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Basic information

Entry
Database: PDB / ID: 8b2q
TitleMatrix-metallopeptidase inhibitor Potempin A (PotA) from Tannerella forsythia in complex with T. forsythia karilysin.
Components
  • Karilysin long form Kly38
  • Tannerella forsythia potempin A (PotA)
KeywordsHYDROLASE INHIBITOR / Metallopeptidase inhibitor
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / collagen catabolic process / extracellular matrix organization / extracellular matrix / metalloendopeptidase activity / proteolysis / extracellular region / zinc ion binding
Similarity search - Function
Secretion system C-terminal sorting domain / Secretion system C-terminal sorting domain / Invasin/intimin cell-adhesion fragments / Peptidase M10A / Peptidase M10A, catalytic domain / Peptidase M10, metallopeptidase / Matrixin / Peptidase, metallopeptidase / Zinc-dependent metalloprotease / Metallopeptidase, catalytic domain superfamily ...Secretion system C-terminal sorting domain / Secretion system C-terminal sorting domain / Invasin/intimin cell-adhesion fragments / Peptidase M10A / Peptidase M10A, catalytic domain / Peptidase M10, metallopeptidase / Matrixin / Peptidase, metallopeptidase / Zinc-dependent metalloprotease / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Lipoprotein / Karilysin
Similarity search - Component
Biological speciesTannerella forsythia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsPotempa, J. / Ksiazek, M. / Goulas, T. / Cuppari, A. / Rodriguez-Banqueri, A. / Arolas, J.L. / Lopez-Pelegrin, M. / Garcia-Ferrer, I. / Guevara, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: Chem Sci / Year: 2023
Title: A unique network of attack, defence and competence on the outer membrane of the periodontitis pathogen Tannerella forsythia.
Authors: Ksiazek, M. / Goulas, T. / Mizgalska, D. / Rodriguez-Banqueri, A. / Eckhard, U. / Veillard, F. / Waligorska, I. / Benedyk-Machaczka, M. / Sochaj-Gregorczyk, A.M. / Madej, M. / Thogersen, I.B. ...Authors: Ksiazek, M. / Goulas, T. / Mizgalska, D. / Rodriguez-Banqueri, A. / Eckhard, U. / Veillard, F. / Waligorska, I. / Benedyk-Machaczka, M. / Sochaj-Gregorczyk, A.M. / Madej, M. / Thogersen, I.B. / Enghild, J.J. / Cuppari, A. / Arolas, J.L. / de Diego, I. / Lopez-Pelegrin, M. / Garcia-Ferrer, I. / Guevara, T. / Dive, V. / Zani, M.L. / Moreau, T. / Potempa, J. / Gomis-Ruth, F.X.
#1: Journal: Front Microbiol / Year: 2015
Title: KLIKK proteases of Tannerella forsythia: putative virulence factors with a unique domain structure.
Authors: Ksiazek, M. / Mizgalska, D. / Eick, S. / Thogersen, I.B. / Enghild, J.J. / Potempa, J.
History
DepositionSep 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._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_author.identifier_ORCID
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Karilysin long form Kly38
I: Tannerella forsythia potempin A (PotA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8408
Polymers29,2902
Non-polymers5506
Water5,495305
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-44 kcal/mol
Surface area12240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.240, 62.940, 108.680
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AI

#1: Protein Karilysin long form Kly38


Mass: 18645.580 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tannerella forsythia (bacteria)
Strain: ATCC 43037 / JCM 10827 / CCUG 21028 A / KCTC 5666 / FDC 338
Gene: kly, BFO_2683 / Production host: Escherichia coli (E. coli) / References: UniProt: D0EM77
#2: Protein Tannerella forsythia potempin A (PotA)


Mass: 10644.170 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tannerella forsythia (bacteria) / Gene: EII40_07620, TFUB20_02189 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1D3UV35

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Non-polymers , 5 types, 311 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.05 Å3/Da / Density % sol: 39.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: The PotA:karilysin complex at 15 mg/mL in 50 mM sodium chloride, 5 mM calcium chloride, 0.02% sodium azide, 5 mM Tris-HCl pH 8.0 was crystallised from 25% (w/v) PEG 6,000, 100 mM MES, pH 6.0.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.35→62.9 Å / Num. obs: 57705 / % possible obs: 98.6 % / Redundancy: 12.4 % / Biso Wilson estimate: 21.9 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.06 / Rrim(I) all: 0.063 / Net I/σ(I): 20.8
Reflection shellResolution: 1.35→1.42 Å / Redundancy: 12.1 % / Rmerge(I) obs: 0.767 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 7901 / CC1/2: 0.9 / Rrim(I) all: 0.8 / % possible all: 97.2

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IN9

4in9


Resolution: 1.35→36.07 Å / Cor.coef. Fo:Fc: 0.9661 / Cor.coef. Fo:Fc free: 0.9693 / SU R Cruickshank DPI: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.051 / SU Rfree Blow DPI: 0.051 / SU Rfree Cruickshank DPI: 0.048
RfactorNum. reflection% reflectionSelection details
Rfree0.1711 762 1.32 %RANDOM
Rwork0.1542 ---
obs0.1545 57704 98.6 %-
Displacement parametersBiso max: 101.6 Å2 / Biso mean: 22.28 Å2 / Biso min: 5.59 Å2
Baniso -1Baniso -2Baniso -3
1--1.8346 Å20 Å20 Å2
2--1.5681 Å20 Å2
3---0.2665 Å2
Refine analyzeLuzzati coordinate error obs: 0.145 Å
Refinement stepCycle: final / Resolution: 1.35→36.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2065 0 56 328 2449
Biso mean--32 32.65 -
Num. residues----260
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d914SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes54HARMONIC2
X-RAY DIFFRACTIONt_gen_planes616HARMONIC5
X-RAY DIFFRACTIONt_it4196HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion287SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies5HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4455SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4196HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg7549HARMONIC21.07
X-RAY DIFFRACTIONt_omega_torsion4.72
X-RAY DIFFRACTIONt_other_torsion14.58
LS refinement shellResolution: 1.35→1.39 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 51 1.23 %
Rwork0.234 4088 -
all0.2343 4139 -
obs--97.02 %
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)
10.6540.1060.09070.7139-0.19750.68370.0301-0.0003-0.0334-0.0192-0.02980.00320.07640.0245-0.00030.02750.00970.0027-0.0135-0.0011-0.00548.6858-125.748108.409
20.1081-0.09210.00610.0044-0.52264.7835-0.0047-0.07560.03540.03930.05290.004-0.27310.1108-0.04820.15840.00660.0050.0958-0.00550.039748.3641-126.993135.037
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|35 - 200 A|301 - 303}A35 - 200
2X-RAY DIFFRACTION1{A|35 - 200 A|301 - 303}A999
3X-RAY DIFFRACTION1{A|35 - 200 A|301 - 303}A998
4X-RAY DIFFRACTION1{A|35 - 200 A|301 - 303}A997
5X-RAY DIFFRACTION2{I|25 - 118}I25 - 118

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