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- PDB-8b2m: Matrix-metallopeptidase inhibitor Potempin A (PotA) from Tannerel... -

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Basic information

Entry
Database: PDB / ID: 8b2m
TitleMatrix-metallopeptidase inhibitor Potempin A (PotA) from Tannerella forsythia
ComponentsTannerella forsythia Potempin A (PotA)
KeywordsHYDROLASE INHIBITOR / Metallopeptidase inhibitor
Function / homologyProkaryotic membrane lipoprotein lipid attachment site profile. / NICKEL (II) ION / Lipoprotein
Function and homology information
Biological speciesTannerella forsythia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 1.2Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tannerella forsythia Potempin A (PotA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3272
Polymers13,2681
Non-polymers591
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-10 kcal/mol
Surface area6350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.210, 76.210, 30.520
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-353-

HOH

21A-430-

HOH

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Components

#1: Protein Tannerella forsythia Potempin A (PotA)


Mass: 13268.493 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
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O
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: 1.93 Å3/Da / Density % sol: 36.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Isolated PotA at 1.8 mg/mL in 50 mM sodium chloride, 5 mM Tris-HCl pH 8.0 was crystallised with 20% (w/v) polyethylene glycol (PEG) 2,000, 10 microM nickel chloride, 100 mM Tris-HCl pH 8.5 as reservoir solution

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.7→65.9 Å / Num. obs: 11454 / % possible obs: 100 % / Redundancy: 18.9 % / Biso Wilson estimate: 31.5 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.114 / Rrim(I) all: 0.117 / Net I/σ(I): 17.1
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 16.4 % / Rmerge(I) obs: 1.379 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 1771 / CC1/2: 0.83 / Rrim(I) all: 1.423 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: XXXX

Resolution: 1.7→65.9 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.959 / SU R Cruickshank DPI: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.118 / SU Rfree Blow DPI: 0.111 / SU Rfree Cruickshank DPI: 0.103
RfactorNum. reflection% reflectionSelection details
Rfree0.214 581 5.07 %RANDOM
Rwork0.177 ---
obs0.179 11454 100 %-
Displacement parametersBiso mean: 33 Å2
Baniso -1Baniso -2Baniso -3
1-1.9116 Å20 Å20 Å2
2--1.9116 Å20 Å2
3----3.8231 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: 1 / Resolution: 1.7→65.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms760 0 1 146 907
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.01790HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.121069HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d382SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes131HARMONIC5
X-RAY DIFFRACTIONt_it790HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.08
X-RAY DIFFRACTIONt_other_torsion2.68
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion113SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies2HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1019SEMIHARMONIC4
LS refinement shellResolution: 1.7→1.72 Å / Total num. of bins used: 29
RfactorNum. reflection% reflection
Rfree0.2915 -7.34 %
Rwork0.2887 366 -
all0.2889 395 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 25.8912 Å / Origin y: -13.7778 Å / Origin z: 4.0586 Å
111213212223313233
T-0.0483 Å20.0092 Å2-0.0337 Å2--0.0458 Å2-0.0156 Å2---0.0241 Å2
L1.9554 °2-0.393 °2-1.021 °2-1.5734 °2-0.154 °2--1.2694 °2
S0.0366 Å °0.087 Å °0.0834 Å °-0.0869 Å °-0.009 Å °0.0757 Å °-0.0645 Å °-0.1178 Å °-0.0276 Å °
Refinement TLS groupSelection details: {A|23 - 118}

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