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- PDB-8ehe: Structure of Tannerella forsythia potempin C in complex with mirolase -

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Basic information

Entry
Database: PDB / ID: 8ehe
TitleStructure of Tannerella forsythia potempin C in complex with mirolase
Components
  • Mirolase
  • Potempin C (PotC)
KeywordsHYDROLASE INHIBITOR / Serine-peptidase inhibitor / HYDROLASE
Function / homology
Function and homology information


serine-type endopeptidase activity / proteolysis
Similarity search - Function
PKD-like domain / PKD-like domain / Secretion system C-terminal sorting domain / Secretion system C-terminal sorting domain / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Peptidase S8, subtilisin-related / Peptidase S8/S53 domain superfamily ...PKD-like domain / PKD-like domain / Secretion system C-terminal sorting domain / Secretion system C-terminal sorting domain / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Peptidase S8, subtilisin-related / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain
Similarity search - Domain/homology
Mirolase / Lipoprotein
Similarity search - Component
Biological speciesTannerella forsythia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsGomis-Ruth, F.X.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: 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.
History
DepositionSep 14, 2022Deposition site: RCSB / Processing site: RCSB
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.year / _citation_author.identifier_ORCID
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mirolase
B: Potempin C (PotC)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,69419
Polymers54,5702
Non-polymers1,12417
Water13,547752
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-70 kcal/mol
Surface area18750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.650, 113.360, 50.200
Angle α, β, γ (deg.)90.00, 112.69, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Mirolase


Mass: 37594.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tannerella forsythia (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0A7KVG3
#2: Protein Potempin C (PotC)


Mass: 16974.893 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tannerella forsythia (bacteria) / Gene: CLI86_13365, TFUB20_02175 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1D3UUC0

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Non-polymers , 5 types, 769 molecules

#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 752 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.2 Å3/Da / Density % sol: 43.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: The PotC:mirolase complex at 10 mg/mL in 2 mM calcium chloride, 50 mM sodium chloride, 5 mM Tris-HCl pH 8.0 was crystallised from 19 % (w/v) PEG 2,000 MME in 100 mM of a mixture of succinic ...Details: The PotC:mirolase complex at 10 mg/mL in 2 mM calcium chloride, 50 mM sodium chloride, 5 mM Tris-HCl pH 8.0 was crystallised from 19 % (w/v) PEG 2,000 MME in 100 mM of a mixture of succinic acid, sodium dihydrogen phosphate, and glycine at molar ratios 2:7:7, pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.1→56.7 Å / Num. obs: 184353 / % possible obs: 96.9 % / Redundancy: 6.3 % / Biso Wilson estimate: 13.8 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.052 / Rrim(I) all: 0.057 / Net I/σ(I): 18.2
Reflection shellResolution: 1.1→1.17 Å / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 26672 / CC1/2: 0.79 / Rrim(I) all: 0.74 / % possible all: 83

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ST3

1st3


Resolution: 1.1→42.87 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.978 / SU R Cruickshank DPI: 0.027 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.028 / SU Rfree Blow DPI: 0.028 / SU Rfree Cruickshank DPI: 0.026
RfactorNum. reflection% reflectionSelection details
Rfree0.148 761 41 %RANDOM
Rwork0.139 ---
obs0.139 184352 97 %-
Displacement parametersBiso mean: 14.46 Å2
Baniso -1Baniso -2Baniso -3
1-1.4873 Å20 Å2-1.0524 Å2
2--1.1293 Å20 Å2
3----2.6166 Å2
Refine analyzeLuzzati coordinate error obs: 0.11 Å
Refinement stepCycle: 1 / Resolution: 1.1→42.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3618 0 71 752 4441
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0087689HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0213886HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2112SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes120HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1193HARMONIC5
X-RAY DIFFRACTIONt_it7689HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion5.22
X-RAY DIFFRACTIONt_other_torsion2.65
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion527SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies27HARMONIC1
X-RAY DIFFRACTIONt_utility_distance1HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9503SEMIHARMONIC4
LS refinement shellResolution: 1.1→1.13 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2597 -46 %
Rwork0.2237 9898 -
all0.2238 9944 -
obs--71 %
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)
10.3275-0.0754-0.0070.3412-0.02640.22970.0039-0.01350.01220.0353-0.0144-0.0147-0.01530.00880.01050.0028-0.0069-0.00370.00150.00020.016315.745827.932430.5022
20.3846-0.1057-0.00180.7738-0.00770.1850.02390.03850.0333-0.0749-0.0401-0.0466-0.0117-0.0150.01610.02790.00720.01210.0141-0.00170.038810.182549.94939.6875
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|183 - 535 A|993 - 999}
2X-RAY DIFFRACTION2{B|24 - 147}

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