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- PDB-6r7w: Tannerella forsythia mature mirolysin in complex with a cleaved p... -

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Basic information

Entry
Database: PDB / ID: 6r7w
TitleTannerella forsythia mature mirolysin in complex with a cleaved peptide.
Components
  • Mirolysin
  • Putative lipoprotein
KeywordsHYDROLASE / metallopeptidase zymogen / metzincin / pappalysin family / Tannerella forsythia / periodontopathogen / periodontal disease
Function / homology
Function and homology information


metallopeptidase activity / metal ion binding
Similarity search - Function
Peptidase M43, pregnancy-associated plasma-A / Pregnancy-associated plasma protein-A / Secretion system C-terminal sorting domain / Secretion system C-terminal sorting domain / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / ETHANOL / Mirolysin / Karilysin / Putative lipoprotein
Similarity search - Component
Biological speciesTannerella forsythia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsRodriguez-Banqueri, A. / Guevara, T. / Ksiazek, M. / Potempa, J. / Gomis-Ruth, F.X.
Citation
Journal: Iucrj / Year: 2020
Title: Structure-based mechanism of cysteine-switch latency and of catalysis by pappalysin-family metallopeptidases.
Authors: Guevara, T. / Rodriguez-Banqueri, A. / Ksiazek, M. / Potempa, J. / Gomis-Ruth, F.X.
#1: Journal: Biol.Chem. / Year: 2017
Title: Mirolysin, a LysargiNase from Tannerella forsythia, proteolytically inactivates the human cathelicidin, LL-37.
Authors: Koneru, L. / Ksiazek, M. / Waligorska, I. / Straczek, A. / Lukasik, M. / Madej, M. / Thogersen, I.B. / Enghild, J.J. / Potempa, J.
History
DepositionMar 29, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year
Revision 1.2Jan 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: Mirolysin
B: Putative lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1298
Polymers32,6992
Non-polymers4306
Water6,269348
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-66 kcal/mol
Surface area12560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.610, 66.490, 96.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Mirolysin


Mass: 30987.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Mature mirolysin spanning segment R55-S331. / Source: (gene. exp.) Tannerella forsythia (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0F7IPS1, UniProt: G8ULV1*PLUS
#2: Protein/peptide Putative lipoprotein /


Mass: 1712.084 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The citrate molecule mimics an amino acid left behind after substrate cleavage and was thus assigned the residue number -1.
Source: (gene. exp.) Tannerella forsythia (strain ATCC 43037 / JCM 10827 / FDC 338) (bacteria)
Strain: ATCC 43037 / JCM 10827 / FDC 338 / Gene: BFO_2662 / Production host: Escherichia coli (E. coli) / References: UniProt: G8ULV2

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Non-polymers , 5 types, 354 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-EOH / ETHANOL / Ethanol


Mass: 46.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O
#6: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 348 / Source method: isolated from a natural source / Formula: H2O

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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: 1.99 Å3/Da / Density % sol: 38.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: Crystals of the mirolysin product complex were obtained at an OD280 of 19.7 in 5 mM Tris-HCl pH 8.0, 50 mM sodium chloride, 5 mM calcium chloride at 4 degrees from drops containing 200 nL of ...Details: Crystals of the mirolysin product complex were obtained at an OD280 of 19.7 in 5 mM Tris-HCl pH 8.0, 50 mM sodium chloride, 5 mM calcium chloride at 4 degrees from drops containing 200 nL of protein solution and 100 nL of reservoir solution, which comprised 40% ethanol, 5% PEG 1000, 0.1 M phosphate-citrate buffer, pH 4.2.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.5→54.7 Å / Num. obs: 41508 / % possible obs: 97.6 % / Redundancy: 12.5 % / Biso Wilson estimate: 25.6 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.038 / Rrim(I) all: 0.04 / Net I/σ(I): 41.3
Reflection shellResolution: 1.5→1.59 Å / Num. unique obs: 6056

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6R7V

6r7v


Resolution: 1.5→54.7 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.967 / SU R Cruickshank DPI: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.071 / SU Rfree Blow DPI: 0.065 / SU Rfree Cruickshank DPI: 0.061
RfactorNum. reflection% reflectionSelection details
Rfree0.158 728 1.75 %RANDOM
Rwork0.144 ---
obs0.144 41508 97.6 %-
Displacement parametersBiso mean: 17.91 Å2
Baniso -1Baniso -2Baniso -3
1--1.7513 Å20 Å20 Å2
2--1.988 Å20 Å2
3----0.2368 Å2
Refine analyzeLuzzati coordinate error obs: 0.14 Å
Refinement stepCycle: 1 / Resolution: 1.5→54.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2239 0 22 348 2609
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012383HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.023249HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1115SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes434HARMONIC5
X-RAY DIFFRACTIONt_it2383HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.67
X-RAY DIFFRACTIONt_other_torsion2.74
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion317SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies1HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3172SEMIHARMONIC4
LS refinement shellResolution: 1.5→1.52 Å / Total num. of bins used: 36
RfactorNum. reflection% reflection
Rfree0.1878 -1.73 %
Rwork0.1491 1133 -
all0.1496 1153 -
obs--78.54 %
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)
10.4564-0.18380.24890.65-0.24970.7431-0.03360.02750.02010.0963-0.0197-0.0998-0.09860.07080.0533-0.0262-0.005-0.018-0.0280.005-0-1.40751.6111-17.4249
20-0.3663-0.30910.4316-0.64791.5975-0.00970.06450.0194-0.05880.0099-0.1094-0.1081-0.0022-0.00010.0047-0.0222-0.0044-0.0042-0.00120.0028-9.417512.5728-33.6086
30.39920.02370.24510.4004-0.25290.905-0.0101-0.0503-0.01730.06890.0063-0.0276-0.0368-0.01840.0038-0.00950.0028-0.007-0.02420.0027-0.0121-8.8183-2.1844-13.4177
40.6098-0.16230.12040.5549-0.0760.7129-0.01620.0261-0.0213-0.03130.01950.0347-0.0257-0.0769-0.0033-0.0038-0.00050.0032-0.00850.0036-0.0052-20.47694.2224-32.3335
54.2688-0.98470.22851.8175-0.52682.2832-0.1212-0.35940.30040.24960.0365-0.0972-0.408-0.0910.08470.08890.0302-0.0417-0.0482-0.0332-0.0494-9.84715.7649-7.3134
61.8742-0.9024-1.278110.58522.44582.3191-0.07940.1608-0.3795-0.4562-0.1076-0.05510.1187-0.24240.187-0.0142-0.04540.0144-0.0407-0.03310.0243-13.602-17.8897-30.4762
71.6748-3.78610.56780.746-1.53280.6369-0.0224-0.4765-0.01430.15430.0088-0.07470.5015-0.02210.01360.012-0.01360.00510.00740.01360.0091-18.8111-5.1651-20.6795
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|58 - 95}
2X-RAY DIFFRACTION2{A|96 - 117}
3X-RAY DIFFRACTION3{A|118 - 234 A|999 - 999}
4X-RAY DIFFRACTION4{A|235 - 307 A|997 - 998}
5X-RAY DIFFRACTION5{A|308 - 327}
6X-RAY DIFFRACTION6{B|1 - 14}
7X-RAY DIFFRACTION7{B|-1 - -1}

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