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- PDB-6r7v: Tannerella forsythia promirolysin mutant E225A -

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Basic information

Entry
Database: PDB / ID: 6r7v
TitleTannerella forsythia promirolysin mutant E225A
ComponentsMirolysin
KeywordsHYDROLASE / metallopeptidase zymogen / metzincin / pappalysin family / Tannerella forsythia / periodontopathogen / periodontal disease
Function / homologyPeptidase M43, pregnancy-associated plasma-A / Pregnancy-associated plasma protein-A / Secretion system C-terminal sorting domain / Secretion system C-terminal sorting domain / Metallopeptidase, catalytic domain superfamily / metallopeptidase activity / metal ion binding / Mirolysin / Karilysin
Function and homology information
Biological speciesTannerella forsythia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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.title / _citation.year
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mirolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8898
Polymers35,3751
Non-polymers5147
Water4,936274
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-24 kcal/mol
Surface area13190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.330, 67.250, 79.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Mirolysin


Mass: 35375.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Extra N-terminal residues glycine-proline result from the cloning strategy.
Source: (gene. exp.) Tannerella forsythia (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0F7IPS1, UniProt: G8ULV1*PLUS
#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 274 / 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: 1.79 Å3/Da / Density % sol: 31.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Promirolysin crystals were obtained at 20 degrees from drops containing 200 nL of protein solution at 0.6 mg/mL in 5 mM Tris-HCl pH 8.0, 50 mM sodium chloride and 100 nL of reservoir ...Details: Promirolysin crystals were obtained at 20 degrees from drops containing 200 nL of protein solution at 0.6 mg/mL in 5 mM Tris-HCl pH 8.0, 50 mM sodium chloride and 100 nL of reservoir solution, which comprised 25% PEG 1500, 0.1 M MIB buffer (malonic acid, imidazole and boric acid at a 2:3:3 molar ratio), 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: 1.2816 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2816 Å / Relative weight: 1
ReflectionResolution: 1.4→51.4 Å / Num. obs: 50157 / % possible obs: 98.7 % / Redundancy: 9.7 % / Biso Wilson estimate: 19.77 Å2 / Net I/σ(I): 13.8
Reflection shellResolution: 1.4→1.48 Å / Mean I/σ(I) obs: 1.8 / Num. unique obs: 7077

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6R7U

6r7u


Resolution: 1.4→20.34 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.96 / SU R Cruickshank DPI: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.064 / SU Rfree Blow DPI: 0.065 / SU Rfree Cruickshank DPI: 0.062
RfactorNum. reflection% reflectionSelection details
Rfree0.188 722 1.44 %RANDOM
Rwork0.161 ---
obs0.161 50134 98.7 %-
Displacement parametersBiso mean: 25.37 Å2
Baniso -1Baniso -2Baniso -3
1-1.731 Å20 Å20 Å2
2---0.2615 Å20 Å2
3----1.4696 Å2
Refine analyzeLuzzati coordinate error obs: 0.16 Å
Refinement stepCycle: 1 / Resolution: 1.4→20.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2430 0 27 274 2731
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012565HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.013492HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1206SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes466HARMONIC5
X-RAY DIFFRACTIONt_it2565HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.38
X-RAY DIFFRACTIONt_other_torsion2.8
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion340SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies11HARMONIC1
X-RAY DIFFRACTIONt_utility_distance2HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3293SEMIHARMONIC4
LS refinement shellResolution: 1.4→1.42 Å / Total num. of bins used: 36
RfactorNum. reflection% reflection
Rfree0.258 -1.22 %
Rwork0.3006 1376 -
all0.3001 1393 -
obs--84.77 %
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)
11.2864-0.6914-0.98562.80881.17272.27780.13740.10350.1457-0.46680.1033-0.4104-0.07990.1326-0.24070.1385-0.00090.04810.1295-0.01090.217752.098731.88648.0495
20.43310.3884-0.01071.68340.16990.6977-0.0327-0.03840.0592-0.0314-0.01330.1995-0.0008-0.07510.046-0.0946-0.0072-0.0067-0.0553-0.0003-0.0427.792436.817118.4563
30.37230.30850.56751.85160.00361.02220.029-0.1580.19970.1498-0.0255-0.036-0.05820.0114-0.0035-0.00430.0008-0.01290.0216-0.0148-0.032842.910746.70729.5161
40.79970.35030.28570.70280.04840.8535-0.02160.0433-0.0864-0.0520.0349-0.00870.084-0.0516-0.01330.014-0.01310.00250.0198-0.00210.018731.673130.864513.3424
51.00210.09210.35651.8834-0.29211.03950.0593-0.0311-0.12730.1631-0.009-0.2810.00440.0364-0.0503-0.0256-0.0077-0.034-0.03250.00420.031750.314636.093525.6427
67.02791.97040.1922.8083-0.63452.5085-0.25210.46690.69-0.36480.19330.1914-0.27150.0390.05880.2343-0.0559-0.04540.16260.05990.09532.621847.61024.727
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|21 - 56}
2X-RAY DIFFRACTION2{A|57 - 95}
3X-RAY DIFFRACTION3{A|96 - 117}
4X-RAY DIFFRACTION4{A|118 - 234 A|999 - 999}
5X-RAY DIFFRACTION5{A|235 - 307 A|997 - 998}
6X-RAY DIFFRACTION6{A|308 - 327}

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