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- PDB-6r7u: Selenomethionine variant of Tannerella forsythia promirolysin mut... -

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Basic information

Entry
Database: PDB / ID: 6r7u
TitleSelenomethionine variant of Tannerella forsythia promirolysin mutant E225A
ComponentsMirolysin
KeywordsHYDROLASE / metallopeptidase zymogen / metzincin / pappalysin family / Tannerella forsythia / periodontopathogen / peridontal disease
Function / homology
Function and homology information


metallopeptidase activity / proteolysis / 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 / Metallopeptidase, catalytic domain superfamily
Similarity search - Domain/homology
BORIC ACID / Mirolysin / Karilysin
Similarity search - Component
Biological speciesTannerella forsythia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mirolysin
B: Mirolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,44113
Polymers71,7202
Non-polymers72111
Water8,017445
1
A: Mirolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2827
Polymers35,8601
Non-polymers4226
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mirolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1606
Polymers35,8601
Non-polymers2995
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.780, 79.210, 75.500
Angle α, β, γ (deg.)90.00, 106.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Mirolysin


Mass: 35860.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Extra N-terminal residues glycine-proline result from the cloning strategy. The N-terminal cysteine is oxidized to S-oxy cysteine.
Source: (gene. exp.) Tannerella forsythia (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0F7IPS1, UniProt: G8ULV1*PLUS

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Non-polymers , 5 types, 456 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 65.409 Da / Num. of mol.: 2 / 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: Chemical ChemComp-BO3 / BORIC ACID / Boric acid


Mass: 61.833 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BH3O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 445 / 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: 1.93 Å3/Da / Density % sol: 36.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Selenomethionine-derivatized 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 ...Details: Selenomethionine-derivatized 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: 1.2815 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: 1.2815 Å / Relative weight: 1
ReflectionResolution: 1.6→53.4 Å / Num. obs: 70233 / % possible obs: 99.1 % / Redundancy: 4.8 % / Biso Wilson estimate: 18.78 Å2 / Net I/σ(I): 10.9
Reflection shellResolution: 1.6→1.7 Å / Mean I/σ(I) obs: 2.4 / Num. unique obs: 11622

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CKI

2cki


Resolution: 1.6→44.97 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.915 / SU R Cruickshank DPI: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.101 / SU Rfree Blow DPI: 0.099 / SU Rfree Cruickshank DPI: 0.098
RfactorNum. reflection% reflectionSelection details
Rfree0.22 688 0.98 %RANDOM
Rwork0.186 ---
obs0.186 70232 99 %-
Displacement parametersBiso mean: 21.74 Å2
Baniso -1Baniso -2Baniso -3
1--4.7316 Å20 Å20.5843 Å2
2--6.8326 Å20 Å2
3----2.101 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: 1 / Resolution: 1.6→44.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4856 0 48 445 5349
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0125085HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.146914HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2370SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes914HARMONIC5
X-RAY DIFFRACTIONt_it5085HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.35
X-RAY DIFFRACTIONt_other_torsion2.84
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion671SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies14HARMONIC1
X-RAY DIFFRACTIONt_utility_distance38HARMONIC1
X-RAY DIFFRACTIONt_utility_angle14HARMONIC1
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6629SEMIHARMONIC4
LS refinement shellResolution: 1.6→1.62 Å / Total num. of bins used: 34
RfactorNum. reflection% reflection
Rfree0.437 -1.06 %
Rwork0.4424 2044 -
all0.4424 2066 -
obs--98.63 %
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)
11.2341-0.94741.24931.01881.62224.7979-0.02890.1402-0.1279-0.0353-0.0850.19230.5055-0.43950.11390.0871-0.00220.00710.1861-0.03320.124-10.369232.478662.9382
20.97540.471-0.22210.7914-0.33620.3854-0.0695-0.0352-0.05950.07970.01-0.04460.02740.02110.0595-0.1364-0.00180.0351-0.00930.0012-0.0497.812843.279579.503
31.7461-0.57970.72.6863-0.92271.4554-0.0274-0.11940.15270.1345-0.03330.0654-0.109-0.05320.0608-0.03280.0240.05260.0983-0.0080.0349-10.633652.257781.1562
40.5696-0.08940.1630.9646-0.02110.5744-0.00920.05160.0074-0.03730.0208-0.06890.05190.0115-0.0116-0.0874-0.00310.04290.04550.00260.01277.853438.758271.949
50.6291-0.04480.03561.4561-0.40080.51650.010.03310.0414-0.02540.00670.1273-0.0325-0.047-0.0167-0.1078-0.00710.03230.0433-0.00490.0195-11.665549.703267.4608
64.8139-0.75811.14541.3728-1.55412.2968-0.0367-0.1596-0.10240.14550.11970.16190.0523-0.0769-0.0830.0360.00120.06650.05840.02390.0874-1.411228.279784.5968
71.87131.109-0.29713.7421-3.43872.04780.1695-0.0583-0.00420.1017-0.3856-0.4399-0.44630.37540.21610.0817-0.05830.01160.2280.04880.156729.554760.213934.4751
81.10720.34020.81771.01510.33181.78050.0004-0.0009-0.04580.06660.01070.1148-0.0655-0.0731-0.0111-0.14550.00680.0412-0.04760.001-0.09494.971249.97239.5067
91.4409-0.6317-0.31661.61070.42621.3296-0.0434-0.1638-0.23910.3016-0.02860.00010.0136-0.02740.072-0.0166-0.00860.02480.03510.00720.007819.727539.249.9388
100.828-0.16580.15740.8863-0.16170.41270.02450.06260.0103-0.059-0.01270.053-0.0299-0.0097-0.0118-0.01440.00580.02750.0548-0.00770.00768.882254.586233.2993
110.5661-0.25430.14631.7240.14540.56030.01130.0495-0.03380.0694-0.0528-0.117-0.00870.11490.0415-0.0655-0.01450.01550.05920.00940.004827.438542.403938.8844
124.80760.740.30680.47360.43221.5369-0.0182-0.20660.15420.24260.02320.1718-0.2022-0.0761-0.0050.0737-0.00220.03740.0323-0.02540.044110.421364.007349.8645
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}
7X-RAY DIFFRACTION7{B|21 - 56}
8X-RAY DIFFRACTION8{B|57 - 95}
9X-RAY DIFFRACTION9{B|96 - 117}
10X-RAY DIFFRACTION10{B|118 - 234 B|999 - 999}
11X-RAY DIFFRACTION11{B|235 - 307 B|997 - 998}
12X-RAY DIFFRACTION12{B|308 - 328}

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