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- PDB-9eyg: Structure of Tannerella forsythia endopeptidase O (TfPepO) -

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Basic information

Entry
Database: PDB / ID: 9eyg
TitleStructure of Tannerella forsythia endopeptidase O (TfPepO)
ComponentsPeptidase family M13
KeywordsHYDROLASE / protease Tannerella forsythia
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / metalloendopeptidase activity / protein processing / metal ion binding / plasma membrane
Similarity search - Function
Peptidase M13 / Peptidase M13, N-terminal domain / Peptidase M13, C-terminal domain / Peptidase M13, domain 2 / Peptidase family M13 / Peptidase family M13 / Neprilysin-like (M13) protease domain profile. / Metallopeptidase, catalytic domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
IMIDAZOLE / DI(HYDROXYETHYL)ETHER / Peptidase family M13
Similarity search - Component
Biological speciesTannerella forsythia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsZak, K.M. / Grudnik, P. / Waligorska, I. / Ksiazek, M.
Funding support Poland, 2items
OrganizationGrant numberCountry
Polish National Science CentreUMO-2019/35/B/NZ1/03118 Poland
Polish National Science CentreUMO-2018/31/N/NZ1/02891 Poland
CitationJournal: To Be Published
Title: Structure of Tannerella forsythia endopeptidase O (TfPepO)
Authors: Zak, K. / Waligorska, I. / Ksiazek, M.
History
DepositionApr 9, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptidase family M13
B: Peptidase family M13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,87535
Polymers149,3362
Non-polymers2,53933
Water14,394799
1
A: Peptidase family M13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,36122
Polymers74,6681
Non-polymers1,69321
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peptidase family M13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,51513
Polymers74,6681
Non-polymers84712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.414, 95.414, 301.900
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 28 through 62 or resid 66...
d_2ens_1(chain "B" and (resid 28 through 66 or resid 68...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ASPASPTHRTHRAA28 - 623 - 37
d_12SERSERSERSERAA6641
d_13PHEPHEASPASPAA68 - 11243 - 87
d_14THRTHRGLUGLUAA114 - 21789 - 192
d_15ALAALAASPASPAA219 - 355194 - 330
d_16LEULEUHISHISAA357 - 383332 - 358
d_17LEULEUVALVALAA385 - 445360 - 420
d_18PHEPHEGLUGLUAA447 - 451422 - 426
d_19LEULEUILEILEAA453 - 483428 - 458
d_110PHEPHEGLUGLUAA485 - 515460 - 490
d_111THRTHRGLUGLUAA517 - 575492 - 550
d_112LEULEUALAALAAA577 - 578552 - 553
d_113TYRTYRALAALAAA580 - 638555 - 613
d_114GLYGLYILEILEAA640 - 676615 - 651
d_115PEGPEGPEGPEGAD702
d_116EDOEDOEDOEDOAE703
d_117EDOEDOEDOEDOAG705
d_118EDOEDOEDOEDOAH706
d_119EDOEDOEDOEDOAI707
d_120EDOEDOEDOEDOAJ708
d_121EDOEDOEDOEDOAK709
d_21ASPASPSERSERBB28 - 663 - 41
d_22PHEPHEASPASPBB68 - 11243 - 87
d_23THRTHRGLUGLUBB114 - 21789 - 192
d_24ALAALAASPASPBB219 - 355194 - 330
d_25LEULEUHISHISBB357 - 383332 - 358
d_26LEULEUVALVALBB385 - 445360 - 420
d_27PHEPHEGLUGLUBB447 - 451422 - 426
d_28LEULEUILEILEBB453 - 483428 - 458
d_29PHEPHEGLUGLUBB485 - 515460 - 490
d_210THRTHRGLUGLUBB517 - 575492 - 550
d_211LEULEUALAALABB577 - 578552 - 553
d_212TYRTYRALAALABB580 - 638555 - 613
d_213GLYGLYILEILEBB640 - 676615 - 651
d_214PEGPEGPEGPEGBY702
d_215EDOEDOEDOEDOBZ703
d_216EDOEDOEDOEDOBBA705
d_217EDOEDOEDOEDOBCA706
d_218EDOEDOEDOEDOBDA707
d_219EDOEDOEDOEDOBEA708
d_220EDOEDOEDOEDOBFA709

NCS oper: (Code: givenMatrix: (-0.994546595776, 0.0613502061254, 0.0843399136764), (0.0532694356421, 0.994057337369, -0.0949335412183), (-0.0896629023451, -0.08992309064, -0.991904431744)Vector: 98. ...NCS oper: (Code: given
Matrix: (-0.994546595776, 0.0613502061254, 0.0843399136764), (0.0532694356421, 0.994057337369, -0.0949335412183), (-0.0896629023451, -0.08992309064, -0.991904431744)
Vector: 98.2180146351, -6.38082911949, -48.8032429666)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Peptidase family M13


Mass: 74667.953 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tannerella forsythia (bacteria) / Gene: BFO_0011 / Production host: Escherichia coli (E. coli)
References: UniProt: G8UQE9, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases

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Non-polymers , 6 types, 832 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H5N2
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 799 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: 2.67 Å3/Da / Density % sol: 53.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.3 M sodium fluoride, 0.3 M sodium bromide, 0.3 M sodium iodide, 0.1M buffer system containing imidazole / MES mix, 40% (v/v) ethylene glycol, 20% (w/v) PEG 8000, pH=6.5

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→48.8 Å / Num. obs: 148384 / % possible obs: 99.96 % / Redundancy: 9.3 % / Biso Wilson estimate: 29.81 Å2 / Rmerge(I) obs: 0.07979 / Net I/σ(I): 16.92
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 9.5 % / Rmerge(I) obs: 1.132 / Num. unique obs: 14612 / % possible all: 99.99

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
Aimlessdata scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→48.75 Å / SU ML: 0.2543 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.4448
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2233 7428 5.01 %RANDOM
Rwork0.1941 140940 --
obs0.1955 148368 99.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.59 Å2
Refinement stepCycle: LAST / Resolution: 1.8→48.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10482 0 153 799 11434
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008910982
X-RAY DIFFRACTIONf_angle_d0.972714815
X-RAY DIFFRACTIONf_chiral_restr0.05841536
X-RAY DIFFRACTIONf_plane_restr0.00851925
X-RAY DIFFRACTIONf_dihedral_angle_d16.12724086
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 2.8778499016 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.41882580.37894579X-RAY DIFFRACTION100
1.82-1.840.36882430.33634675X-RAY DIFFRACTION99.98
1.84-1.860.34542610.31194596X-RAY DIFFRACTION99.98
1.86-1.890.33292600.2864602X-RAY DIFFRACTION99.98
1.89-1.910.36022310.30384694X-RAY DIFFRACTION99.94
1.91-1.940.32012320.28734637X-RAY DIFFRACTION99.88
1.94-1.970.25172600.24084650X-RAY DIFFRACTION99.98
1.97-20.29132570.23384611X-RAY DIFFRACTION100
2-2.030.27372540.22944679X-RAY DIFFRACTION99.96
2.03-2.060.25542650.23464618X-RAY DIFFRACTION100
2.06-2.10.29322410.26284619X-RAY DIFFRACTION99.94
2.1-2.130.29522490.23554668X-RAY DIFFRACTION100
2.13-2.180.22062270.20814751X-RAY DIFFRACTION100
2.18-2.220.2392480.24652X-RAY DIFFRACTION99.98
2.22-2.270.23132100.21084654X-RAY DIFFRACTION99.98
2.27-2.320.2312660.2054651X-RAY DIFFRACTION99.96
2.32-2.380.23972690.19494688X-RAY DIFFRACTION99.96
2.38-2.440.24092160.1944692X-RAY DIFFRACTION100
2.44-2.510.22892390.19964722X-RAY DIFFRACTION99.98
2.51-2.60.24182550.19474629X-RAY DIFFRACTION100
2.6-2.690.22422470.20164700X-RAY DIFFRACTION99.96
2.69-2.80.25412810.21144715X-RAY DIFFRACTION99.98
2.8-2.920.23212330.20314683X-RAY DIFFRACTION100
2.92-3.080.22862790.20084749X-RAY DIFFRACTION99.98
3.08-3.270.22052380.19694710X-RAY DIFFRACTION99.98
3.27-3.520.21712340.18934773X-RAY DIFFRACTION99.96
3.52-3.880.18692190.16114761X-RAY DIFFRACTION99.88
3.88-4.440.17222350.14854824X-RAY DIFFRACTION100
4.44-5.590.18252610.15174882X-RAY DIFFRACTION100
5.59-48.750.1732600.17275076X-RAY DIFFRACTION99.83
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)
10.877802542269-0.7565103299171.103558836090.878597103281-0.8200764019080.944976264832-0.0109011074693-0.1907023671240.1369433950950.2299129390650.0269714280902-0.149380457522-0.117095607388-0.0578984215122-0.04020978136870.331190964029-0.03458967067630.009279516038230.31867331651-0.0048016348390.34117352756751.6906617215-1.22001751480.594828402767
21.07015591521-0.0131684941479-0.3093718617981.232433303020.1547970665810.9579808610610.0897375074191-0.0417345976874-0.052814881723-0.0398551667799-0.007100828092160.02010412387690.062596200044-0.0529258767919-0.07700655769740.1735289802360.00181170272892-0.01486390598630.212773137134-0.004454283408920.23730619956916.6704042092-5.319833669-11.0345990051
30.548179117295-0.271654085551-0.06845282067451.11777632673-0.7185348518420.8652124998550.1001597509110.1133160887690.0576404450118-0.125786269053-0.219880818295-0.1411651379690.1460342985170.03290225132670.1086231782350.288802754486-0.01650258294120.02219964072290.2387120140950.005661033216160.18350312459850.951588005-16.7698001255-14.9382423857
40.431289434449-0.9428855744660.2205952549660.824025493228-0.4370600618320.272154540550.1095696968650.07885800887380.1032499348860.0242114554226-0.1601881987080.05316106908290.114156324643-0.004849168441910.04919428446810.285114216962-0.03495667520460.007371043959950.2637248023510.01539925439120.24346411336444.244022342-16.7969582391-11.5029480466
51.262583485790.5246876274350.1809547717182.098956618420.3720238568312.293122594530.025541880276-0.2463922590570.01851683061120.234395284156-0.141177296103-0.06992172777210.177719559916-0.1224065421680.1072320710830.229862203835-0.0160987041489-0.02605263693330.2048617667310.01948383673110.18004677477456.8899659002-25.09460429128.56683700997
60.3828045290970.8494761887261.20926723560.9944186078241.564424391940.97713506647-0.069720979930.08273037981860.0163742358611-0.187592969539-0.01232079862380.051764373712-0.2097004825990.03185775729060.05342537292230.3567793362720.06294966962470.02940439838950.3698271141950.02622359029580.28905904711145.7793927577-5.18116400783-53.3388824897
71.3141268342-0.2770035004230.01908851486561.3506863242-0.2434275503710.994881825520.08250504422670.136914767291-0.167553691797-0.0169940590671-0.0560462416873-0.0860397311580.1640839955610.117738679044-0.02458663062380.2206127365330.0642325325248-0.02269480202670.230926062333-0.002868536569090.22756331358680.2382851976-9.45469770599-38.9907850674
80.1257817163020.4704235863890.1586006309380.6636190798050.5809799372960.4160427848960.0494345813743-0.0348396302537-0.01570734516090.156954302912-0.132564107704-0.01395748901850.2609139214470.01682226182020.0768853521710.3694542001070.0579017625620.05031839086870.2214455368530.004703069600480.2238640298949.0251677447-19.3794412923-38.5222730487
91.91282293909-0.9489448801660.02977754173762.209333120280.06299714654772.454515014810.03289412903840.23842940861-0.005363152351590.0567873598858-0.1548432173530.07056616414430.1977901001680.1152756728170.1059782890830.2059949248510.0305426547370.03622021529280.196240952952-0.02345768939720.16969743209940.8185417079-29.2270453928-60.0850227983
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 28 through 111 )AA28 - 1111 - 84
22chain 'A' and (resid 112 through 356 )AA112 - 35685 - 329
33chain 'A' and (resid 357 through 436 )AA357 - 436330 - 409
44chain 'A' and (resid 437 through 538 )AA437 - 538410 - 511
55chain 'A' and (resid 539 through 677 )AA539 - 677512 - 650
66chain 'B' and (resid 26 through 110 )BR26 - 1101 - 82
77chain 'B' and (resid 111 through 356 )BR111 - 35683 - 328
88chain 'B' and (resid 357 through 538 )BR357 - 538329 - 510
99chain 'B' and (resid 539 through 677 )BR539 - 677511 - 649

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