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- PDB-9fma: Structure of Porphyromonas gingivalis endopeptidase (PgPepO) -

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Basic information

Entry
Database: PDB / ID: 9fma
TitleStructure of Porphyromonas gingivalis endopeptidase (PgPepO)
ComponentsEndopeptidase PepO
KeywordsHYDROLASE / protease / Porphyromonas gingivalis
Function / homology
Function and homology information


protein processing / metalloendopeptidase activity / 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
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.76 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
DepositionJun 5, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 17, 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: Endopeptidase PepO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,7673
Polymers76,6391
Non-polymers1272
Water9,116506
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-34 kcal/mol
Surface area28230 Å2
Unit cell
Length a, b, c (Å)93.222, 93.222, 182.506
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-1050-

HOH

21A-1306-

HOH

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Components

#1: Protein Endopeptidase PepO


Mass: 76639.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Gene: pepO, PG_0159 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7MXL5
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 506 / Source method: isolated from a natural source / Formula: H2O
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: 2.59 Å3/Da / Density % sol: 52.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Tris pH=7.5, 0.2 M magnesium chloride, 40% (v/v) ethylene glycol, 15% (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: BESSY / Beamline: 14.1 / Wavelength: 1.282416 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.282416 Å / Relative weight: 1
ReflectionResolution: 1.76→46.61 Å / Num. obs: 80690 / % possible obs: 99.96 % / Redundancy: 14.4 % / Biso Wilson estimate: 27.81 Å2 / CC1/2: 0.99 / Net I/σ(I): 13.2
Reflection shellResolution: 1.76→1.823 Å / Num. unique obs: 7885 / CC1/2: 0.39

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.76→46.61 Å / SU ML: 0.2177 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.9707
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2144 2100 2.6 %
Rwork0.1877 78590 -
obs0.1884 80690 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.92 Å2
Refinement stepCycle: LAST / Resolution: 1.76→46.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5272 0 5 506 5783
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00515413
X-RAY DIFFRACTIONf_angle_d0.65837313
X-RAY DIFFRACTIONf_chiral_restr0.0441758
X-RAY DIFFRACTIONf_plane_restr0.0059962
X-RAY DIFFRACTIONf_dihedral_angle_d16.35062010
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.80.34211370.33495123X-RAY DIFFRACTION99.1
1.8-1.840.32971370.29545134X-RAY DIFFRACTION100
1.84-1.890.33741380.27515182X-RAY DIFFRACTION99.96
1.89-1.950.28841380.24795177X-RAY DIFFRACTION99.96
1.95-2.010.26961380.23135153X-RAY DIFFRACTION100
2.01-2.080.24321390.20995194X-RAY DIFFRACTION100
2.08-2.170.22761390.20225210X-RAY DIFFRACTION100
2.17-2.260.21131390.18255182X-RAY DIFFRACTION100
2.27-2.380.21321390.17685206X-RAY DIFFRACTION99.96
2.38-2.530.25181400.17975245X-RAY DIFFRACTION100
2.53-2.730.2251400.1885232X-RAY DIFFRACTION100
2.73-30.22261410.19375283X-RAY DIFFRACTION99.96
3-3.440.23121410.18525274X-RAY DIFFRACTION99.94
3.44-4.330.17121430.15495379X-RAY DIFFRACTION99.95
4.33-46.610.17261510.17235616X-RAY DIFFRACTION99.79
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)
10.322794601912-0.237927040291-0.5722438288790.1589416945850.3778348962751.55754133588-1.69812150257E-50.209362629018-0.1882153627950.05640870085660.04692700051090.11328438415-0.076536587605-0.188799541828-0.02494902078910.207219495134-0.003912748144120.04035118211690.2318603385180.00129310564560.36349672378438.714753892216.7519266961101.664972594
20.655889658714-0.135919660549-0.3839653877820.4250834574350.1630460493950.3787381986960.01884831901390.06009332858460.02445663600120.00135998045165-0.00667454521414-0.0501340464735-0.03288536675970.0102079140931-0.01455836724620.185803712347-0.01622654714620.008051983364940.25131963856-0.02041414173290.34906705843360.999242776233.275134721378.9479174262
31.28212035512-0.6726820138210.1903497145451.42779548175-0.6633738365631.2802731209-0.03626615054980.0582790138316-0.0762355122385-0.0412511372657-0.0278927624773-0.1784867827040.05326748755150.1156730716340.001834820324010.171462887815-0.03037958882810.04806390918040.265509055036-0.0792111568520.36226078797874.405835391620.619668880970.955862906
40.4099693650030.395706028501-0.08383928916290.9249685037780.3952943356380.999051926140.01903984232150.1059097765320.0573804427659-0.0218101628568-0.04032173625180.0756721881535-0.12531498246-0.14251888317-0.01262948335660.195318210080.0132307225903-0.007319762240950.25836451106-0.02025164738470.32823924345453.205887548933.795662645676.2635234005
51.63276310636-1.886518928590.3172685257287.48671072119-2.373187598272.91184383631-0.177610100552-0.333410244158-0.07724196056340.7655715775930.0464256625159-0.111630450485-0.2938909825820.06421429540220.03222228954250.135791946718-0.0297129475042-0.04542632420650.295427876973-0.02019267657250.30008675641263.325237987625.1388981064109.733545295
61.08441155109-0.511335181760.1492991712062.052398798-0.4783468737661.775599131060.00106041198299-0.0906161839489-0.02341885920350.362305957755-0.154584331267-0.352798041486-0.000212191343960.3130655180130.22026381990.108643583422-0.0030344481442-0.008800903870950.337740037154-0.0207326757010.38038284011972.051565119523.5959279088100.633448001
70.2792412472190.450243529139-0.30605280010.590571497954-0.5517834951950.6046769506050.0565336551312-0.0547953123743-0.03136537652550.06892087862-0.0579654392503-0.143419326833-0.06344967104660.1457601340210.007847843805430.1967516815330.00763128945126-0.001928202354160.252190855215-0.01873166041630.36449457772267.45856155523.660790254897.7674968924
83.11431829031-0.696595390124-0.3556233602251.60848759313-0.151164689311.0400408558-0.132999703722-0.143772897404-0.2946832722750.06168090316950.0669164606863-0.01140093923660.2399195842350.2299366222620.07160759740720.195411201662-3.97917404959E-50.03000032665650.1259809536710.004843459739610.38747650575755.35264494886.45660940795102.226875138
91.18151493022-0.350299461755-0.08856393224281.45893128935-0.3910046130411.58335981566-0.1326715241970.0718212021446-0.3184753580480.03850768628620.0211496859664-0.01425042237240.2327899262540.02590294894740.09622053202120.215645461474-0.02008250242720.06335101478470.207843574072-0.06600335691560.3938912656249.62752276886.06329044296.4059988059
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 13 through 52 )13 - 521 - 40
22chain 'A' and (resid 53 through 201 )53 - 20141 - 189
33chain 'A' and (resid 202 through 287 )202 - 287190 - 275
44chain 'A' and (resid 288 through 343 )288 - 343276 - 331
55chain 'A' and (resid 344 through 382 )344 - 382332 - 370
66chain 'A' and (resid 383 through 423 )383 - 423371 - 411
77chain 'A' and (resid 424 through 525 )424 - 525412 - 513
88chain 'A' and (resid 526 through 605 )526 - 605514 - 593
99chain 'A' and (resid 606 through 664 )606 - 664594 - 652

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