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- PDB-9kn2: Crystallization of zinc metalloproteinase PepO from Porphyromonas... -

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Basic information

Entry
Database: PDB / ID: 9kn2
TitleCrystallization of zinc metalloproteinase PepO from Porphyromonas gingivalis
ComponentsEndopeptidase PepO
KeywordsMETAL BINDING PROTEIN / zinc metalloproteinase / Inhibitor / Complex / Peptidase M13 family
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
Chem-RDF / Endopeptidase PepO
Similarity search - Component
Biological speciesPorphyromonas gingivalis W83 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsFeng, C.Y. / Feng, C.Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2025
Title: Structural and biochemical characterization of a zinc metallopeptidase from Porphyromonas gingivalis.
Authors: Feng, C. / Yu, W. / Jiang, Y. / Xia, R.
History
DepositionNov 18, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 1, 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)77,1665
Polymers76,3651
Non-polymers8014
Water17,348963
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.190, 121.190, 199.018
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-804-

HOH

21A-1585-

HOH

31A-1726-

HOH

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Components

#1: Protein Endopeptidase PepO / PHOSPHORAMIDON


Mass: 76364.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis W83 (bacteria)
Gene: pepO, PG_0159
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q7MXL5
#2: Chemical ChemComp-RDF / N-ALPHA-L-RHAMNOPYRANOSYLOXY(HYDROXYPHOSPHINYL)-L-LEUCYL-L-TRYPTOPHAN / PHOSPHORAMIDON


Type: peptide-like / Mass: 543.504 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H34N3O10P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 963 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 4.78 Å3/Da / Density % sol: 74.29 %
Crystal growTemperature: 287.15 K / Method: vapor diffusion, hanging drop / Details: 2.4 M ammonium sulfate, 0.1 M HEPES pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 4, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.04→31.84 Å / Num. obs: 92725 / % possible obs: 98.42 % / Redundancy: 20.4 % / Rmerge(I) obs: 0.128 / Net I/σ(I): 14.2
Reflection shellResolution: 2.04→2.12 Å / Rmerge(I) obs: 0.836 / Mean I/σ(I) obs: 5.6 / Num. unique obs: 8111 / % possible all: 87.24

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
MLPHAREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.04→31.84 Å / SU ML: 0.1739 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.843
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1901 4579 4.94 %
Rwork0.1639 88146 -
obs0.1652 92725 98.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.59 Å2
Refinement stepCycle: LAST / Resolution: 2.04→31.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5263 0 48 963 6274
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01025429
X-RAY DIFFRACTIONf_angle_d0.99047338
X-RAY DIFFRACTIONf_chiral_restr0.0562762
X-RAY DIFFRACTIONf_plane_restr0.0097956
X-RAY DIFFRACTIONf_dihedral_angle_d6.8642723
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.04-2.070.2515880.20411888X-RAY DIFFRACTION63.82
2.07-2.090.24911630.19822908X-RAY DIFFRACTION98.94
2.09-2.120.21211620.18542902X-RAY DIFFRACTION98.93
2.12-2.140.20751450.18542915X-RAY DIFFRACTION99.06
2.14-2.170.24421260.18262940X-RAY DIFFRACTION99.16
2.17-2.20.21071330.17312945X-RAY DIFFRACTION99.16
2.2-2.230.18981390.16642900X-RAY DIFFRACTION99.15
2.23-2.270.21971510.17442938X-RAY DIFFRACTION99.26
2.27-2.30.22971540.17152939X-RAY DIFFRACTION99.55
2.3-2.340.19881410.17012956X-RAY DIFFRACTION99.39
2.34-2.380.23161680.17342935X-RAY DIFFRACTION99.52
2.38-2.420.19211850.17522903X-RAY DIFFRACTION99.52
2.42-2.470.20711560.17482920X-RAY DIFFRACTION99.55
2.47-2.520.20831640.1732944X-RAY DIFFRACTION99.46
2.52-2.570.21331540.17872944X-RAY DIFFRACTION99.77
2.57-2.630.21691640.17892964X-RAY DIFFRACTION99.59
2.63-2.70.19981460.1822952X-RAY DIFFRACTION99.68
2.7-2.770.21021410.17942976X-RAY DIFFRACTION99.71
2.77-2.850.21911560.18032968X-RAY DIFFRACTION99.81
2.85-2.950.18311630.17642965X-RAY DIFFRACTION99.84
2.95-3.050.20331420.17822981X-RAY DIFFRACTION99.87
3.05-3.170.19921450.17613005X-RAY DIFFRACTION99.81
3.17-3.320.18631730.16942960X-RAY DIFFRACTION99.94
3.32-3.490.18061590.16023010X-RAY DIFFRACTION100
3.49-3.710.17811730.14772984X-RAY DIFFRACTION99.97
3.71-40.17311740.13783006X-RAY DIFFRACTION99.91
4-4.40.15131290.13273068X-RAY DIFFRACTION100
4.4-5.030.16961490.13073079X-RAY DIFFRACTION100
5.03-6.330.19361690.17023091X-RAY DIFFRACTION99.97
6.33-31.840.15141670.16633260X-RAY DIFFRACTION99.83

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