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- PDB-9isp: DUF2436 domain which is frequently found in virulence proteins fr... -

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Basic information

Entry
Database: PDB / ID: 9isp
TitleDUF2436 domain which is frequently found in virulence proteins from Porphyromonas gingivalis
ComponentsProtease PrtH
KeywordsUNKNOWN FUNCTION / Porphyromonas gingivalis / oral pathogen / DUF2436
Function / homology
Function and homology information


biosynthetic process / cysteine-type peptidase activity / cytoplasmic vesicle / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / proteolysis
Similarity search - Function
Cleaved adhesin / Peptidase C25, gingipain, C-terminal / Cleaved Adhesin Domain / Domain of unknown function (DUF2436) / Formyl transferase, N-terminal / Formyl transferase / Formyl transferase, N-terminal domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesPorphyromonas gingivalis W83 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsKim, B. / Hwang, J. / Do, H. / Lee, J.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2024
Title: First crystal structure of the DUF2436 domain of virulence proteins from Porphyromonas gingivalis.
Authors: Kim, B. / Hwang, J. / Im, S. / Do, H. / Shim, Y.S. / Lee, J.H.
History
DepositionJul 18, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protease PrtH


Theoretical massNumber of molelcules
Total (without water)23,7991
Polymers23,7991
Non-polymers00
Water1,63991
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.275, 101.275, 70.168
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein Protease PrtH


Mass: 23799.244 Da / Num. of mol.: 1 / Fragment: DUF2436 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis W83 (bacteria)
Gene: prtH / Production host: Escherichia coli (E. coli)
References: UniProt: P46071, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O
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: 4.36 Å3/Da / Density % sol: 71.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M Sodium Chloride, 0.1 M Tris-HCl (pH 7), 1 M sodium Citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Dec 26, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.21→29.24 Å / Num. obs: 21191 / % possible obs: 99.89 % / Redundancy: 19.8 % / Biso Wilson estimate: 39.03 Å2 / CC1/2: 0.987 / Net I/σ(I): 22.29
Reflection shellResolution: 2.21→2.289 Å / Num. unique obs: 2066 / CC1/2: 0.483

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.21→29.24 Å / SU ML: 0.3005 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.6813
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2586 1023 4.83 %
Rwork0.2378 20168 -
obs0.2388 21191 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.12 Å2
Refinement stepCycle: LAST / Resolution: 2.21→29.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1183 0 0 91 1274
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011211
X-RAY DIFFRACTIONf_angle_d1.24951652
X-RAY DIFFRACTIONf_chiral_restr0.0711181
X-RAY DIFFRACTIONf_plane_restr0.0058221
X-RAY DIFFRACTIONf_dihedral_angle_d16.8976426
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.21-2.320.3351510.2962801X-RAY DIFFRACTION98.89
2.32-2.470.3441420.2822876X-RAY DIFFRACTION99.93
2.47-2.660.30961430.26372851X-RAY DIFFRACTION100
2.66-2.930.26781600.25012842X-RAY DIFFRACTION100
2.93-3.350.23371480.23372877X-RAY DIFFRACTION100
3.35-4.220.2481270.21482932X-RAY DIFFRACTION100
4.22-100.23261520.22462989X-RAY DIFFRACTION99.81

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