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- PDB-9arc: Crystal Structure of C0362 (TDE_0362 [TDE0362] resi 205-647) -

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Basic information

Entry
Database: PDB / ID: 9arc
TitleCrystal Structure of C0362 (TDE_0362 [TDE0362] resi 205-647)
ComponentsBacterial Ig-like domain protein C0362
KeywordsHYDROLASE / Papain-superfamily cysteine protease / virulence factor / TDE_0362 / alpha/beta hydrolase
Function / homology
Function and homology information


Ig protease IdeS / Mac 1 / Bacterial Ig-like domain (group 2) / Bacterial Ig-like domain 2 / Invasin/intimin cell-adhesion fragments / Bacterial Ig-like domain, group 2 / Papain-like cysteine peptidase superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
: / Bacterial Ig-like domain protein
Similarity search - Component
Biological speciesTreponema denticola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsClark, N.D. / Malkowski, M.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)5R01DE023080-10 United States
CitationJournal: Embo J. / Year: 2025
Title: A bipartite bacterial virulence factor targets the complement system and neutrophil activation.
Authors: Kurniyati, K. / Clark, N.D. / Wang, H. / Deng, Y. / Sze, C.W. / Visser, M.B. / Malkowski, M.G. / Li, C.
History
DepositionFeb 23, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 5, 2025Group: 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

Downloads & links

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Assembly

Deposited unit
A: Bacterial Ig-like domain protein C0362
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6394
Polymers55,5211
Non-polymers1173
Water4,504250
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.598, 99.258, 121.310
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-850-

HOH

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Components

#1: Protein Bacterial Ig-like domain protein C0362


Mass: 55521.414 Da / Num. of mol.: 1 / Fragment: residues 205-647
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Treponema denticola (bacteria) / Gene: TDE_0362 / Plasmid: pET101/D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIL / References: UniProt: Q73QT1
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.26 Å3/Da / Density % sol: 45.46 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 20% PEG 20K, 0.1 M Tris, pH 8.0, 100 mM KBr

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.77→39.35 Å / Num. obs: 49945 / % possible obs: 99.9 % / Redundancy: 8.4 % / Biso Wilson estimate: 32.33 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.04881 / Rpim(I) all: 0.01791 / Rrim(I) all: 0.05208 / Net I/σ(I): 18.32
Reflection shellResolution: 1.77→1.833 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.8283 / Mean I/σ(I) obs: 1.77 / Num. unique obs: 4929 / CC1/2: 0.894 / CC star: 0.972 / Rpim(I) all: 0.3113 / Rrim(I) all: 0.8862 / % possible all: 99.88

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Coot0.9.8.92model building
PHASER2.8.3phasing
cctbx.xfeldata reduction
Aimless0.7.7data scaling
DIALS2.2.10data reduction
xia20.6.475data reduction
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→39.35 Å / SU ML: 0.1981 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.0664
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2269 4710 4.97 %Random
Rwork0.198 90077 --
obs0.1994 49918 99.53 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.77 Å2
Refinement stepCycle: LAST / Resolution: 1.77→39.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3485 0 3 250 3738
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00753730
X-RAY DIFFRACTIONf_angle_d0.92935078
X-RAY DIFFRACTIONf_chiral_restr0.0614516
X-RAY DIFFRACTIONf_plane_restr0.0072667
X-RAY DIFFRACTIONf_dihedral_angle_d9.5912504
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.790.39211440.34492654X-RAY DIFFRACTION88.04
1.79-1.810.33091740.31543076X-RAY DIFFRACTION99.85
1.81-1.830.27591430.27162951X-RAY DIFFRACTION99.84
1.83-1.850.29871580.25993005X-RAY DIFFRACTION99.84
1.85-1.880.24471690.24853037X-RAY DIFFRACTION99.94
1.88-1.90.28391380.24523018X-RAY DIFFRACTION99.94
1.9-1.930.36961580.28842964X-RAY DIFFRACTION99.52
1.93-1.960.25441690.24293043X-RAY DIFFRACTION99.88
1.96-1.990.28951790.24133024X-RAY DIFFRACTION99.94
1.99-2.020.31131180.23173029X-RAY DIFFRACTION99.94
2.02-2.060.29561620.22542991X-RAY DIFFRACTION99.87
2.06-2.090.2471730.21953044X-RAY DIFFRACTION99.91
2.09-2.130.26471570.21532978X-RAY DIFFRACTION99.97
2.13-2.180.27071460.21713023X-RAY DIFFRACTION99.97
2.18-2.230.28121380.22553000X-RAY DIFFRACTION100
2.23-2.280.26751760.22843020X-RAY DIFFRACTION99.69
2.28-2.330.28951900.21663002X-RAY DIFFRACTION100
2.33-2.40.26951470.20723007X-RAY DIFFRACTION99.97
2.4-2.470.28621300.22453039X-RAY DIFFRACTION100
2.47-2.550.26531430.23143016X-RAY DIFFRACTION100
2.55-2.640.22551700.22723015X-RAY DIFFRACTION100
2.64-2.740.26281720.21943031X-RAY DIFFRACTION100
2.74-2.870.26051650.21612953X-RAY DIFFRACTION100
2.87-3.020.2211280.21923064X-RAY DIFFRACTION100
3.02-3.210.23651830.20253019X-RAY DIFFRACTION100
3.21-3.460.2081560.19693017X-RAY DIFFRACTION100
3.46-3.80.20091730.17193003X-RAY DIFFRACTION100
3.81-4.360.15841670.15322977X-RAY DIFFRACTION100
4.36-5.490.17381270.14443055X-RAY DIFFRACTION100
5.49-39.350.20561570.18583022X-RAY DIFFRACTION99.75
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)
10.633987805929-1.02693627078-0.820299771153.1454790392.539743070181.929091469730.116697773193-0.02149583209470.0129325260551-0.199141720058-0.203108474980.0908925645457-0.354111710168-0.1383222583440.08231765796390.4028385641280.0256100170028-0.0574882992390.2628105527880.01887453639780.22497273180718.941273772340.669357918318.3560935037
20.9068349408070.1100281041821.193400442711.434463623010.6572208744634.38382912569-0.06215675431350.155343060126-0.131061305265-0.07696179482910.054192531224-0.266555662860.03800574914650.5566923905470.003805595139860.17822613296-0.0409296809475-0.004858705717270.283589658607-0.003122837267290.29283896445236.18408561888.73920492297-11.0709915178
31.49627136955-0.133949569347-0.2962499811062.388694779580.8601677898892.56536786657-0.07022719606150.2346297180730.198706749305-0.412131740814-0.0452575023358-0.114759817449-0.94999397158-0.02001965669630.07945774745710.478065069834-0.0481530165784-0.08915503303520.2526408141770.04930537345490.30925677505825.798613744325.1816731514-7.25314112108
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 211 through 383 )211 - 3831 - 170
22chain 'A' and (resid 384 through 475 )384 - 475171 - 262
33chain 'A' and (resid 476 through 650 )476 - 650263 - 431

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