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- PDB-9mdk: Crystal Structure of E64-inhibited C0362 (TDE_0362 [TDE0362] resi... -

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Basic information

Entry
Database: PDB / ID: 9mdk
TitleCrystal Structure of E64-inhibited C0362 (TDE_0362 [TDE0362] resi 205-647)
ComponentsBacterial Ig-like domain protein C0362
KeywordsHYDROLASE / Inhibitor complex / 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
Chem-E64 / Bacterial Ig-like domain protein
Similarity search - Component
Biological speciesTreponema denticola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 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)DE030667 United States
Citation
Journal: Acta Crystallogr.,Sect.F / Year: 2025
Title: Structural insights into the role of the prosegment binding loop in a papain-superfamily cysteine protease from Treponema denticola.
Authors: Clark, N.D. / Li, C. / Malkowski, M.G.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionDec 5, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 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: Bacterial Ig-like domain protein C0362
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1146
Polymers55,5051
Non-polymers6095
Water6,648369
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.684, 99.366, 121.224
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-908-

HOH

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Components

#1: Protein Bacterial Ig-like domain protein C0362


Mass: 55505.414 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 BL21(DE3) (bacteria) / Strain (production host): BL21-CodonPlus (DE3)-RIL / References: UniProt: Q73QT1
#2: Chemical ChemComp-E64 / N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE


Mass: 360.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H30N5O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 45.61 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M Tris, pH 8.0, 100 mM Potassium Bromide, 20% PEG 20,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.93→76.85 Å / Num. obs: 250587 / % possible obs: 98.55 % / Redundancy: 6.5 % / Biso Wilson estimate: 27.62 Å2 / CC1/2: 0.889 / CC star: 0.97 / Rmerge(I) obs: 0.137 / Net I/σ(I): 9.85
Reflection shellResolution: 1.93→1.95 Å / Redundancy: 5.3 % / Rmerge(I) obs: 1.535 / Mean I/σ(I) obs: 2.22 / Num. unique obs: 1323 / CC1/2: 0.542 / CC star: 0.838 / % possible all: 87

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Processing

Software
NameVersionClassification
DIALS2.2.10data reduction
xia20.6.475data reduction
Aimlessdata scaling
pointlessdata scaling
PHENIXphasing
PHASER1.19.2phasing
Cootmodel building
PHENIX1.21_5207refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→76.85 Å / SU ML: 0.2523 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.4509
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.228 3662 5.05 %
Rwork0.1853 68792 -
obs0.1874 72454 98.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.5 Å2
Refinement stepCycle: LAST / Resolution: 1.93→76.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3536 0 41 369 3946
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00753770
X-RAY DIFFRACTIONf_angle_d0.86065120
X-RAY DIFFRACTIONf_chiral_restr0.0588522
X-RAY DIFFRACTIONf_plane_restr0.0074671
X-RAY DIFFRACTIONf_dihedral_angle_d17.62811392
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.950.34181230.30982326X-RAY DIFFRACTION87.03
1.95-1.980.34411400.27552640X-RAY DIFFRACTION97.2
1.98-2.010.28211290.2482634X-RAY DIFFRACTION98.71
2.01-2.040.29751490.24942593X-RAY DIFFRACTION97.89
2.04-2.070.30431600.23042694X-RAY DIFFRACTION98.75
2.07-2.10.27911610.21642611X-RAY DIFFRACTION99.11
2.1-2.140.26581210.21352659X-RAY DIFFRACTION99
2.14-2.180.27221350.21942680X-RAY DIFFRACTION99.12
2.18-2.220.27411590.2152670X-RAY DIFFRACTION99.12
2.22-2.270.25011530.21112586X-RAY DIFFRACTION98.6
2.27-2.310.25931360.20772737X-RAY DIFFRACTION99.38
2.31-2.370.23011050.20652648X-RAY DIFFRACTION98.57
2.37-2.430.27221440.20932643X-RAY DIFFRACTION98.59
2.43-2.490.27481430.21942633X-RAY DIFFRACTION97.78
2.49-2.570.27771220.20822690X-RAY DIFFRACTION99.43
2.57-2.650.28331480.20592666X-RAY DIFFRACTION99.82
2.65-2.740.27951630.19612665X-RAY DIFFRACTION99.51
2.74-2.850.19171410.19852656X-RAY DIFFRACTION99.75
2.85-2.980.24441560.20722695X-RAY DIFFRACTION99.69
2.98-3.140.26241580.19472621X-RAY DIFFRACTION99.46
3.14-3.340.26271280.18322686X-RAY DIFFRACTION99.43
3.34-3.60.21091300.16292673X-RAY DIFFRACTION99.15
3.6-3.960.21691220.16062707X-RAY DIFFRACTION99.68
3.96-4.530.12721590.13012643X-RAY DIFFRACTION99.72
4.53-5.70.17271410.142698X-RAY DIFFRACTION99.96
5.71-76.850.1931360.17822638X-RAY DIFFRACTION97.74
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)
10.197222794098-0.423779436608-0.3874065842932.912267050082.588148571661.525629945580.12301250068-0.002700107493950.0136975440593-0.42431712012-0.2360353639610.0709517598922-0.458276987743-0.2073819456610.0881945566260.5161292152280.085085760528-0.04999612636040.2587063640.00167350373920.232814928093-4.1060155041745.696307918420.8698136705
22.79059389723-0.272622514988-0.2752739354211.29094516202-0.5431582189281.352054605260.06176493705330.212213453484-0.1262125301830.121360246173-0.0187434828574-0.393877436505-0.06588766456180.445917989987-0.02714389730840.149268014193-0.0394600377567-0.09774356186410.319678173755-0.02212091400620.34553218300718.378582780712.4303888548-0.247607517095
30.823945261954-0.226890740306-0.4214162621452.182904344170.8627351939043.31550445270.02830572090790.1336471549640.0640343976141-0.207622510469-0.0951567278253-0.172036938764-0.6786505304570.04729837674120.05582950195210.245679866069-0.0250244578906-0.03958163255010.2061619860410.03453494697430.2493575944776.8913084168220.3258914528-8.52529804224
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 212 through 356 )212 - 3561 - 145
22chain 'A' and (resid 357 through 411 )357 - 411146 - 200
33chain 'A' and (resid 412 through 650 )412 - 650201 - 439

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