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- PDB-9qte: Simkania negevensis CE-clan virulence factor SnCE1 wildtype -

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Basic information

Entry
Database: PDB / ID: 9qte
TitleSimkania negevensis CE-clan virulence factor SnCE1 wildtype
ComponentsDeubiquitinase and deneddylase ChlaDub2
KeywordsHYDROLASE / cysteine protease / CE-clan / Ubl protease / deSUMOylase / SUMO pathway / virulence factor / bacterial virulence / pathogenesis
Function / homology
Function and homology information


cysteine-type peptidase activity / host cell / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / proteolysis / extracellular region / membrane
Similarity search - Function
Ulp1 protease family, C-terminal catalytic domain / Ubiquitin-like protease family profile. / Ulp1 protease family, C-terminal catalytic domain / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
MALONATE ION / DeSUMOylase CE1
Similarity search - Component
Biological speciesSimkania negevensis Z (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.821 Å
AuthorsSchmoeker, O. / Girbardt, B. / Palm, G.J. / Hoppen, J. / Schulze, S. / Lammers, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)443535983 Germany
CitationJournal: Nat Commun / Year: 2026
Title: Reprogramming of bacterial virulence by lysine acetylation.
Authors: Schmoker, O. / Girbardt, B. / Schulze, S. / Palm, G.J. / Berndt, L. / Hoppen, J. / Kara, N. / Schops, X. / Al-Abdulla, R. / Garz, K. / Junker, H. / Wolfgramm, S. / Steil, L. / Hentschker, C. ...Authors: Schmoker, O. / Girbardt, B. / Schulze, S. / Palm, G.J. / Berndt, L. / Hoppen, J. / Kara, N. / Schops, X. / Al-Abdulla, R. / Garz, K. / Junker, H. / Wolfgramm, S. / Steil, L. / Hentschker, C. / Schoknecht, K. / Mayer, L.M. / Speth, L. / Lachmayer, V. / Dorr, M. / Kemnitz, S. / Muller, S. / Lackmann, J.W. / Kruger, M. / Hofmann, K. / Bornscheuer, U.T. / Volker, U. / Kruger, E. / Kozjak-Pavlovic, V. / Lammers, M.
History
DepositionApr 8, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release
Revision 1.1May 6, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Deubiquitinase and deneddylase ChlaDub2
B: Deubiquitinase and deneddylase ChlaDub2
C: Deubiquitinase and deneddylase ChlaDub2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,5415
Polymers75,3373
Non-polymers2042
Water18010
1
A: Deubiquitinase and deneddylase ChlaDub2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2142
Polymers25,1121
Non-polymers1021
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Deubiquitinase and deneddylase ChlaDub2


Theoretical massNumber of molelcules
Total (without water)25,1121
Polymers25,1121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Deubiquitinase and deneddylase ChlaDub2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2142
Polymers25,1121
Non-polymers1021
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.645, 105.645, 122.086
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21B
32A
42C
53B
63C

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: GLN / End label comp-ID: GLN / Auth seq-ID: 34 - 229 / Label seq-ID: 9 - 204

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
32AA
42CC
53BB
63CC

NCS ensembles :
IDDetails (eV)
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6

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Components

#1: Protein Deubiquitinase and deneddylase ChlaDub2


Mass: 25112.441 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: Starting amino acids correspond to expression tag, amino acids 206/209 to 212 not resolved
Source: (gene. exp.) Simkania negevensis Z (bacteria) / Gene: cdu2, SNE_A10940 / Plasmid: pGEX6P.1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F8L4W9
#2: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.26 Å3/Da / Density % sol: 45.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.18 M sodium malonate pH 5.0, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 13, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.82→47.27 Å / Num. obs: 15908 / % possible obs: 98.4 % / Redundancy: 12.9 % / Biso Wilson estimate: 48.3 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.228 / Rpim(I) all: 0.095 / Rrim(I) all: 0.247 / Χ2: 1.05 / Net I/σ(I): 8.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
8.92-47.2711.80.10318.15280.9960.0440.1121.0399.4
2.82-2.977.50.941220580.5690.4971.0730.9489.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Coot0.9.6model building
PHASERphasing
XDSdata reduction
XDSdata scaling
MxCuBEdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.821→44.1 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.876 / SU B: 49.506 / SU ML: 0.418 / Cross valid method: FREE R-VALUE / ESU R Free: 0.449
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2687 749 4.715 %
Rwork0.2467 15138 -
all0.248 --
obs-15887 98.256 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 59.341 Å2
Baniso -1Baniso -2Baniso -3
1--1.681 Å20 Å20 Å2
2---1.681 Å2-0 Å2
3---3.362 Å2
Refinement stepCycle: LAST / Resolution: 2.821→44.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5057 0 14 10 5081
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0135222
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164825
X-RAY DIFFRACTIONr_ext_dist_refined_d0.2630.181570
X-RAY DIFFRACTIONr_angle_refined_deg1.5721.6517047
X-RAY DIFFRACTIONr_angle_other_deg1.2871.58911110
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9265592
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.43722.571319
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.86915902
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9621530
X-RAY DIFFRACTIONr_chiral_restr0.0780.2600
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025908
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021340
X-RAY DIFFRACTIONr_nbd_refined0.1930.2843
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1780.24045
X-RAY DIFFRACTIONr_nbtor_refined0.1750.22511
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.22456
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.270
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2330.222
X-RAY DIFFRACTIONr_nbd_other0.2480.2101
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.4650.23
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1260.21
X-RAY DIFFRACTIONr_mcbond_it1.9923.6292377
X-RAY DIFFRACTIONr_mcbond_other1.9923.632376
X-RAY DIFFRACTIONr_mcangle_it3.2565.4412966
X-RAY DIFFRACTIONr_mcangle_other3.2555.4412967
X-RAY DIFFRACTIONr_scbond_it1.7743.7692845
X-RAY DIFFRACTIONr_scbond_other1.7733.7692842
X-RAY DIFFRACTIONr_scangle_it3.0025.5894081
X-RAY DIFFRACTIONr_scangle_other3.0025.5894082
X-RAY DIFFRACTIONr_lrange_it7.577133.59382855
X-RAY DIFFRACTIONr_lrange_other7.577133.59282856
X-RAY DIFFRACTIONr_ncsr_local_group_10.0820.056823
X-RAY DIFFRACTIONr_ncsr_local_group_20.0850.056790
X-RAY DIFFRACTIONr_ncsr_local_group_30.0890.056775
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.081820.0501
12BX-RAY DIFFRACTIONLocal ncs0.081820.0501
23AX-RAY DIFFRACTIONLocal ncs0.085310.0501
24CX-RAY DIFFRACTIONLocal ncs0.085310.0501
35BX-RAY DIFFRACTIONLocal ncs0.088880.0501
36CX-RAY DIFFRACTIONLocal ncs0.088880.0501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.821-2.8940.357400.348877X-RAY DIFFRACTION79.6007
2.894-2.9740.352680.3031072X-RAY DIFFRACTION98.1912
2.974-3.060.317450.2661117X-RAY DIFFRACTION100
3.06-3.1540.272460.2451033X-RAY DIFFRACTION100
3.154-3.2570.307490.2531017X-RAY DIFFRACTION100
3.257-3.3710.423350.244989X-RAY DIFFRACTION100
3.371-3.4980.281380.251958X-RAY DIFFRACTION99.8997
3.498-3.6410.263460.263907X-RAY DIFFRACTION99.8952
3.641-3.8020.3500.273872X-RAY DIFFRACTION100
3.802-3.9870.288510.253819X-RAY DIFFRACTION100
3.987-4.2020.237450.242795X-RAY DIFFRACTION100
4.202-4.4570.208500.226741X-RAY DIFFRACTION100
4.457-4.7630.222500.223698X-RAY DIFFRACTION100
4.763-5.1430.246180.202663X-RAY DIFFRACTION100
5.143-5.6320.212210.218625X-RAY DIFFRACTION100
5.632-6.2930.199110.22563X-RAY DIFFRACTION99.308
6.293-7.2590.284260.248479X-RAY DIFFRACTION99.2141
7.259-8.8720.224300.25421X-RAY DIFFRACTION99.1209
8.872-12.470.256140.225313X-RAY DIFFRACTION98.7915
12.47-44.10.404160.304179X-RAY DIFFRACTION96.0591
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)
15.18160.4758-0.23663.7139-0.4442.4196-0.1495-0.4884-0.03130.32110.0611-0.25740.23480.18430.08840.09790.0155-0.01650.1131-0.00570.020625.92862.966310.6541
23.225-0.62-0.51575.37010.01792.20730.09090.2305-0.2151-0.3931-0.0914-0.1460.13210.14670.00050.0767-0.0044-0.01430.0876-0.0150.03549.753126.8737-7.8388
33.15591.5904-0.41334.5321-0.66262.24270.00250.2803-0.0927-0.26240.0371-0.3511-0.240.2501-0.03960.2455-0.00420.00990.3905-0.05420.220726.05541.7349-27.4791
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA34 - 233
2X-RAY DIFFRACTION2ALLB34 - 230
3X-RAY DIFFRACTION3ALLC33 - 230

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