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- PDB-6fdu: Structure of Chlamydia trachomatis effector protein Cdu1 bound to... -

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Basic information

Entry
Database: PDB / ID: 6fdu
TitleStructure of Chlamydia trachomatis effector protein Cdu1 bound to Compound 3
ComponentsDeubiquitinase and deneddylase Dub1
KeywordsHYDROLASE / ChlaDUB1 / CE protease / DUB / Ubiquitin / covalent inhibitor.
Function / homology
Function and homology information


deNEDDylase activity / protein deneddylation / protein deubiquitination / host cell / cysteine-type deubiquitinase activity / 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
Chem-D5W / Deubiquitinase and deneddylase Dub1
Similarity search - Component
Biological speciesChlamydia trachomatis serovar L2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsRamirez, Y. / Kisker, C. / Altmann, E.
Funding support Germany, 1items
OrganizationGrant numberCountry
GSLS University of Wuerzburg Germany
CitationJournal: ChemMedChem / Year: 2018
Title: Structural Basis of Substrate Recognition and Covalent Inhibition of Cdu1 from Chlamydia trachomatis.
Authors: Ramirez, Y.A. / Adler, T.B. / Altmann, E. / Klemm, T. / Tiesmeyer, C. / Sauer, F. / Kathman, S.G. / Statsyuk, A.V. / Sotriffer, C. / Kisker, C.
History
DepositionDec 26, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Deubiquitinase and deneddylase Dub1
B: Deubiquitinase and deneddylase Dub1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,6195
Polymers61,0692
Non-polymers5503
Water2,630146
1
A: Deubiquitinase and deneddylase Dub1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5702
Polymers30,5341
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Deubiquitinase and deneddylase Dub1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0493
Polymers30,5341
Non-polymers5152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.080, 57.093, 116.381
Angle α, β, γ (deg.)90.00, 96.00, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 163 - 400 / Label seq-ID: 28 - 265

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Deubiquitinase and deneddylase Dub1 / ChlaDub1


Mass: 30534.355 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydia trachomatis serovar L2 (strain 434/Bu / ATCC VR-902B) (bacteria)
Gene: cdu1, CTL0247
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: B0B9A0, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-D5W / (2~{S},3~{S})-2-[[(2~{S})-2-[3,5-bis(chloranyl)phenyl]-2-(dimethylamino)ethanoyl]amino]-~{N}-[[2-(iminomethyl)pyrimidin-4-yl]methyl]-3-methyl-pentanamide


Mass: 479.403 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H28Cl2N6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O
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: 2.51 Å3/Da / Density % sol: 51.09 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 100 mM Bicine pH 9.0, 10% PEG 20000, 2% 1, 4 dioxane

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.3→43.84 Å / Num. obs: 25773 / % possible obs: 99.59 % / Redundancy: 2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.04711 / Rpim(I) all: 0.04711 / Rrim(I) all: 0.06663 / Net I/σ(I): 8.96
Reflection shellResolution: 2.279→2.3 Å / Redundancy: 2 % / Num. unique obs: 2743 / CC1/2: 0.785 / % possible all: 78.12

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B5Q

5b5q


Resolution: 2.3→43.84 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.925 / SU B: 17.279 / SU ML: 0.198 / Cross valid method: THROUGHOUT / ESU R: 0.334 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23996 1351 5.2 %RANDOM
Rwork0.19988 ---
obs0.20208 24390 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.361 Å2
Baniso -1Baniso -2Baniso -3
1--0.92 Å2-0 Å2-0.65 Å2
2--0.49 Å2-0 Å2
3---0.56 Å2
Refinement stepCycle: 1 / Resolution: 2.3→43.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3860 0 34 146 4040
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0144062
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173697
X-RAY DIFFRACTIONr_angle_refined_deg1.7831.6635542
X-RAY DIFFRACTIONr_angle_other_deg1.0121.6388682
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1935493
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.47422.969192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.99515692
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4991517
X-RAY DIFFRACTIONr_chiral_restr0.0860.2522
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024490
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02771
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0872.7071936
X-RAY DIFFRACTIONr_mcbond_other2.0022.7061935
X-RAY DIFFRACTIONr_mcangle_it3.4124.0442420
X-RAY DIFFRACTIONr_mcangle_other3.4234.0472421
X-RAY DIFFRACTIONr_scbond_it2.1912.8822126
X-RAY DIFFRACTIONr_scbond_other2.1912.8822127
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7024.2323116
X-RAY DIFFRACTIONr_long_range_B_refined6.13731.2634650
X-RAY DIFFRACTIONr_long_range_B_other6.12931.1334631
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 7800 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 107 -
Rwork0.282 1765 -
obs--99.89 %
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)
12.93020.25551.84660.0911-0.14322.5715-0.04970.2003-0.3153-0.07950.0239-0.05190.20170.11340.02580.22580.0504-0.09490.0315-0.070.2442-41.5385-12.8027122.4561
21.3038-0.18130.93340.11040.06381.3267-0.04450.0627-0.1092-0.00260.0604-0.0104-0.25610.1352-0.01590.2357-0.0137-0.10520.0836-0.03330.1864-39.3689-2.5419120.4092
31.7699-1.03171.56580.9599-1.46292.3699-0.0686-0.1272-0.02010.04910.0514-0.01-0.2152-0.03910.01720.2390.0054-0.11840.0455-0.02710.1795-48.1132.9757132.721
40.91730.14820.37370.4979-1.15873.40250.2082-0.0809-0.3075-0.078-0.01270.02980.4-0.034-0.19540.25510.0037-0.11650.01110.0070.289-45.9419-17.3865131.8856
51.52030.22450.22441.2880.16330.7928-0.0454-0.146-0.14260.00350.08540.12860.1052-0.032-0.040.2191-0.0149-0.08150.07270.02910.1808-31.6438-0.542166.13
65.15740.9817.04921.45942.341510.4529-0.17670.16510.21120.076-0.11510.1214-0.09620.14490.29190.1907-0.0139-0.0440.1244-0.00840.1842-28.28716.6769170.1371
72.1512.23641.22824.54461.13691.14390.2055-0.3086-0.07310.2297-0.14580.3313-0.03350.0515-0.05970.2258-0.0641-0.02840.20230.03970.1181-29.699210.1254179.5386
80.48970.76410.00851.21310.01680.0015-0.0296-0.02610.1436-0.04030.01590.18690.01460.00530.01370.2225-0.0059-0.08280.1665-0.00630.1892-36.177.7667159.2368
94.12760.82941.38830.6703-0.11830.79710.2643-0.6615-0.1019-0.1587-0.11690.10210.2374-0.197-0.14740.2046-0.0822-0.10030.22880.04190.1838-42.37593.3227158.4295
102.8891.88722.52352.49782.30742.5518-0.14710.17030.1641-0.10650.06030.0365-0.10770.11120.08680.2592-0.0609-0.10350.04540.05720.1386-24.870115.0568155.7136
110.2750.0930.64160.55171.2223.47570.01280.0568-0.1085-0.02950.1132-0.0085-0.05410.2827-0.1260.1955-0.0345-0.06780.1254-0.00830.1967-23.834-1.8986151.7262
121.2132-0.9065-0.87710.711.07236.2766-0.05640.0172-0.21310.0971-0.04080.13790.603-0.35210.09720.259-0.0314-0.06970.03150.03740.201-28.2397-9.8162163.3382
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A162 - 198
2X-RAY DIFFRACTION2A199 - 282
3X-RAY DIFFRACTION3A283 - 331
4X-RAY DIFFRACTION4A332 - 401
5X-RAY DIFFRACTION5B163 - 198
6X-RAY DIFFRACTION6B199 - 215
7X-RAY DIFFRACTION7B216 - 238
8X-RAY DIFFRACTION8B239 - 254
9X-RAY DIFFRACTION9B255 - 282
10X-RAY DIFFRACTION10B283 - 331
11X-RAY DIFFRACTION11B332 - 371
12X-RAY DIFFRACTION12B372 - 401

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