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

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Basic information

Entry
Database: PDB / ID: 6fdq
TitleStructure of Chlamydia trachomatis effector protein Cdu1 bound to Compound 5
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-2UQ / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)61,5494
Polymers61,0692
Non-polymers4812
Water2,756153
1
A: Deubiquitinase and deneddylase Dub1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7752
Polymers30,5341
Non-polymers2401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Deubiquitinase and deneddylase Dub1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7752
Polymers30,5341
Non-polymers2401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.590, 57.037, 114.593
Angle α, β, γ (deg.)90.00, 94.73, 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)
Strain: 434/Bu / ATCC VR-902B / 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-2UQ / N-benzyl-2-[(Z)-iminomethyl]pyrimidine-5-carboxamide


Mass: 240.261 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H12N4O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O

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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: 2.32 Å3/Da / Density % sol: 47.09 %
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→43.44 Å / Num. obs: 24597 / % possible obs: 97.56 % / Redundancy: 1.9 % / CC1/2: 0.994 / Rmerge(I) obs: 0.07289 / Rrim(I) all: 0.1031 / Net I/σ(I): 3.57
Reflection shellResolution: 2.3→2.382 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 1.08 / Num. unique obs: 2391 / CC1/2: 0.755 / Rrim(I) all: 0.693 / % possible all: 95.66

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B5Q

5b5q


Resolution: 2.3→43.44 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.906 / SU B: 27.398 / SU ML: 0.313 / Cross valid method: FREE R-VALUE / ESU R: 0.419 / ESU R Free: 0.281 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28397 1142 4.6 %RANDOM
Rwork0.22924 ---
obs0.23185 23430 97.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 46.786 Å2
Baniso -1Baniso -2Baniso -3
1-2 Å2-0 Å2-0.12 Å2
2---1.92 Å20 Å2
3----0.06 Å2
Refinement stepCycle: 1 / Resolution: 2.3→43.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3920 0 36 153 4109
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0194106
X-RAY DIFFRACTIONr_bond_other_d0.010.023795
X-RAY DIFFRACTIONr_angle_refined_deg2.0181.9765595
X-RAY DIFFRACTIONr_angle_other_deg1.2138839
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3585492
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.95624.091176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.23515695
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8291518
X-RAY DIFFRACTIONr_chiral_restr0.1130.2607
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214518
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02846
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_it0.8591.1361956
X-RAY DIFFRACTIONr_mcbond_other0.8591.1361955
X-RAY DIFFRACTIONr_mcangle_it1.5211.7012446
X-RAY DIFFRACTIONr_mcangle_other1.5211.72447
X-RAY DIFFRACTIONr_scbond_it1.0811.2052150
X-RAY DIFFRACTIONr_scbond_other1.0811.2062151
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8651.7683148
X-RAY DIFFRACTIONr_long_range_B_refined6.86314.0134827
X-RAY DIFFRACTIONr_long_range_B_other6.83913.6884797
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 16002 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 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
Rfree0.41 70 -
Rwork0.364 1633 -
obs--94.77 %
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)
11.12870.30791.03682.59930.10061.7677-0.0812-0.0134-0.1148-0.0240.0165-0.48930.1878-0.0750.06460.37840.0417-0.30750.2747-0.07170.5728-73.8595-5.07817.4492
21.8561-1.1030.92711.2385-0.43961.2158-0.0784-0.03330.2222-0.03080.0622-0.217-0.0413-0.06780.01620.2972-0.0095-0.34990.3205-0.02130.5645-71.10944.26576.4078
33.3401-2.14242.72852.1764-2.44232.8454-0.0866-0.27520.15970.07250.0681-0.0319-0.0789-0.18830.01840.36320.0898-0.36060.347-0.04950.4911-80.587210.194917.7486
40.8245-0.13690.58050.8915-1.09974.6997-0.038-0.1701-0.2081-0.08520.0494-0.06860.1574-0.2224-0.01130.2751-0.0008-0.30290.3676-0.01960.4937-79.3556-10.109116.9312
50.88580.41581.6141.43030.88882.96370.06-0.0606-0.0675-0.03140.07290.30120.1507-0.0588-0.13290.3866-0.0662-0.48510.2930.1030.6608-64.7346-19.531547.3008
67.50730.55256.5840.04290.44888.0901-0.25090.0880.115-0.02310.03140.0095-0.320.00470.21950.4314-0.0111-0.10850.3271-0.01990.4794-58.0339-0.192555.1827
74.06452.09981.21566.73140.64330.37420.1315-0.46160.28870.2023-0.14660.31430.0562-0.1480.01510.39670.0227-0.24270.38690.04460.5328-58.0713-6.92564.2376
86.6815-0.32924.22470.2145-0.3153.3415-0.9735-0.2706-0.36310.06990.3346-0.1349-0.8537-0.43520.63890.22670.1082-0.24510.5223-0.34781.127-67.949-8.396145.2965
96.896-0.64040.3780.55410.33291.0161-0.2777-0.187-0.2237-0.15090.25460.1538-0.0931-0.28770.02310.3104-0.0075-0.24150.46660.08620.394-74.4441-12.394445.63
103.75722.09553.51971.29471.80683.631-0.11570.36220.01230.05470.1561-0.0095-0.26130.207-0.04030.3370.0081-0.33210.34580.01290.5051-56.6901-1.700840.3955
112.1472-0.13911.08991.93780.41892.70790.31510.5048-0.45190.03440.0221-0.16590.24840.2102-0.33710.3230.0291-0.37670.3487-0.06170.5022-57.5711-18.772735.9356
121.04770.19230.77231.85730.846.51510.0503-0.0605-0.26460.20190.08380.08361.0077-0.0735-0.13410.379-0.0739-0.24590.28660.07080.5317-61.0647-26.335747.9864
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 DIFFRACTION5B155 - 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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