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- PDB-6xom: DCN1 bound to 8 -

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Basic information

Entry
Database: PDB / ID: 6xom
TitleDCN1 bound to 8
ComponentsLysozyme, DCN1-like protein 1 chimera
KeywordsLIGASE/LIGASE INHIBITOR / Inhibitor / LIGASE / LIGASE-LIGASE INHIBITOR complex
Function / homology
Function and homology information


positive regulation of protein neddylation / ubiquitin-like protein binding / regulation of protein neddylation / protein neddylation / ubiquitin conjugating enzyme binding / cullin family protein binding / regulation of protein ubiquitination / ubiquitin ligase complex / viral release from host cell by cytolysis / peptidoglycan catabolic process ...positive regulation of protein neddylation / ubiquitin-like protein binding / regulation of protein neddylation / protein neddylation / ubiquitin conjugating enzyme binding / cullin family protein binding / regulation of protein ubiquitination / ubiquitin ligase complex / viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / Neddylation / host cell cytoplasm / defense response to bacterium / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Potentiating neddylation domain / Defective-in-cullin neddylation protein / DCN1-like, PONY binding domain / Cullin binding / DCUN1 domain profile. / UBA-like domain / UBA-like superfamily / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 ...Potentiating neddylation domain / Defective-in-cullin neddylation protein / DCN1-like, PONY binding domain / Cullin binding / DCUN1 domain profile. / UBA-like domain / UBA-like superfamily / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Lysozyme-like domain superfamily
Similarity search - Domain/homology
Chem-H8V / Endolysin / DCN1-like protein 1
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsStuckey, J.A.
CitationJournal: Nat Commun / Year: 2021
Title: Selective inhibition of cullin 3 neddylation through covalent targeting DCN1 protects mice from acetaminophen-induced liver toxicity.
Authors: Zhou, H. / Lu, J. / Chinnaswamy, K. / Stuckey, J.A. / Liu, L. / McEachern, D. / Yang, C.Y. / Bernard, D. / Shen, H. / Rui, L. / Sun, Y. / Wang, S.
History
DepositionJul 7, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysozyme, DCN1-like protein 1 chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0233
Polymers44,3471
Non-polymers6762
Water4,306239
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Mass Spectometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.721, 86.698, 126.082
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Lysozyme, DCN1-like protein 1 chimera / / Endolysin / Lysis protein / Muramidase / DCUN1 domain-containing protein 1 / Defective in cullin ...Endolysin / Lysis protein / Muramidase / DCUN1 domain-containing protein 1 / Defective in cullin neddylation protein 1-like protein 1 / Squamous cell carcinoma-related oncogene


Mass: 44347.434 Da / Num. of mol.: 1 / Mutation: C54T,C97A,D127A,A146T,R154A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus), (gene. exp.) Homo sapiens (human)
Gene: e, T4Tp126, DCUN1D1, DCN1, DCUN1L1, RP42, SCCRO / Production host: Escherichia coli (E. coli) / References: UniProt: D9IEF7, UniProt: Q96GG9, lysozyme
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-H8V / (2R)-N-[(2S)-2-cyclohexyl-2-({N-propanoyl-3-[6-(propan-2-yl)-1,3-benzothiazol-2-yl]-L-alanyl}amino)ethyl]-2-methyl-4-(morpholin-4-yl)butanamide


Mass: 613.854 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H51N5O4S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 239 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.07 Å3/Da / Density % sol: 40.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 28 - 33% PEG 3350, 200 mM ammonium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 22472 / % possible obs: 100 % / Redundancy: 7.1 % / Biso Wilson estimate: 27.52 Å2 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.023 / Rrim(I) all: 0.061 / Χ2: 0.966 / Net I/σ(I): 11 / Num. measured all: 159935
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.146.30.56510840.8720.2450.6170.796100
2.14-2.186.70.48610940.8920.2010.5270.826100
2.18-2.227.30.42511140.9430.1680.4570.862100
2.22-2.267.30.38311060.9440.1510.4120.938100
2.26-2.317.30.30810650.960.1220.3310.948100
2.31-2.377.40.28211080.9640.1120.3040.96100
2.37-2.427.30.22811430.9710.0910.2460.998100
2.42-2.497.30.19410770.9820.0770.2090.999100
2.49-2.567.30.16811220.9840.0670.1811.04100
2.56-2.657.30.14511000.9880.0580.1561.032100
2.65-2.747.30.12611100.990.050.1361.121100
2.74-2.857.30.10811260.9940.0430.1171.191100
2.85-2.987.30.09211040.9940.0370.0991.283100
2.98-3.147.20.07811270.9950.0310.0841.239100
3.14-3.337.20.06311470.9960.0260.0681.102100
3.33-3.597.20.05311090.9980.0210.0570.974100
3.59-3.957.10.05211400.9970.0210.0561.129100
3.95-4.526.90.04311540.9980.0180.0470.971100
4.52-5.770.03111830.9990.0120.0330.488100
5.7-506.30.02712590.9980.0120.030.35899.7

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5V83

5v83


Resolution: 2.1→37.82 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.903 / SU R Cruickshank DPI: 0.234 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.257 / SU Rfree Blow DPI: 0.197 / SU Rfree Cruickshank DPI: 0.191
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1108 4.95 %RANDOM
Rwork0.195 ---
obs0.198 22377 99.6 %-
Displacement parametersBiso max: 110.67 Å2 / Biso mean: 31.47 Å2 / Biso min: 7.48 Å2
Baniso -1Baniso -2Baniso -3
1-2.4203 Å20 Å20 Å2
2---0.3493 Å20 Å2
3----2.071 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: final / Resolution: 2.1→37.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2837 0 97 239 3173
Biso mean--35.89 35.35 -
Num. residues----357
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1069SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes521HARMONIC5
X-RAY DIFFRACTIONt_it3010HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion380SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3708SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3010HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4117HARMONIC20.98
X-RAY DIFFRACTIONt_omega_torsion2.7
X-RAY DIFFRACTIONt_other_torsion16.39
LS refinement shellResolution: 2.1→2.12 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3101 29 6.47 %
Rwork0.1977 419 -
all0.2046 448 -
obs--84.81 %
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)
11.5266-1.3247-1.28082.76961.87422.08760.3522-0.08350.0443-0.4743-0.1526-0.1147-0.48220.1236-0.19960.0745-0.0733-0.0197-0.1201-0.0032-0.1567-5.01389.97636.6242
21.42440.6440.7911.96981.03131.68120.0314-0.01320.05140.0461-0.02640.08080.09640.0038-0.005-0.08350.08420.019-0.03580.0401-0.08736.21217.896539.2948
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|-6 - 1063}A-6 - 1063
2X-RAY DIFFRACTION2{A|1064 - 1251}A1064 - 1251

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