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- PDB-3pg6: The carboxyl terminal domain of human deltex 3-like -

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Basic information

Entry
Database: PDB / ID: 3pg6
TitleThe carboxyl terminal domain of human deltex 3-like
ComponentsE3 ubiquitin-protein ligase DTX3L
KeywordsLIGASE / DNA-DAMAGE / METAL-BINDING / NUCLEUS / PHOSPHORYLATION / CHROMATIN REGULATOR / UBL CONJUGATION PATHWAY / ZINC-FINGER / STRUCTURAL GENOMICS CONSORTIUM / SGC
Function / homology
Function and homology information


histone H4K91 ubiquitin ligase activity / protein ADP-ribosyltransferase-substrate adaptor activity / histone ubiquitin ligase activity / positive regulation of protein localization to early endosome / negative regulation of ubiquitin-protein transferase activity / enzyme inhibitor activity / positive regulation of chromatin binding / DNA repair-dependent chromatin remodeling / STAT family protein binding / positive regulation of receptor catabolic process ...histone H4K91 ubiquitin ligase activity / protein ADP-ribosyltransferase-substrate adaptor activity / histone ubiquitin ligase activity / positive regulation of protein localization to early endosome / negative regulation of ubiquitin-protein transferase activity / enzyme inhibitor activity / positive regulation of chromatin binding / DNA repair-dependent chromatin remodeling / STAT family protein binding / positive regulation of receptor catabolic process / endosome to lysosome transport / ubiquitin-like protein ligase binding / protein autoubiquitination / protein K48-linked ubiquitination / Notch signaling pathway / positive regulation of defense response to virus by host / DNA damage checkpoint signaling / RING-type E3 ubiquitin transferase / positive regulation of protein localization to nucleus / ubiquitin-protein transferase activity / double-strand break repair / protein transport / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of protein binding / early endosome membrane / histone binding / ubiquitin-dependent protein catabolic process / defense response to virus / lysosome / lysosomal membrane / innate immune response / positive regulation of DNA-templated transcription / enzyme binding / protein-containing complex / nucleoplasm / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Enolase-like; domain 1 - #130 / DTX3L, RING-HC finger / : / : / DTX3L, alpha/beta domain / DTX3L, KH-like domain / Deltex, C-terminal / Deltex family / Deltex, C-terminal domain superfamily / Deltex C-terminal domain ...Enolase-like; domain 1 - #130 / DTX3L, RING-HC finger / : / : / DTX3L, alpha/beta domain / DTX3L, KH-like domain / Deltex, C-terminal / Deltex family / Deltex, C-terminal domain superfamily / Deltex C-terminal domain / Zinc finger, C3HC4 type (RING finger) / Enolase-like; domain 1 / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Nucleotide-binding alpha-beta plait domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / DI(HYDROXYETHYL)ETHER / E3 ubiquitin-protein ligase DTX3L
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsWalker, J.R. / Obiero, J. / Kania, J. / Schuler, H. / Bountra, C. / Weigelt, J. / Edwards, A.M. / Arrowsmith, C.H. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: Proteins / Year: 2012
Title: Fold of the conserved DTC domain in Deltex proteins.
Authors: Obiero, J. / Walker, J.R. / Dhe-Paganon, S.
History
DepositionOct 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 28, 2012Group: Database references
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase DTX3L
B: E3 ubiquitin-protein ligase DTX3L
C: E3 ubiquitin-protein ligase DTX3L
D: E3 ubiquitin-protein ligase DTX3L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,67012
Polymers71,5774
Non-polymers1,0938
Water10,935607
1
A: E3 ubiquitin-protein ligase DTX3L
D: E3 ubiquitin-protein ligase DTX3L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1795
Polymers35,7892
Non-polymers3903
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-10 kcal/mol
Surface area13100 Å2
MethodPISA
2
B: E3 ubiquitin-protein ligase DTX3L
C: E3 ubiquitin-protein ligase DTX3L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4917
Polymers35,7892
Non-polymers7035
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-7 kcal/mol
Surface area12580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.323, 76.146, 138.753
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
E3 ubiquitin-protein ligase DTX3L / B-lymphoma- and BAL-associated protein / Protein deltex-3-like / Rhysin-2 / Rhysin2


Mass: 17894.252 Da / Num. of mol.: 4 / Fragment: carboxyl terminal domain (UNP residues 601-740)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BBAP, DTX3L / Plasmid: PET28A-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: Q8TDB6, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 607 / 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: 3.05 Å3/Da / Density % sol: 59.65 %
Description: THE SE-MET DATA SET USED FOR PHASING WAS COLLECTED AT A WAVELENGTH OF 0.97946
Crystal growTemperature: 293 K / pH: 6
Details: 22% PEG3350, 0.2 M TRI-LITHIUM CITRATE PH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97949, 0.97946
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 22, 2010
RadiationMonochromator: DOUBLE CRYSTAL CRYO-COOLED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979491
20.979461
ReflectionResolution: 1.7→30 Å / Num. obs: 88378 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Rsym value: 0.074 / Net I/σ(I): 31.6279
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 2.73 % / Mean I/σ(I) obs: 7.4 / Rsym value: 0.643 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXC/D/Emodel building
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXC/D/Ephasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.427 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18621 2043 2.3 %RANDOM
Rwork0.16506 ---
obs0.16558 86249 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.972 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20 Å20 Å2
2---0.28 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4259 0 72 607 4938
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224607
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5461.9836251
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8615578
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.46623.2200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.515784
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4491532
X-RAY DIFFRACTIONr_chiral_restr0.1070.2647
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213568
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.8431.52787
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.57724545
X-RAY DIFFRACTIONr_scbond_it2.67931820
X-RAY DIFFRACTIONr_scangle_it4.5184.51701
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.214 6368 -
Rfree-0 -
obs--99.55 %
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)
10.73950.20290.14311.38390.03470.8290.0404-0.099-0.02380.055-0.0294-0.01580.1007-0.0415-0.0110.05650.0055-0.02880.0313-0.0130.03761.1238.001-26.999
21.9944-0.35660.81530.70580.41581.0754-0.12420.18070.164-0.16140.0355-0.0304-0.21870.19520.08860.0705-0.0388-0.02740.10010.02810.078224.49861.785-11.114
30.91940.35531.10030.91480.90552.07110.0862-0.207-0.06390.1274-0.07850.01190.2607-0.2236-0.00770.074-0.0289-0.02830.12590.01030.069113.35650.3281.162
40.46750.04540.2572.50290.37810.5183-0.04060.12240.0389-0.31610.0488-0.1617-0.0430.0718-0.00820.1186-0.00250.01160.0434-0.00590.05689.02149.245-42.093
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A606 - 740
2X-RAY DIFFRACTION2B607 - 740
3X-RAY DIFFRACTION3C606 - 740
4X-RAY DIFFRACTION4D607 - 740

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