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- PDB-6iet: The crystal structure of TRIM66 PHD-Bromo domain -

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Basic information

Entry
Database: PDB / ID: 6iet
TitleThe crystal structure of TRIM66 PHD-Bromo domain
ComponentsTripartite motif-containing protein 66
KeywordsTRANSCRIPTION / TRIM66 / PHD-Bromo
Function / homology
Function and homology information


chromatin / zinc ion binding / nucleus
Similarity search - Function
Tripartite motif-containing protein 66 / B-box, C-terminal / B-Box C-terminal domain / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, PHD-type, conserved site ...Tripartite motif-containing protein 66 / B-box, C-terminal / B-Box C-terminal domain / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Bromodomain-like / Histone Acetyltransferase; Chain A / Zinc finger, FYVE/PHD-type / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Tripartite motif-containing protein 66
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.101 Å
AuthorsChen, J.
CitationJournal: Nat Commun / Year: 2019
Title: TRIM66 reads unmodified H3R2K4 and H3K56ac to respond to DNA damage in embryonic stem cells.
Authors: Chen, J. / Wang, Z. / Guo, X. / Li, F. / Wei, Q. / Chen, X. / Gong, D. / Xu, Y. / Chen, W. / Liu, Y. / Kang, J. / Shi, Y.
History
DepositionSep 17, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2020Group: 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 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: Tripartite motif-containing protein 66
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7393
Polymers22,6081
Non-polymers1312
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area40 Å2
ΔGint-8 kcal/mol
Surface area9070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.192, 54.192, 108.310
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Tripartite motif-containing protein 66


Mass: 22607.797 Da / Num. of mol.: 1 / Fragment: UNP residues 968-1160
Mutation: L1002T, C1026S, C1030S, H1031Y, M1036K, I1089T, C1135S, V1138N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM66 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O15016
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.03 Å3/Da / Density % sol: 39.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 30%(w/v)5000 MME, 100mM Tris base/ Hydrochloric acid pH 8.0, 200mM Lithium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.101→27.096 Å / Num. obs: 10413 / % possible obs: 99.04 % / Redundancy: 20.5 % / Biso Wilson estimate: 37.01 Å2 / Rmerge(I) obs: 0.128 / Net I/σ(I): 34.33
Reflection shellResolution: 2.101→2.176 Å / Rmerge(I) obs: 0.434 / Num. unique obs: 1026

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
SCALA3.3.22data scaling
PDB_EXTRACT3.24data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3O33

3o33


Resolution: 2.101→27.096 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.43 / Phase error: 27.93
RfactorNum. reflection% reflection
Rfree0.2561 494 4.75 %
Rwork0.2063 --
obs0.2087 10410 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 76.75 Å2 / Biso mean: 40.1332 Å2 / Biso min: 21.67 Å2
Refinement stepCycle: final / Resolution: 2.101→27.096 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1254 0 2 56 1312
Biso mean--35.99 41.63 -
Num. residues----161
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081288
X-RAY DIFFRACTIONf_angle_d0.8391747
X-RAY DIFFRACTIONf_chiral_restr0.049190
X-RAY DIFFRACTIONf_plane_restr0.006224
X-RAY DIFFRACTIONf_dihedral_angle_d9.502777
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1011-2.31250.27311230.194424862609100
2.3125-2.64680.27181140.211924902604100
2.6468-3.33380.27821440.23652474261899
3.3338-27.09820.23711130.19382466257998

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