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- PDB-5j3e: Crystal Structure of Human THYN1 protein in complex with 5-methyl... -

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Basic information

Entry
Database: PDB / ID: 5j3e
TitleCrystal Structure of Human THYN1 protein in complex with 5-methylcytosine containing DNA
Components
  • 5-methylcytosine containing DNA
  • Thymocyte nuclear protein 1
KeywordsNUCLEAR PROTEIN/DNA / protein-DNA complex / modified DNA / 5-methylcytosine containing DNA / Structural Genomics Consortium / SGC / NUCLEAR PROTEIN-DNA complex
Function / homology
Function and homology information


: / EVE domain / EVE domain / ph1033 like fold / ph1033 like domains / PUA-like superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Thymocyte nuclear protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsHalabelian, L. / Tempel, W. / Li, Y. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Structural Genomics Consortium (SGC)
CitationJournal: To be published
Title: Crystal Structure of Human THYN1 protein in complex with 5-methylcytosine containing DNA
Authors: Halabelian, L. / Tempel, W. / Li, Y. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H.
History
DepositionMar 30, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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

Downloads & links

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Assembly

Deposited unit
A: Thymocyte nuclear protein 1
B: Thymocyte nuclear protein 1
C: 5-methylcytosine containing DNA
D: 5-methylcytosine containing DNA
E: 5-methylcytosine containing DNA
F: 5-methylcytosine containing DNA


Theoretical massNumber of molelcules
Total (without water)66,19014
Polymers66,1906
Non-polymers08
Water18010
1
A: Thymocyte nuclear protein 1
E: 5-methylcytosine containing DNA
F: 5-methylcytosine containing DNA


Theoretical massNumber of molelcules
Total (without water)33,0956
Polymers33,0953
Non-polymers03
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-5 kcal/mol
Surface area11790 Å2
MethodPISA
2
B: Thymocyte nuclear protein 1
C: 5-methylcytosine containing DNA
D: 5-methylcytosine containing DNA


Theoretical massNumber of molelcules
Total (without water)33,0958
Polymers33,0953
Non-polymers05
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-4 kcal/mol
Surface area11460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.327, 73.232, 108.201
Angle α, β, γ (deg.)90.000, 91.180, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 2 / Auth seq-ID: 218 - 222 / Label seq-ID: 218 - 222

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

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Components

#1: Protein Thymocyte nuclear protein 1 / Thymocyte protein Thy28


Mass: 25740.361 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: THYN1, THY28, HSPC144, MDS012, My0054 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V3R-pRARE2 / References: UniProt: Q9P016
#2: DNA chain
5-methylcytosine containing DNA / 5-methylcytosine containing DNA


Mass: 3677.419 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: Synthesized by IDTDNA / Source: (synth.) Homo sapiens (human)
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 8 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.41 Å3/Da / Density % sol: 49.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: 0.1M TRISODIUM CITRATE, 0.2M NaCl, 30% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.6→43.51 Å / Num. obs: 19516 / % possible obs: 99.8 % / Redundancy: 3.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.056 / Rrim(I) all: 0.11 / Net I/σ(I): 12.8 / Num. measured all: 73091
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) all% possible all
2.6-2.723.80.7292.1914824090.7640.4350.85100
9.01-43.513.40.02438.516744890.9990.0150.02897.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
Aimless0.5.9data scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EOP

3eop


Resolution: 2.6→43.51 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.919 / WRfactor Rfree: 0.2235 / WRfactor Rwork: 0.1826 / FOM work R set: 0.7527 / SU B: 32.564 / SU ML: 0.294 / SU R Cruickshank DPI: 0.5723 / SU Rfree: 0.2964 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.572 / ESU R Free: 0.296 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: Molecular Replacement
RfactorNum. reflection% reflectionSelection details
Rfree0.2488 941 4.8 %RANDOM
Rwork0.2087 ---
obs0.2106 18559 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 100.03 Å2 / Biso mean: 54.604 Å2 / Biso min: 24.21 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å21.34 Å2
2---1.17 Å2-0 Å2
3---1.54 Å2
Refinement stepCycle: final / Resolution: 2.6→43.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2728 976 8 10 3722
Biso mean--34.78 42.19 -
Num. residues----391
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0173942
X-RAY DIFFRACTIONr_bond_other_d0.0040.023137
X-RAY DIFFRACTIONr_angle_refined_deg1.3791.7375550
X-RAY DIFFRACTIONr_angle_other_deg1.07837259
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7875341
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.80624.37135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.83415471
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.411514
X-RAY DIFFRACTIONr_chiral_restr0.0790.2547
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213767
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02891
X-RAY DIFFRACTIONr_mcbond_it0.8632.1421370
X-RAY DIFFRACTIONr_mcbond_other0.8592.141369
X-RAY DIFFRACTIONr_mcangle_it1.4663.2091709
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
37MEDIUM POSITIONAL0.020.5
30TIGHT THERMAL3.070.5
37MEDIUM THERMAL3.362
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.42 85 -
Rwork0.343 1356 -
all-1441 -
obs--99.93 %
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)
12.9126-0.3452-1.76572.1566-0.81425.1837-0.04010.416-0.0125-0.3068-0.09250.01330.0630.03530.13250.29170.0190.11670.1453-0.01660.2618-18.501813.9421-48.056
23.621-1.0565-2.68632.79561.62014.5242-0.2003-0.0004-0.11050.1735-0.19050.53080.2996-0.15090.39080.2569-0.03790.34570.0204-0.0760.5197-39.728910.3239-6.3277
37.1109-2.1821.52882.1841-0.48890.34970.11380.2336-0.00970.0552-0.10730.2153-0.0146-0.0318-0.00640.13480.04520.11770.5077-0.09940.777-53.324728.8705-15.3184
411.8755-0.1477-0.26660.9305-0.60120.41350.0190.2273-0.03160.0973-0.0866-0.0451-0.11340.01830.06750.2355-0.032-0.07430.4732-0.05840.6812-52.995227.556-15.5761
511.39821.4224-0.06951.01840.03970.2666-0.42520.29021.1335-0.13620.20680.1805-0.13670.16230.21840.1856-0.034-0.06150.53130.05340.4932-7.185330.2953-38.011
610.82560.5455-0.96821.09760.61060.4992-0.07390.36480.1270.05910.02660.04680.0234-0.00610.04730.16290.0326-0.00740.56470.07840.4252-7.028831.75-38.2
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A53 - 224
2X-RAY DIFFRACTION2B54 - 224
3X-RAY DIFFRACTION3C1 - 12
4X-RAY DIFFRACTION4D1 - 12
5X-RAY DIFFRACTION5E1 - 12
6X-RAY DIFFRACTION6F1 - 12

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