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- PDB-3ted: Crystal structure of the Chd1 DNA-binding domain in complex with ... -

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Basic information

Entry
Database: PDB / ID: 3ted
TitleCrystal structure of the Chd1 DNA-binding domain in complex with a DNA duplex
Components
  • 5'-D(*CP*CP*AP*TP*AP*TP*AP*TP*AP*TP*GP*C)-3'
  • 5'-D(*GP*CP*AP*TP*AP*TP*AP*TP*AP*TP*GP*G)-3'
  • Chromo domain-containing protein 1
KeywordsDNA binding protein/DNA / PROTEIN-DNA complex / DOUBLE HELIX / DNA DUPLEX / SANT and SLIDE domains / chromatin remodeling / DNA binding / nuclear / DNA binding protein-DNA complex
Function / homology
Function and homology information


nucleolar chromatin / regulation of transcriptional start site selection at RNA polymerase II promoter / negative regulation of DNA-templated DNA replication / regulation of chromatin organization / SLIK (SAGA-like) complex / rDNA binding / DNA double-strand break processing / nucleosome organization / ATP-dependent chromatin remodeler activity / SAGA complex ...nucleolar chromatin / regulation of transcriptional start site selection at RNA polymerase II promoter / negative regulation of DNA-templated DNA replication / regulation of chromatin organization / SLIK (SAGA-like) complex / rDNA binding / DNA double-strand break processing / nucleosome organization / ATP-dependent chromatin remodeler activity / SAGA complex / sister chromatid cohesion / termination of RNA polymerase II transcription / termination of RNA polymerase I transcription / ATP-dependent activity, acting on DNA / methylated histone binding / helicase activity / transcription elongation by RNA polymerase II / double-strand break repair via homologous recombination / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / chromatin DNA binding / site of double-strand break / histone binding / transcription cis-regulatory region binding / chromatin remodeling / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / ATP hydrolysis activity / mitochondrion / DNA binding / ATP binding / nucleus
Similarity search - Function
Helix Hairpins - #1440 / Chromodomain helicase DNA-binding domain / Chromodomain helicase DNA-binding domain 1 / Chromodomain-helicase-DNA-binding protein 1-like, C-terminal domain / Chromodomain-helicase-DNA-binding protein 1-like, C-terminal / DUF4208 / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain ...Helix Hairpins - #1440 / Chromodomain helicase DNA-binding domain / Chromodomain helicase DNA-binding domain 1 / Chromodomain-helicase-DNA-binding protein 1-like, C-terminal domain / Chromodomain-helicase-DNA-binding protein 1-like, C-terminal / DUF4208 / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Helix Hairpins / Homeodomain-like / Helix non-globular / Special / Helicase conserved C-terminal domain / Homeobox-like domain superfamily / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Arc Repressor Mutant, subunit A / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Chromo domain-containing protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSharma, A. / Jenkins, K.R. / Heroux, A. / Bowman, G.D.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: DNA-binding domain of Chd1 in complex with a DNA duplex
Authors: Sharma, A. / Jenkins, K.R. / Heroux, A. / Bowman, G.D.
History
DepositionAug 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chromo domain-containing protein 1
B: 5'-D(*CP*CP*AP*TP*AP*TP*AP*TP*AP*TP*GP*C)-3'
C: 5'-D(*GP*CP*AP*TP*AP*TP*AP*TP*AP*TP*GP*G)-3'


Theoretical massNumber of molelcules
Total (without water)37,8293
Polymers37,8293
Non-polymers00
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-18 kcal/mol
Surface area17410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.670, 61.426, 76.771
Angle α, β, γ (deg.)90.00, 104.17, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Chromo domain-containing protein 1 / ATP-dependent helicase CHD1


Mass: 30505.826 Da / Num. of mol.: 1
Fragment: SANT/SLIDE DNA-binding domain, UNP residues 1006-1274
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CHD1, SYGP-ORF4, YER164W / Plasmid: pDEST17 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 star (DE3)
References: UniProt: P32657, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: DNA chain 5'-D(*CP*CP*AP*TP*AP*TP*AP*TP*AP*TP*GP*C)-3'


Mass: 3621.392 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: artificial AT-rich sequence; synthesized by Integrated DNA Technologies
#3: DNA chain 5'-D(*GP*CP*AP*TP*AP*TP*AP*TP*AP*TP*GP*G)-3'


Mass: 3701.440 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: artificial AT-rich sequence; synthesized by Integrated DNA Technologies
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.34 Å3/Da / Density % sol: 47.37 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 14-18% PEG 400 0.1 M BisTris, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 24, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 22675 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 18.2 % / Rsym value: 0.079 / Net I/σ(I): 37.2
Reflection shellResolution: 2→2.07 Å / Redundancy: 15 % / Rmerge(I) obs: 0.768 / Mean I/σ(I) obs: 3.2 / Rsym value: 0.768 / % possible all: 99.6

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Processing

Software
NameVersionClassification
CBASSdata collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2XB0

2xb0


Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.936 / SU B: 8.26 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.177 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24898 1214 5.1 %RANDOM
Rwork0.19262 ---
obs0.19546 22413 99.56 %-
all-21134 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.726 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å20 Å2-1.74 Å2
2--0.11 Å2-0 Å2
3----0.51 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1857 486 0 169 2512
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0182434
X-RAY DIFFRACTIONr_bond_other_d0.0010.021611
X-RAY DIFFRACTIONr_angle_refined_deg1.121.8343370
X-RAY DIFFRACTIONr_angle_other_deg1.2733933
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8045227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.3824.94387
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.68515380
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3041510
X-RAY DIFFRACTIONr_chiral_restr0.0790.2346
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022322
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02472
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_it0.3961.51137
X-RAY DIFFRACTIONr_mcbond_other0.0931.5463
X-RAY DIFFRACTIONr_mcangle_it0.74221826
X-RAY DIFFRACTIONr_scbond_it1.0831297
X-RAY DIFFRACTIONr_scangle_it1.6354.51544
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 84 -
Rwork0.281 1571 -
obs--96.56 %
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)
16.58911.13122.99322.60110.82114.2922-0.13120.15520.4582-0.1490.0624-0.1335-0.39190.3490.06880.1693-0.0618-0.02790.03590.0060.06915.975913.532225.7692
26.551.41784.54983.83421.00345.39120.16140.199-0.4079-0.2445-0.02480.08550.3926-0.4059-0.13660.3019-0.074-0.00350.33150.04510.1636-24.09034.3015-0.0857
312.01113.3319-1.35158.51220.23747.9698-0.21830.73440.3612-0.68920.1278-0.3277-0.37350.50440.09040.2038-0.0789-0.07910.13220.08280.1184-0.209911.068113.7996
43.0011-0.5891-0.0465.65140.91283.3309-0.223-0.0893-0.13910.3040.13660.42310.1448-0.16380.08640.03860.00320.02360.01760.01450.0402-6.8763-6.954631.8164
52.79961.95072.2244.37020.62872.8025-0.15490.30630.0388-0.32960.00820.0575-0.03870.08420.14670.1216-0.00430.0450.2135-0.03310.0439-3.4494-8.053110.9382
65.4962.3767-1.97263.6494-0.38822.8177-0.20830.3021-0.0438-0.3060.1132-0.2505-0.02460.12190.0950.1536-0.0017-0.03380.19580.00590.0484-2.1013-6.743711.2584
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1006 - 1063
2X-RAY DIFFRACTION2A1064 - 1117
3X-RAY DIFFRACTION3A1118 - 1132
4X-RAY DIFFRACTION4A1133 - 1266
5X-RAY DIFFRACTION5B1 - 12
6X-RAY DIFFRACTION6C1 - 12

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