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- PDB-2h1e: Tandem chromodomains of budding yeast CHD1 -

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Basic information

Entry
Database: PDB / ID: 2h1e
TitleTandem chromodomains of budding yeast CHD1
ComponentsChromo domain protein 1
KeywordsHYDROLASE / CHD1 / chromodomain / tandem chromodomains / three-stranded antiparallel b-sheet
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 / rDNA binding / nucleosome organization / SLIK (SAGA-like) complex / sister chromatid cohesion / 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 / rDNA binding / nucleosome organization / SLIK (SAGA-like) complex / sister chromatid cohesion / ATP-dependent chromatin remodeler activity / SAGA complex / 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 / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / chromatin DNA binding / histone binding / transcription cis-regulatory region binding / chromatin remodeling / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / ATP hydrolysis activity / mitochondrion / DNA binding / ATP binding / nucleus
Similarity search - Function
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. ...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. / : / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / Chromo/chromo shadow domain / Chromatin organization modifier domain / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Chromo-like domain superfamily / Helicase conserved C-terminal domain / Homeobox-like domain superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / 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 / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Chromo domain-containing protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsFlanagan IV, J.F. / Khorasanizadeh, S.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Molecular Implications of Evolutionary Differences in CHD Double Chromodomains.
Authors: Flanagan, J.F. / Blus, B.J. / Kim, D. / Clines, K.L. / Rastinejad, F. / Khorasanizadeh, S.
History
DepositionMay 16, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 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
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). ACCORDING TO AUTHORS, THE BIOLOGICAL UNIT OF THE PROTEIN IN VIVO IS UNKNOWN

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chromo domain protein 1
B: Chromo domain protein 1


Theoretical massNumber of molelcules
Total (without water)42,8922
Polymers42,8922
Non-polymers00
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-9 kcal/mol
Surface area19130 Å2
MethodPISA
2
A: Chromo domain protein 1
B: Chromo domain protein 1

A: Chromo domain protein 1
B: Chromo domain protein 1


Theoretical massNumber of molelcules
Total (without water)85,7844
Polymers85,7844
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_665-x+1,-y+1,z1
Buried area8910 Å2
ΔGint-25 kcal/mol
Surface area33780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.185, 136.185, 57.516
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11A-228-

HOH

21B-187-

HOH

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Components

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


Mass: 21446.033 Da / Num. of mol.: 2 / Fragment: chromodomain, residues 174-339
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CHD1 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 lysogen pLysS
References: UniProt: P32657, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 3.11 Å3/Da / Density % sol: 60.43 %
Crystal growTemperature: 283 K / pH: 8
Details: 10mM BTP, 12mM NaCl, 5mM TCEP, 0.9M ammonium sulfate, 3.75% isopropanol, 4.5mg/ml yeast CHD1 tandem chromodomains, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 283K, pH 8.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 12, 2005
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→19.57 Å / Num. obs: 25838 / % possible obs: 95.7 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rsym value: 0.104 / Net I/σ(I): 10.8
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2 % / Mean I/σ(I) obs: 1.7 / Rsym value: 0.449 / % possible all: 80.9

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Phasing

Phasing MRRfactor: 0.537 / Cor.coef. Fo:Fc: 0.293
Highest resolutionLowest resolution
Rotation4 Å43.09 Å
Translation4 Å43.09 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2B2Y, CHAIN A WITHOUT B1-B2 LOOP

2b2y


Resolution: 2.2→19.57 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.909 / SU B: 8.541 / SU ML: 0.139 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.208 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1299 5 %RANDOM
Rwork0.189 ---
obs0.192 25796 95.7 %-
all-25934 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.85 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2740 0 0 194 2934
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0222791
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2261.9383778
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg28.1265327
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.94124.78159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.40815508
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2821521
X-RAY DIFFRACTIONr_chiral_restr0.2660.2411
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022143
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2730.31306
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3180.51893
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2460.5305
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2660.385
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2230.527
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.251.51694
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.33822661
X-RAY DIFFRACTIONr_scbond_it4.38331258
X-RAY DIFFRACTIONr_scangle_it6.1894.51117
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.25 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 66 -
Rwork0.227 1436 -
obs--78.11 %
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)
13.65940.5781-1.83862.65880.7385.4953-0.26150.1116-0.4682-0.06880.0583-0.13030.5421-0.07110.2032-0.0862-0.01110.0081-0.16390.0222-0.072261.3443.2756.838
21.3981.6446-0.25482.10770.1091.01180.2871-0.18220.1040.3429-0.35170.1090.16360.07730.0646-0.009-0.05920.0103-0.0058-0.0076-0.127253.77553.72320.585
32.33833.21043.02816.53064.02654.9703-0.25310.3394-0.4014-0.7520.3672-0.4224-0.21590.3631-0.11410.013-0.03780.1258-0.0599-0.10650.004169.65843.608-12.869
43.40410.5676-1.35342.89261.76333.72430.0261-0.05670.16570.0573-0.12460.38630.1453-0.30230.0985-0.1511-0.0008-0.0199-0.11460.0046-0.084244.06260.9896.881
50.46510.50640.16720.94321.03331.9097-0.2080.10660.0204-0.14040.19570.0709-0.0513-0.08350.0123-0.0388-0.0650.0066-0.0543-0.0037-0.109153.73653.754-6.585
64.37791.8877-0.46360.97690.1971.5087-0.06380.19230.3186-0.24210.09290.2818-0.23610.0224-0.0291-0.0316-0.0382-0.0438-0.1040.0515-0.072455.97269.33-2.493
77.04272.2548-5.23682.136-3.10768.07440.1642-0.69390.29510.2718-0.10560.4027-0.11420.0205-0.0586-0.0546-0.03630.08870.0218-0.14220.002343.48969.74126.871
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 15
2X-RAY DIFFRACTION1A39 - 66
3X-RAY DIFFRACTION2A16 - 38
4X-RAY DIFFRACTION3A113 - 161
5X-RAY DIFFRACTION4B13 - 15
6X-RAY DIFFRACTION4B39 - 66
7X-RAY DIFFRACTION5B16 - 38
8X-RAY DIFFRACTION6B67 - 112
9X-RAY DIFFRACTION7B113 - 161

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