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- PDB-3mwy: Crystal structure of the chromodomain-ATPase portion of the yeast... -

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Basic information

Entry
Database: PDB / ID: 3mwy
TitleCrystal structure of the chromodomain-ATPase portion of the yeast Chd1 chromatin remodeler
ComponentsChromo domain-containing protein 1
KeywordsHYDROLASE / SWI2/SNF2 ATPase / double chromodomains
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 / nucleosome organization / rDNA binding / SLIK (SAGA-like) complex / SAGA complex / ATP-dependent chromatin remodeler activity / sister chromatid cohesion ...nucleolar chromatin / regulation of transcriptional start site selection at RNA polymerase II promoter / negative regulation of DNA-templated DNA replication / regulation of chromatin organization / nucleosome organization / rDNA binding / SLIK (SAGA-like) complex / SAGA complex / ATP-dependent chromatin remodeler activity / 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 / 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
Tandem AAA-ATPase domain / 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 ...Tandem AAA-ATPase domain / 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 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / 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 / P-loop containing nucleotide triphosphate hydrolases / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Chromo domain-containing protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.7 Å
AuthorsHauk, G. / Bowman, G.D.
CitationJournal: Mol.Cell / Year: 2010
Title: The chromodomains of the Chd1 chromatin remodeler regulate DNA access to the ATPase motor.
Authors: Hauk, G. / McKnight, J.N. / Nodelman, I.M. / Bowman, G.D.
History
DepositionMay 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 30, 2013Group: Non-polymer description
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Sep 6, 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 / 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

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Assembly

Deposited unit
W: Chromo domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,9662
Polymers92,4431
Non-polymers5231
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
W: Chromo domain-containing protein 1
hetero molecules

W: Chromo domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,9334
Polymers184,8872
Non-polymers1,0462
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_675x-y+1,-y+2,-z1
Buried area4440 Å2
ΔGint-23 kcal/mol
Surface area67240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.333, 94.333, 450.088
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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


Mass: 92443.250 Da / Num. of mol.: 1
Fragment: double chromodomains and ATPase motor (UNP residues 142-939)
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(DE3)star
References: UniProt: P32657, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM

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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: 3.13 Å3/Da / Density % sol: 60.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 18% PEG 3350; 400 mM K+/Na+ tartrate; 5% xylitol; 10 mM MgCl2; 1 mM ATPgammaS, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792,0.9611
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 29, 2008
RadiationMonochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.96111
ReflectionResolution: 3.7→50 Å / Num. all: 24026 / Num. obs: 20114 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.5 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 20.9
Reflection shellResolution: 3.7→3.83 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.402 / Mean I/σ(I) obs: 4.5 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0091refinement
SOLVEphasing
SHARPphasing
PHENIXrefinement
CBASSdata collection
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD
Starting model: PDB ENTRIES 2H1E,1Z63,1Z3I

2h1e

1z63

1z3i


Resolution: 3.7→50 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.909 / SU B: 127.855 / SU ML: 0.786
Isotropic thermal model: overall temperature factors, with three TLS groups
Cross valid method: THROUGHOUT / ESU R Free: 0.797
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31772 688 5 %RANDOM
Rwork0.26186 ---
obs0.26462 12949 99.94 %-
all-12949 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 126.878 Å2
Baniso -1Baniso -2Baniso -3
1-3.44 Å21.72 Å20 Å2
2--3.44 Å20 Å2
3----5.16 Å2
Refine analyzeLuzzati coordinate error free: 0.798 Å
Refinement stepCycle: LAST / Resolution: 3.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5712 0 31 0 5743
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0225857
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6281.9617908
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4055689
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.41124.379306
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.559151079
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.411544
X-RAY DIFFRACTIONr_chiral_restr0.1110.2862
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214420
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.7→3.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 54 -
Rwork0.347 920 -
obs--99.9 %
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)
11.1540.1480.16529.6003-2.7360.991-0.16740.1874-0.5455-1.02310.3305-0.41110.82110.1982-0.16312.20140.7287-0.30160.6957-0.04490.874832.06642.039-4.393
26.65991.2729-1.32937.21562.19369.78890.2848-0.10440.0232-0.1290.39351.4037-0.6495-1.1769-0.67831.32560.8189-0.07090.78870.51021.308321.56535.62832.048
35.2001-1.82080.93039.9823-1.89759.2525-0.0717-0.1444-0.20910.41910.55550.39870.49380.7088-0.48380.5160.26810.00780.20530.05990.419932.31375.13418.9
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1W175 - 341
2X-RAY DIFFRACTION2W2000 - 2001
3X-RAY DIFFRACTION2W342 - 606
4X-RAY DIFFRACTION2W905 - 922
5X-RAY DIFFRACTION3W607 - 904

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