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- PDB-2r0v: Structure of the Rsc4 tandem bromodomain acetylated at K25 -

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Basic information

Entry
Database: PDB / ID: 2r0v
TitleStructure of the Rsc4 tandem bromodomain acetylated at K25
ComponentsChromatin structure-remodeling complex protein RSC4
KeywordsTRANSCRIPTION / bromodomain / chromatin / remodeler / RSC / histone / acetylation / Chromatin regulator / Nucleus / Phosphorylation / Transcription regulation
Function / homology
Function and homology information


nucleosome disassembly / RSC-type complex / transcription elongation by RNA polymerase II / lysine-acetylated histone binding / chromatin remodeling / chromatin binding / chromatin
Similarity search - Function
Remodelling complex subunit Rsc/polybromo / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily ...Remodelling complex subunit Rsc/polybromo / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chromatin structure-remodeling complex subunit RSC4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å
AuthorsVanDemark, A.P. / Kasten, M.M. / Ferris, E. / Heroux, A. / Hill, C.P. / Cairns, B.R.
CitationJournal: Mol.Cell / Year: 2007
Title: Autoregulation of the rsc4 tandem bromodomain by gcn5 acetylation.
Authors: VanDemark, A.P. / Kasten, M.M. / Ferris, E. / Heroux, A. / Hill, C.P. / Cairns, B.R.
History
DepositionAug 21, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chromatin structure-remodeling complex protein RSC4
B: Chromatin structure-remodeling complex protein RSC4
C: Chromatin structure-remodeling complex protein RSC4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,8248
Polymers120,3443
Non-polymers4805
Water7,332407
1
A: Chromatin structure-remodeling complex protein RSC4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4034
Polymers40,1151
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Chromatin structure-remodeling complex protein RSC4


Theoretical massNumber of molelcules
Total (without water)40,1151
Polymers40,1151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Chromatin structure-remodeling complex protein RSC4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3073
Polymers40,1151
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)123.246, 83.169, 127.059
Angle α, β, γ (deg.)90.00, 109.27, 90.00
Int Tables number5
Space group name H-MC121
DetailsThere are 3 biological units in the asmmetric unit (chain A, chain B, and Chain C)

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Components

#1: Protein Chromatin structure-remodeling complex protein RSC4 / Remodel the structure of chromatin complex subunit 4


Mass: 40114.727 Da / Num. of mol.: 3 / Fragment: Rsc4 TBD (1-340)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RSC4 / Plasmid: pET151-D/TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Codon+ / References: UniProt: Q02206
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 407 / 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: 2.55 Å3/Da / Density % sol: 51.84 %
Crystal growTemperature: 298 K / pH: 8
Details: 0.1M Tris, 0.2M ammonium sulfate, 22% PEG 4000, pH 8.0, VAPOR DIFFUSION, temperature 298K, pH 8.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2005
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 50527 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 13.8
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.503 / % possible all: 99.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å46.64 Å
Translation2.5 Å46.64 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→50 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.94 / SU B: 13.215 / SU ML: 0.162 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.289 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23 2569 5.1 %RANDOM
Rwork0.178 ---
obs0.18 50522 99.4 %-
all-50781 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.38 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20 Å2-0.42 Å2
2--0.63 Å20 Å2
3----1.17 Å2
Refinement stepCycle: LAST / Resolution: 2.35→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7269 0 25 407 7701
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0227484
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2831.98210127
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4875870
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.32525.752379
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.915151371
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2751515
X-RAY DIFFRACTIONr_chiral_restr0.0930.21093
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025650
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1990.23426
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.25106
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2435
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2090.275
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.551.54526
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.98527168
X-RAY DIFFRACTIONr_scbond_it1.61233339
X-RAY DIFFRACTIONr_scangle_it2.6184.52959
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.41 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 207 -
Rwork0.237 3513 -
obs--98.54 %

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