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- PDB-2byk: Histone fold heterodimer of the Chromatin Accessibility Complex -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 2byk
TitleHistone fold heterodimer of the Chromatin Accessibility Complex
Components
  • CHRAC-14
  • CHRAC-16
KeywordsDNA BINDING PROTEIN / CHRAC-14 / NUCLEOSOME SLIDING / HISTONE FOLD / CHRAC-16 / DNA-BINDING PROTEIN
Function / homology
Function and homology information


DNA replication initiation / PCNA-Dependent Long Patch Base Excision Repair / Termination of translesion DNA synthesis / Recognition of DNA damage by PCNA-containing replication complex / Dual Incision in GG-NER / Dual incision in TC-NER / CHRAC / Activation of the pre-replicative complex / epsilon DNA polymerase complex / CENP-A containing chromatin assembly ...DNA replication initiation / PCNA-Dependent Long Patch Base Excision Repair / Termination of translesion DNA synthesis / Recognition of DNA damage by PCNA-containing replication complex / Dual Incision in GG-NER / Dual incision in TC-NER / CHRAC / Activation of the pre-replicative complex / epsilon DNA polymerase complex / CENP-A containing chromatin assembly / ATAC complex / leading strand elongation / heterochromatin formation / cellular response to gamma radiation / chromatin DNA binding / DNA-templated DNA replication / nucleic acid binding / molecular adaptor activity / chromatin remodeling / protein heterodimerization activity / DNA damage response / nucleus
Similarity search - Function
Transcription factor CBF/NF-Y/archaeal histone domain / Histone-like transcription factor (CBF/NF-Y) and archaeal histone / Histone, subunit A / Histone, subunit A / Histone-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA polymerase epsilon subunit 3 / Chromatin accessibility complex 16kD protein
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsFernandez-Tornero, C. / Hartlepp, K.F. / Grune, T. / Eberharter, A. / Becker, P.B. / Muller, C.W.
CitationJournal: Mol.Cell.Biol. / Year: 2005
Title: The Histone Fold Subunits of Drosophila Chrac Facilitate Nucleosome Sliding Through Dynamic DNA Interactions.
Authors: Hartlepp, K.F. / Fernandez-Tornero, C. / Eberharter, A. / Grune, T. / Muller, C.W. / Becker, P.B.
History
DepositionAug 3, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 9, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CHRAC-16
B: CHRAC-14
C: CHRAC-16
D: CHRAC-14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0557
Polymers59,7674
Non-polymers2883
Water68538
1
A: CHRAC-16
B: CHRAC-14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0754
Polymers29,8832
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: CHRAC-16
D: CHRAC-14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9793
Polymers29,8832
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)76.010, 76.010, 166.080
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.30632, 0.77157, 0.55754), (0.77331, -0.13986, 0.61841), (0.55512, 0.62059, -0.55382)-77.62991, -29.83781, 138.90033
2given(-0.29615, 0.77932, 0.55223), (0.77507, -0.14179, 0.61576), (0.55817, 0.61038, -0.56204)-77.5948, -29.77311, 139.9268

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Components

#1: Protein CHRAC-16 / CG32956-PA ISOFORM A / CG32956-PE / ISOFORM E


Mass: 16020.667 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Plasmid: PGEX2T-CHRAC14/16 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9V452
#2: Protein CHRAC-14 / RE59557P / CG15736-PA


Mass: 13862.586 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Plasmid: PGEX2T-CHRAC14/16 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9V444
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsPROTEOLYTIC CLEAVAGE IN THE CRYSTALLIZATION DROP MIGHT HAVE OCCURRED BUT ATTEMPTS TO CHARACTERIZE ...PROTEOLYTIC CLEAVAGE IN THE CRYSTALLIZATION DROP MIGHT HAVE OCCURRED BUT ATTEMPTS TO CHARACTERIZE IT WERE UNSUCCESSFUL.

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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: 2.31 Å3/Da / Density % sol: 46.3 %
Crystal growpH: 3.5 / Details: 2M AMMONIUM SULFATE, 0.1M CITRIC ACID, PH 3.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 2.4→24 Å / Num. obs: 22490 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Biso Wilson estimate: 51.6 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 4.4
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BYM

2bym


Resolution: 2.4→23.83 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1896010.14 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.278 2231 9.9 %RANDOM
Rwork0.237 ---
obs0.237 22445 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 73.8532 Å2 / ksol: 0.388442 e/Å3
Displacement parametersBiso mean: 66 Å2
Baniso -1Baniso -2Baniso -3
1-11.61 Å210.29 Å20 Å2
2--11.61 Å20 Å2
3----23.22 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 2.4→23.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2465 0 15 38 2518
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.351.5
X-RAY DIFFRACTIONc_mcangle_it2.422
X-RAY DIFFRACTIONc_scbond_it2.212
X-RAY DIFFRACTIONc_scangle_it3.632.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.345 391 10.6 %
Rwork0.35 3300 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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