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- PDB-8dei: Structure of the Cac1 KER domain -

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Basic information

Entry
Database: PDB / ID: 8dei
TitleStructure of the Cac1 KER domain
ComponentsMaltodextrin-binding protein,Chromatin assembly factor 1 subunit p90 fusion
KeywordsDNA BINDING PROTEIN / chromatin / DNA binding
Function / homology
Function and homology information


CAF-1 complex / DNA replication-dependent chromatin assembly / chromosome, centromeric region / carbohydrate transmembrane transporter activity / nucleosome / nucleosome assembly / chromatin organization / outer membrane-bounded periplasmic space / DNA replication / DNA repair ...CAF-1 complex / DNA replication-dependent chromatin assembly / chromosome, centromeric region / carbohydrate transmembrane transporter activity / nucleosome / nucleosome assembly / chromatin organization / outer membrane-bounded periplasmic space / DNA replication / DNA repair / chromatin / nucleus
Similarity search - Function
: / Chromatin assembly factor 1 subunit Cac1, C-terminal domain / Chromatin assembly factor 1 subunit A / Chromatin assembly factor 1 subunit A / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Maltodextrin-binding protein / Chromatin assembly factor 1 subunit p90
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsRosas, R. / Churchill, M.E.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM135604 United States
CitationJournal: Elife / Year: 2023
Title: A novel single alpha-helix DNA-binding domain in CAF-1 promotes gene silencing and DNA damage survival through tetrasome-length DNA selectivity and spacer function.
Authors: Rosas, R. / Aguilar, R.R. / Arslanovic, N. / Seck, A. / Smith, D.J. / Tyler, J.K. / Churchill, M.E.A.
History
DepositionJun 20, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / citation_author
Revision 1.2Oct 25, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.3Feb 14, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Maltodextrin-binding protein,Chromatin assembly factor 1 subunit p90 fusion
B: Maltodextrin-binding protein,Chromatin assembly factor 1 subunit p90 fusion
C: Maltodextrin-binding protein,Chromatin assembly factor 1 subunit p90 fusion
D: Maltodextrin-binding protein,Chromatin assembly factor 1 subunit p90 fusion
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,15011
Polymers222,4334
Non-polymers7187
Water19811
1
A: Maltodextrin-binding protein,Chromatin assembly factor 1 subunit p90 fusion


Theoretical massNumber of molelcules
Total (without water)55,6081
Polymers55,6081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Maltodextrin-binding protein,Chromatin assembly factor 1 subunit p90 fusion
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8203
Polymers55,6081
Non-polymers2122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Maltodextrin-binding protein,Chromatin assembly factor 1 subunit p90 fusion
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0075
Polymers55,6081
Non-polymers3994
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Maltodextrin-binding protein,Chromatin assembly factor 1 subunit p90 fusion
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7142
Polymers55,6081
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.586, 165.249, 116.149
Angle α, β, γ (deg.)90.000, 96.475, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Maltodextrin-binding protein,Chromatin assembly factor 1 subunit p90 fusion / CAF-1 90 kDa subunit / RAP1 localization factor 2


Mass: 55608.172 Da / Num. of mol.: 4 / Fragment: KER domain, residues 136-225
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: malE, malE_1, malE_2, RLF2, CAC1, YPR018W, YP9531.12 / Strain: ATCC 204508 / S288c / Production host: Escherichia coli (E. coli) / References: UniProt: C3SHQ8, UniProt: Q12495
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.3 Å3/Da / Density % sol: 46.46 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Phosphate/citrate pH 4.2 and 30 % PEG 300

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Mar 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.81→28.68 Å / Num. obs: 48320 / % possible obs: 99 % / Redundancy: 3.9 % / Biso Wilson estimate: 46.75 Å2 / CC1/2: 0.979 / Net I/σ(I): 7.3
Reflection shellResolution: 2.81→2.91 Å / Redundancy: 3 % / Num. unique obs: 13259 / CC1/2: 0.695 / % possible all: 90.9

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Processing

Software
NameVersionClassification
Cootmodel building
PHENIX1.17.1_3660refinement
CrysalisProdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PEB

1peb


Resolution: 2.81→28.68 Å / SU ML: 0.4341 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.7751
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2825 4768 9.99 %
Rwork0.233 42974 -
obs0.238 47742 97.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.56 Å2
Refinement stepCycle: LAST / Resolution: 2.81→28.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14659 0 43 11 14713
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001114988
X-RAY DIFFRACTIONf_angle_d0.342220201
X-RAY DIFFRACTIONf_chiral_restr0.03482166
X-RAY DIFFRACTIONf_plane_restr0.00232630
X-RAY DIFFRACTIONf_dihedral_angle_d16.1035685
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.81-2.840.38361370.29091220X-RAY DIFFRACTION84.08
2.84-2.880.37591430.31541293X-RAY DIFFRACTION90.54
2.88-2.910.31381570.27341411X-RAY DIFFRACTION95.55
2.91-2.950.31181590.26961446X-RAY DIFFRACTION99.14
2.95-2.990.40181660.28011490X-RAY DIFFRACTION99.58
2.99-3.030.33961530.28341406X-RAY DIFFRACTION99.24
3.03-3.070.36111640.27721460X-RAY DIFFRACTION99.69
3.07-3.120.33851600.26391451X-RAY DIFFRACTION99.38
3.12-3.160.37081660.27581494X-RAY DIFFRACTION99.88
3.16-3.220.35621590.28631420X-RAY DIFFRACTION99.37
3.22-3.270.32271610.26061445X-RAY DIFFRACTION99.69
3.27-3.330.34711640.26071473X-RAY DIFFRACTION99.39
3.33-3.390.31921580.26661454X-RAY DIFFRACTION99.26
3.39-3.460.30821580.2451426X-RAY DIFFRACTION99.25
3.46-3.540.28311600.24141478X-RAY DIFFRACTION98.91
3.54-3.620.29091580.23561435X-RAY DIFFRACTION99.38
3.62-3.710.27641590.22321441X-RAY DIFFRACTION99.56
3.71-3.810.2511640.22511477X-RAY DIFFRACTION98.8
3.81-3.920.28291570.2351392X-RAY DIFFRACTION97.42
3.92-4.050.30151630.22711427X-RAY DIFFRACTION96.77
4.05-4.190.27351580.22291410X-RAY DIFFRACTION96.37
4.19-4.360.26551610.19981443X-RAY DIFFRACTION98.65
4.36-4.560.23951600.1961423X-RAY DIFFRACTION97.84
4.56-4.80.21571590.19471428X-RAY DIFFRACTION97.18
4.8-5.10.24811610.19411444X-RAY DIFFRACTION98.53
5.1-5.490.24491640.21021462X-RAY DIFFRACTION99.03
5.49-6.040.30341570.22991454X-RAY DIFFRACTION98.9
6.04-6.90.27751610.23011452X-RAY DIFFRACTION99.26
6.9-8.650.22981620.20921465X-RAY DIFFRACTION98.25
8.65-28.680.22271590.22481454X-RAY DIFFRACTION96.76

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