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- PDB-5jxr: Crystal structure of MtISWI -

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Basic information

Entry
Database: PDB / ID: 5jxr
TitleCrystal structure of MtISWI
ComponentsChromatin-remodeling complex ATPase-like protein
KeywordsTRANSCRIPTION / chromatin remodeler / ISWI
Function / homology
Function and homology information


ATP-dependent chromatin remodeler activity / nucleosome binding / hydrolase activity / DNA binding / ATP binding / nucleus
Similarity search - Function
Isw1/2, N-terminal / ISWI, HAND domain / SLIDE domain / ISWI, HAND domain superfamily / HAND / SLIDE / SANT domain profile. / SANT domain / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal ...Isw1/2, N-terminal / ISWI, HAND domain / SLIDE domain / ISWI, HAND domain superfamily / HAND / SLIDE / SANT domain profile. / SANT domain / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Helicase conserved C-terminal domain / Homeobox-like domain superfamily / 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 nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chromatin-remodeling complex ATPase-like protein
Similarity search - Component
Biological speciesMyceliophthora thermophila (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.404 Å
AuthorsChen, Z. / Yan, L.
CitationJournal: Nature / Year: 2016
Title: Structure and regulation of the chromatin remodeller ISWI
Authors: Yan, L. / Wang, L. / Tian, Y. / Xia, X. / Chen, Z.
History
DepositionMay 13, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2017Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chromatin-remodeling complex ATPase-like protein
B: Chromatin-remodeling complex ATPase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,8424
Polymers166,7712
Non-polymers712
Water6,377354
1
A: Chromatin-remodeling complex ATPase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,4212
Polymers83,3861
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-10 kcal/mol
Surface area32430 Å2
MethodPISA
2
B: Chromatin-remodeling complex ATPase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,4212
Polymers83,3861
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-10 kcal/mol
Surface area32470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.767, 127.767, 106.666
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Chromatin-remodeling complex ATPase-like protein


Mass: 83385.672 Da / Num. of mol.: 2 / Fragment: UNP residues 81-803
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myceliophthora thermophila (strain ATCC 42464 / BCRC 31852 / DSM 1799) (fungus)
Strain: ATCC 42464 / BCRC 31852 / DSM 1799 / Gene: MYCTH_2307364 / Production host: Escherichia coli (E. coli) / References: UniProt: G2QFM3
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 354 / 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: 3.01 Å3/Da / Density % sol: 59.19 %
Crystal growTemperature: 277 K / Method: evaporation / Details: PEG3350,200 mM NaAc

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 75016 / % possible obs: 99.05 % / Redundancy: 5.2 % / Net I/σ(I): 27

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
HKL-2000v705adata reduction
HKL-2000v705adata scaling
PHASERv7.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.404→32.91 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 25.56
RfactorNum. reflection% reflection
Rfree0.2255 3770 5.03 %
Rwork0.1947 --
obs0.1963 75016 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.404→32.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10098 0 2 354 10454
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00410268
X-RAY DIFFRACTIONf_angle_d0.79613828
X-RAY DIFFRACTIONf_dihedral_angle_d13.53940
X-RAY DIFFRACTIONf_chiral_restr0.0561516
X-RAY DIFFRACTIONf_plane_restr0.0031808
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4043-2.43480.31141410.28062517X-RAY DIFFRACTION94
2.4348-2.46680.33391210.28132611X-RAY DIFFRACTION99
2.4668-2.50060.31341450.27362688X-RAY DIFFRACTION100
2.5006-2.53630.32871360.25872650X-RAY DIFFRACTION100
2.5363-2.57410.28271480.26012646X-RAY DIFFRACTION100
2.5741-2.61430.31511640.2392711X-RAY DIFFRACTION100
2.6143-2.65720.28011460.23292597X-RAY DIFFRACTION100
2.6572-2.7030.31791270.23772703X-RAY DIFFRACTION100
2.703-2.75210.30641500.23452601X-RAY DIFFRACTION100
2.7521-2.8050.31881310.23272737X-RAY DIFFRACTION100
2.805-2.86220.28421260.22332653X-RAY DIFFRACTION100
2.8622-2.92440.28921260.23242714X-RAY DIFFRACTION100
2.9244-2.99240.28211280.22582664X-RAY DIFFRACTION100
2.9924-3.06720.26331360.22512653X-RAY DIFFRACTION100
3.0672-3.15010.25961300.21712693X-RAY DIFFRACTION100
3.1501-3.24270.23851260.22592641X-RAY DIFFRACTION100
3.2427-3.34730.24171640.21112661X-RAY DIFFRACTION100
3.3473-3.46680.24361750.20712638X-RAY DIFFRACTION100
3.4668-3.60540.26691360.19162650X-RAY DIFFRACTION100
3.6054-3.76930.22311460.19012682X-RAY DIFFRACTION100
3.7693-3.96770.19991320.1782683X-RAY DIFFRACTION100
3.9677-4.21580.18881500.17562636X-RAY DIFFRACTION100
4.2158-4.54050.1921410.1632661X-RAY DIFFRACTION100
4.5405-4.9960.18511440.15672653X-RAY DIFFRACTION100
4.996-5.71570.20131510.18232658X-RAY DIFFRACTION100
5.7157-7.18880.21261300.19582677X-RAY DIFFRACTION100
7.1888-32.9130.17171200.16492168X-RAY DIFFRACTION82

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