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- PDB-5hzr: Crystal structure of MtSnf2 -

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Basic information

Entry
Database: PDB / ID: 5hzr
TitleCrystal structure of MtSnf2
ComponentsSNF2-family ATP dependent chromatin remodeling factor like protein
KeywordsTRANSCRIPTION / Swi2/Snf2 / chromatin remodeling
Function / homology
Function and homology information


ATP-dependent chromatin remodeler activity => GO:0140658 / histone binding / regulation of DNA-templated transcription / ATP binding / nucleus
Similarity search - Function
Glutamine-Leucine-Glutamine, QLQ / QLQ / QLQ domain profile. / QLQ / Snf2, ATP coupling domain / Snf2-ATP coupling, chromatin remodelling complex / Snf2-ATP coupling, chromatin remodelling complex / HSA domain / Helicase/SANT-associated domain / HSA domain profile. ...Glutamine-Leucine-Glutamine, QLQ / QLQ / QLQ domain profile. / QLQ / Snf2, ATP coupling domain / Snf2-ATP coupling, chromatin remodelling complex / Snf2-ATP coupling, chromatin remodelling complex / HSA domain / Helicase/SANT-associated domain / HSA domain profile. / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Helicase conserved C-terminal domain / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like 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
3-(1-methylpiperidinium-1-yl)propane-1-sulfonate / SNF2-family ATP dependent chromatin remodeling factor like protein
Similarity search - Component
Biological speciesMyceliophthora thermophila ATCC 42464 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.33 Å
AuthorsChen, Z.C. / Xia, X.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Key Research Plan-Protein Sciences2014CB910100 China
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2016
Title: Structure of chromatin remodeler Swi2/Snf2 in the resting state
Authors: Xia, X. / Liu, X. / Li, T. / Fang, X. / Chen, Z.C.
History
DepositionFeb 2, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2016Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SNF2-family ATP dependent chromatin remodeling factor like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,7499
Polymers84,5521
Non-polymers1,1968
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-18 kcal/mol
Surface area27030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.613, 144.266, 121.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1424-

HOH

21A-1433-

HOH

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Components

#1: Protein SNF2-family ATP dependent chromatin remodeling factor like protein / MtSnf2


Mass: 84552.289 Da / Num. of mol.: 1 / Fragment: UNP residues 445-1176
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myceliophthora thermophila ATCC 42464 (fungus)
Strain: ATCC 42464 / Gene: MYCTH_115909 / Production host: Escherichia coli (E. coli) / References: UniProt: G2QDW1
#2: Chemical
ChemComp-KH2 / 3-(1-methylpiperidinium-1-yl)propane-1-sulfonate


Mass: 221.317 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H19NO3S
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 136 / 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: 3.17 Å3/Da / Density % sol: 61.22 %
Crystal growTemperature: 277 K / Method: evaporation / Details: ammonium sulfate, protamine, NDSB-221

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.3→62 Å / Num. obs: 41149 / % possible obs: 85.74 % / Redundancy: 5.1 % / Net I/σ(I): 24.6

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000V705data reduction
HKL-2000V705data scaling
PHASERphasing
RefinementResolution: 2.33→44.769 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2131 2048 5.03 %
Rwork0.1944 --
obs0.1953 40707 88.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.33→44.769 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4516 0 72 136 4724
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044662
X-RAY DIFFRACTIONf_angle_d0.7156284
X-RAY DIFFRACTIONf_dihedral_angle_d14.6952860
X-RAY DIFFRACTIONf_chiral_restr0.043699
X-RAY DIFFRACTIONf_plane_restr0.004786
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.33-2.38420.2674460.231076X-RAY DIFFRACTION37
2.3842-2.44390.2264830.20631571X-RAY DIFFRACTION54
2.4439-2.50990.2268970.22521909X-RAY DIFFRACTION66
2.5099-2.58380.23211250.23532253X-RAY DIFFRACTION78
2.5838-2.66720.23931450.23372583X-RAY DIFFRACTION89
2.6672-2.76250.27141570.24562855X-RAY DIFFRACTION99
2.7625-2.87310.23221590.24112910X-RAY DIFFRACTION100
2.8731-3.00380.27261590.22322891X-RAY DIFFRACTION100
3.0038-3.16210.26931680.22572906X-RAY DIFFRACTION100
3.1621-3.36020.22811500.21172927X-RAY DIFFRACTION100
3.3602-3.61950.20731530.19252915X-RAY DIFFRACTION100
3.6195-3.98360.19461390.1692936X-RAY DIFFRACTION100
3.9836-4.55950.16851530.15382961X-RAY DIFFRACTION100
4.5595-5.74260.1861400.16832994X-RAY DIFFRACTION100
5.7426-44.77690.2151740.20972972X-RAY DIFFRACTION97
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)
16.7604-2.9699-3.41824.67882.11155.6867-0.3680.1142-0.86820.06150.2186-0.40030.74190.40390.13340.451-0.0916-0.04280.405-0.14210.599147.86998.16816.3623
22.1402-0.2821-0.46852.5913-0.99893.3357-0.05190.33430.0359-0.1750.03390.4045-0.1275-0.98440.02470.29850.054-0.04660.5786-0.07130.322727.956729.93699.4636
37.8548-0.648-1.38475.6045-1.56876.75810.05030.88630.5229-0.6288-0.165-0.2955-0.57250.22560.10280.4460.0268-0.04710.57030.06280.405742.136336.96663.3499
42.7615-2.6274-0.41944.69030.87882.92760.02320.58030.0395-0.56580.0759-0.5493-0.0351-0.193-0.11390.5161-0.1090.02460.4329-0.0720.445242.229613.5792-1.5539
54.09611.02130.00453.6206-0.414.37-0.0739-0.15690.33920.24620.02470.1376-0.30.25470.06610.33670.1018-0.0150.31380.01140.303119.663645.2396-18.9299
69.6205-0.083-3.95561.09510.3114.4588-0.02310.35380.4570.1894-0.07980.4445-0.0219-0.50820.12420.33980.03390.010.2961-0.00420.35831.51141.0439-18.1785
77.21310.90331.87473.55110.73364.57540.2728-1.0194-0.34050.7317-0.27540.4070.0188-0.2715-0.0430.52910.06010.04570.55710.08460.381511.008837.6936-9.0467
82.32631.4264-1.04272.8541-2.43154.3148-0.2755-0.1192-0.6417-0.0768-0.0464-0.53090.92070.57960.29120.67890.22160.05030.5420.02930.520324.367329.3432-23.1533
92.7206-1.9829-0.33325.69830.43534.0218-0.16070.18811.0696-1.143-0.51190.3438-1.0741-0.12910.68031.0704-0.1823-0.1320.92890.11531.277426.760562.523-24.7736
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 461:544)
2X-RAY DIFFRACTION2(chain A and resid 545:634)
3X-RAY DIFFRACTION3(chain A and resid 635:707)
4X-RAY DIFFRACTION4(chain A and resid 708:791)
5X-RAY DIFFRACTION5(chain A and resid 792:897)
6X-RAY DIFFRACTION6(chain A and resid 898:938)
7X-RAY DIFFRACTION7(chain A and resid 939:1009)
8X-RAY DIFFRACTION8(chain A and resid 1055:1112)
9X-RAY DIFFRACTION9(chain A and resid 1113:1126)

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