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- PDB-1z3i: Structure of the SWI2/SNF2 chromatin remodeling domain of eukaryo... -

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Basic information

Entry
Database: PDB / ID: 1z3i
TitleStructure of the SWI2/SNF2 chromatin remodeling domain of eukaryotic Rad54
Componentssimilar to RAD54-like
KeywordsRecombination/DNA binding / Recombination ATPase helicase / Recombination-DNA binding COMPLEX
Function / homology
Function and homology information


double-strand break repair via synthesis-dependent strand annealing / ATP-dependent chromatin remodeler activity => GO:0140658 / DNA translocase activity / reciprocal meiotic recombination / ATP-dependent activity, acting on DNA / DNA helicase activity / DNA helicase / DNA binding / ATP binding / nucleus
Similarity search - Function
SWI2/SNF2 ATPases, N-terminal domain / Tandem AAA-ATPase domain / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / Helicase conserved C-terminal domain / 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. ...SWI2/SNF2 ATPases, N-terminal domain / Tandem AAA-ATPase domain / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / Helicase conserved C-terminal domain / 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 nucleotide triphosphate hydrolases / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA repair and recombination protein RAD54-like / DNA repair and recombination protein RAD54-like
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 Å
AuthorsThoma, N.H. / Czyzewski, B.K. / Alexeev, A.A. / Mazin, A.V. / Kowalczykowski, S.C. / Pavletich, N.P.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2005
Title: Structure of the SWI2/SNF2 chromatin-remodeling domain of eukaryotic Rad54.
Authors: Thoma, N.H. / Czyzewski, B.K. / Alexeev, A.A. / Mazin, A.V. / Kowalczykowski, S.C. / Pavletich, N.P.
History
DepositionMar 12, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: similar to RAD54-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,96311
Polymers73,0331
Non-polymers93010
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
X: similar to RAD54-like
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)443,77866
Polymers438,1986
Non-polymers5,58060
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area27840 Å2
ΔGint-771 kcal/mol
Surface area158290 Å2
MethodPISA
3
X: similar to RAD54-like
hetero molecules

X: similar to RAD54-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,92622
Polymers146,0662
Non-polymers1,86020
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
MethodPQS
Unit cell
Length a, b, c (Å)205.046, 205.046, 189.958
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein similar to RAD54-like


Mass: 73033.062 Da / Num. of mol.: 1 / Fragment: Proteolytic Fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q7ZV09, UniProt: F1Q8K0*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4

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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: 5.26 Å3/Da / Density % sol: 76.62 %
Crystal growTemperature: 298 K / pH: 6
Details: Ammonium Sulfate, Malonate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 6.00

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
1,21
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONAPS 17-ID11.041
SYNCHROTRONAPS 17-ID21.03909, 1.04013, 1.02635
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDJun 1, 2004
2
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1INSERTION DEVICESINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.0411
21.039091
31.040131
41.026351
ReflectionResolution: 3→20 Å / Num. all: 31235 / Num. obs: 31235 / Observed criterion σ(I): 2
Reflection shellResolution: 3→3.11 Å / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXSphasing
RefinementMethod to determine structure: MAD / Resolution: 3→20 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.912 / SU B: 26.423 / SU ML: 0.221 / Cross valid method: THROUGHOUT / ESU R: 0.461 / ESU R Free: 0.299 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2343 1545 5 %RANDOM
Rwork0.19773 ---
obs0.19957 29139 99.97 %-
all-29139 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 72.171 Å2
Baniso -1Baniso -2Baniso -3
1-1.54 Å20.77 Å20 Å2
2--1.54 Å20 Å2
3----2.31 Å2
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5052 0 46 0 5098
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0225184
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2361.9777013
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8695643
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.46923.612227
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.515932
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0121542
X-RAY DIFFRACTIONr_chiral_restr0.0850.2785
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023841
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2180.22458
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.23480
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2141
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0940.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1840.252
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.260.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.93813267
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.651.55169
X-RAY DIFFRACTIONr_scbond_it2.16922107
X-RAY DIFFRACTIONr_scangle_it3.60131844
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.076 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 98 -
Rwork0.327 2105 -
obs--100 %

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