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- PDB-4o66: Crystal Structure of SMARCAL1 HARP substrate recognition domain -

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Basic information

Entry
Database: PDB / ID: 4o66
TitleCrystal Structure of SMARCAL1 HARP substrate recognition domain
ComponentsSWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1
KeywordsDNA BINDING PROTEIN / DNA Repair DNA Replication
Function / homology
Function and homology information


DNA rewinding / : / DNA replication factor A complex / ATP-dependent DNA/DNA annealing activity / DNA metabolic process / replication fork processing / nuclear replication fork / ATP-dependent activity, acting on DNA / DNA helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement ...DNA rewinding / : / DNA replication factor A complex / ATP-dependent DNA/DNA annealing activity / DNA metabolic process / replication fork processing / nuclear replication fork / ATP-dependent activity, acting on DNA / DNA helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / double-strand break repair via nonhomologous end joining / site of double-strand break / DNA repair / DNA damage response / regulation of transcription by RNA polymerase II / ATP binding / nucleus
Similarity search - Function
HARP domain / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1 / HepA-related protein (HARP) / HARP domain profile. / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. ...HARP domain / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1 / HepA-related protein (HARP) / HARP domain profile. / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / 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 nucleoside triphosphate hydrolase
Similarity search - Domain/homology
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsMason, A.C. / Eichman, B.F.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: A structure-specific nucleic acid-binding domain conserved among DNA repair proteins.
Authors: Mason, A.C. / Rambo, R.P. / Greer, B. / Pritchett, M. / Tainer, J.A. / Cortez, D. / Eichman, B.F.
History
DepositionDec 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2014Group: Database references
Revision 1.2Feb 28, 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_ref_seq_dif / 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_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_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_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _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
A: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1
B: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1
C: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1
D: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,90310
Polymers34,4004
Non-polymers5036
Water3,099172
1
A: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,6962
Polymers8,6001
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1


Theoretical massNumber of molelcules
Total (without water)8,6001
Polymers8,6001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9845
Polymers8,6001
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,6232
Polymers8,6001
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1
B: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2963
Polymers17,2002
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-46 kcal/mol
Surface area7210 Å2
MethodPISA
6
C: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1
D: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6077
Polymers17,2002
Non-polymers4075
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-84 kcal/mol
Surface area7250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.511, 56.634, 104.321
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and (resseq 202:268 )
21chain B and (resseq 202:268 )
31chain C and (resseq 202:268 )
41chain D and (resseq 202:268 )

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and (resseq 202:268 )A0
211chain B and (resseq 202:268 )B0
311chain C and (resseq 202:268 )C0
411chain D and (resseq 202:268 )D0

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Components

#1: Protein
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1 / HepA-related protein / mharp / Sucrose nonfermenting protein 2-like 1


Mass: 8599.902 Da / Num. of mol.: 4 / Fragment: HARP domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Smarcal1, Harp / Production host: Escherichia coli (E. coli)
References: UniProt: Q8BJL0, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.43 Å3/Da / Density % sol: 49.31 %
Crystal growTemperature: 294.2 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M ammonium sulfate, 0.1M MES, 30% PEG monomethyl ether 5,000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 294.2K

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Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 6, 2011
RadiationMonochromator: Kohzu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 26465 / Num. obs: 26465 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.093 / Net I/σ(I): 26.2
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.464 / Mean I/σ(I) obs: 4.4 / % possible all: 96.4

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Processing

Software
NameVersionClassification
MD2data collection
SHARPphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.9→49.772 Å / σ(F): 1.96 / Phase error: 28.38 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.1966 1367 5.17 %Random 5%
Rwork0.1685 ---
obs0.1713 26465 96.97 %-
all-26465 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→49.772 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2181 0 26 172 2379
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142249
X-RAY DIFFRACTIONf_angle_d1.3063030
X-RAY DIFFRACTIONf_dihedral_angle_d12.582810
X-RAY DIFFRACTIONf_chiral_restr0.056334
X-RAY DIFFRACTIONf_plane_restr0.006369
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A532X-RAY DIFFRACTIONPOSITIONAL0.086
12B532X-RAY DIFFRACTIONPOSITIONAL0.086
13C528X-RAY DIFFRACTIONPOSITIONAL0.089
14D530X-RAY DIFFRACTIONPOSITIONAL0.097
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8952-1.9710.25311250.19852745X-RAY DIFFRACTION93
1.971-2.06070.20831480.18432713X-RAY DIFFRACTION91
2.0607-2.16930.21581550.1822717X-RAY DIFFRACTION91
2.1693-2.30510.20221370.1772725X-RAY DIFFRACTION91
2.3051-2.48290.2031350.17392746X-RAY DIFFRACTION91
2.4829-2.73240.22221650.18042696X-RAY DIFFRACTION90
2.7324-3.1270.20051500.16822822X-RAY DIFFRACTION93
3.127-3.93680.17811470.15422904X-RAY DIFFRACTION95
3.9368-23.68190.1821680.16143045X-RAY DIFFRACTION95

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