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- PDB-4hw0: Crystal structure of Sso10a-2, a DNA-binding protein from Sulfolo... -

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Basic information

Entry
Database: PDB / ID: 4hw0
TitleCrystal structure of Sso10a-2, a DNA-binding protein from Sulfolobus solfataricus
ComponentsDNA-binding protein Sso10a-2
KeywordsDNA BINDING PROTEIN / Winged-helix / DNA-binding domain / two-stranded antiparallel coiled-coil / DNA/RNA-binding 3-helical bundle
Function / homologyArnR1-like, winged helix-turn-helix domain / Winged helix-turn-helix / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha / ArnR1-like winged helix-turn-helix domain-containing protein
Function and homology information
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsWaterreus, W.J. / Goosen, N. / Moolenaar, G.F. / Driessen, R.P.C. / Dame, R.T. / Pannu, N.S.
CitationJournal: Sci Rep / Year: 2016
Title: Diverse architectural properties of Sso10a proteins: Evidence for a role in chromatin compaction and organization.
Authors: Driessen, R.P. / Lin, S.N. / Waterreus, W.J. / van der Meulen, A.L. / van der Valk, R.A. / Laurens, N. / Moolenaar, G.F. / Pannu, N.S. / Wuite, G.J. / Goosen, N. / Dame, R.T.
History
DepositionNov 7, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2017Group: Database references
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-binding protein Sso10a-2
B: DNA-binding protein Sso10a-2
C: DNA-binding protein Sso10a-2


Theoretical massNumber of molelcules
Total (without water)37,1103
Polymers37,1103
Non-polymers00
Water1,910106
1
A: DNA-binding protein Sso10a-2

A: DNA-binding protein Sso10a-2


Theoretical massNumber of molelcules
Total (without water)24,7402
Polymers24,7402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2360 Å2
ΔGint-28 kcal/mol
Surface area11900 Å2
MethodPISA
2
B: DNA-binding protein Sso10a-2
C: DNA-binding protein Sso10a-2


Theoretical massNumber of molelcules
Total (without water)24,7402
Polymers24,7402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2200 Å2
ΔGint-27 kcal/mol
Surface area11130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.221, 69.538, 80.727
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number17
Space group name H-MP2122
Components on special symmetry positions
IDModelComponents
11A-210-

HOH

21C-205-

HOH

31C-220-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRAA8 - 1018 - 101
21THRTHRBB8 - 1018 - 101
12LEULEUAA8 - 998 - 99
22LEULEUCC8 - 998 - 99
13LEULEUBB8 - 998 - 99
23LEULEUCC8 - 998 - 99

NCS ensembles :
ID
1
2
3

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Components

#1: Protein DNA-binding protein Sso10a-2


Mass: 12369.967 Da / Num. of mol.: 3 / Fragment: UNP residues 28-130
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: AAK42937.1, SSO2827 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q97V10
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.28 Å3/Da / Density % sol: 45.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Succinic acid, HEPES, PEG MME 2000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 8, 2012
RadiationMonochromator: Diamond(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2→40.36 Å / Num. all: 21998 / Num. obs: 21998 / % possible obs: 93.28 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 6 / Redundancy: 13.46 % / Rmerge(I) obs: 0.039 / Net I/σ(I): 39.6302
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allDiffraction-ID% possible all
2-2.119.570.48306613204195.21
2.11-2.2413.190.31330342505178.05
2.24-2.3914.320.17330832310177.18
2.39-2.5814.70.124158728301100
2.58-2.8314.660.073800125921100
2.83-3.1614.550.04348372394199.96
3.16-3.6514.320.033009421021100
3.65-4.4714.010.022513117941100
4.47-6.3213.590.02195001435199.96
6.32-40.3612.20.0210150832199.05

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Processing

Software
NameVersionClassificationNB
SCALACCP4_3.3.20data scaling
REFMACrefmac_5.7.0029refinement
PDB_EXTRACT3.11data extraction
XDSdata scaling
XSCALEdata scaling
CRANKphasing
RefinementMethod to determine structure: SAD / Resolution: 2→40.36 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.936 / WRfactor Rfree: 0.24 / WRfactor Rwork: 0.199 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 8.577 / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.2 / ESU R Free: 0.175 / Stereochemistry target values: Engh & Huber
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2449 1118 5.1 %RANDOM
Rwork0.2046 ---
all0.2065 21980 --
obs0.2065 21980 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 104.82 Å2 / Biso mean: 45.4661 Å2 / Biso min: 22.05 Å2
Baniso -1Baniso -2Baniso -3
1-3.38 Å2-0 Å2-0 Å2
2---0.22 Å20 Å2
3----3.16 Å2
Refinement stepCycle: LAST / Resolution: 2→40.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2331 0 0 106 2437
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0192367
X-RAY DIFFRACTIONr_bond_other_d0.0080.022431
X-RAY DIFFRACTIONr_angle_refined_deg1.7141.9963170
X-RAY DIFFRACTIONr_angle_other_deg1.3423.0025582
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2925285
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.68323.761109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.06615482
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6731522
X-RAY DIFFRACTIONr_chiral_restr0.0970.2364
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022575
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02513
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A56340.16
12B56340.16
21A54350.17
22C54350.17
31B53740.18
32C53740.18
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.0520.289930.2531476171491.54
2.052-2.1080.3760.2421549166497.656
2.108-2.1690.305860.23915311617100
2.169-2.2360.256390.245858160056.063
2.236-2.3090.292440.252800152955.199
2.309-2.390.251730.2213831456100
2.39-2.480.268800.22113711451100
2.48-2.5810.263780.23113031381100
2.581-2.6960.269760.22512421318100
2.696-2.8270.272590.23112121271100
2.827-2.980.294470.2211831230100
2.98-3.1610.27800.231086116799.914
3.161-3.3790.292480.22510301078100
3.379-3.6490.23520.2029611013100
3.649-3.9960.249360.19290794899.473
3.996-4.4660.155460.153810856100
4.466-5.1550.205390.15772776799.87
5.155-6.3070.239330.199630663100
6.307-8.8920.244200.181504524100
8.892-80.7270.174130.20729932695.706
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)
10.7151-0.03810.42130.5058-0.44773.6518-0.0391-0.0561-0.00750.00020.0236-0.01440.0167-0.21520.01540.0095-0.01350.01360.1849-0.01130.2614-4.098-0.82516.388
20.61730.3671-0.22130.3084-0.05951.30290.13220.05460.0356-0.0194-0.0358-0.03040.37640.0055-0.09650.39520.0743-0.04760.22550.00110.385715.602-18.4929.021
30.27620.32510.25890.6932-0.72575.0560.09660.0183-0.0294-0.03160.0170.08190.7652-0.1494-0.11350.35620.09870.03220.2718-0.01440.359311.953-25.823-26.052
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999
3X-RAY DIFFRACTION3C-10 - 9999

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