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- PDB-1r7j: Crystal structure of the DNA-binding protein Sso10a from Sulfolob... -

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Basic information

Entry
Database: PDB / ID: 1r7j
TitleCrystal structure of the DNA-binding protein Sso10a from Sulfolobus solfataricus
ComponentsConserved hypothetical protein Sso10a
KeywordsDNA BINDING PROTEIN / Winged helix-turn-helix / two-stranded antiparallel coiled coil / Structural Genomics / PSI / Protein Structure Initiative / Southeast Collaboratory for Structural Genomics / SECSG
Function / homology
Function and homology information


ArnR1-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
Similarity search - Domain/homology
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Sulfur-SAS on Cr X-ray source / Resolution: 1.47 Å
AuthorsChen, L. / Chen, L.R. / Zhou, X.E. / Wang, Y. / Kahsai, M.A. / Clark, A.T. / Edmondson, S.P. / Liu, Z.-J. / Rose, J.P. / Wang, B.C. ...Chen, L. / Chen, L.R. / Zhou, X.E. / Wang, Y. / Kahsai, M.A. / Clark, A.T. / Edmondson, S.P. / Liu, Z.-J. / Rose, J.P. / Wang, B.C. / Shriver, J.W. / Meehan, E.J. / Southeast Collaboratory for Structural Genomics (SECSG)
CitationJournal: J.Mol.Biol. / Year: 2004
Title: The hyperthermophile protein Sso10a is a dimer of winged helix DNA-binding domains linked by an antiparallel coiled coil rod.
Authors: Chen, L. / Chen, L.R. / Zhou, X.E. / Wang, Y. / Kahsai, M.A. / Clark, A.T. / Edmondson, S.P. / Liu, Z.J. / Rose, J.P. / Wang, B.C. / Meehan, E.J. / Shriver, J.W.
History
DepositionOct 21, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE AUTHORS INFORMED THAT THE DIFFERENCES BETWEEN THEIR SEQUENCE AND THE DATABASE REFERENCE ...SEQUENCE AUTHORS INFORMED THAT THE DIFFERENCES BETWEEN THEIR SEQUENCE AND THE DATABASE REFERENCE SEQUENCE WERE DUE TO THEIR USING A SLIGHTLY DIFFERENT STRAIN IN CLONING.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Conserved hypothetical protein Sso10a


Theoretical massNumber of molelcules
Total (without water)11,1031
Polymers11,1031
Non-polymers00
Water3,153175
1
A: Conserved hypothetical protein Sso10a

A: Conserved hypothetical protein Sso10a


Theoretical massNumber of molelcules
Total (without water)22,2062
Polymers22,2062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area2050 Å2
ΔGint-26 kcal/mol
Surface area10950 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)57.940, 72.300, 30.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Conserved hypothetical protein Sso10a


Mass: 11103.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: Sso10a / Plasmid: pETBlue-2 / Production host: Escherichia coli (E. coli) / Strain (production host): RossetaBlue(DE3)pLacI (Novagen) / References: UniProt: Q5W1E8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.86 Å3/Da / Density % sol: 56.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: PEG 3350, potassium fluoride, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 10, 2003 / Details: Mirrors
RadiationMonochromator: Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.47→18.86 Å / Num. all: 21672 / Num. obs: 21672 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.8 % / Biso Wilson estimate: 19.8 Å2 / Rmerge(I) obs: 0.042 / Rsym value: 0.042 / Net I/σ(I): 18.4
Reflection shellResolution: 1.47→1.52 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.264 / Mean I/σ(I) obs: 4.6 / Num. unique all: 1538 / Rsym value: 0.264 / % possible all: 69.2

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Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
ISASphasing
ARP/wARPmodel building
RefinementMethod to determine structure: Sulfur-SAS on Cr X-ray source
Resolution: 1.47→18.86 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 699335.84 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.244 1021 4.9 %RANDOM
Rwork0.232 ---
all0.232 20838 --
obs0.232 20838 93.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.7247 Å2 / ksol: 0.429311 e/Å3
Displacement parametersBiso mean: 21.5 Å2
Baniso -1Baniso -2Baniso -3
1-1.54 Å20 Å20 Å2
2---5.18 Å20 Å2
3---3.64 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.47→18.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms729 0 0 175 904
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d17.2
X-RAY DIFFRACTIONc_improper_angle_d0.67
X-RAY DIFFRACTIONc_mcbond_it1.221.5
X-RAY DIFFRACTIONc_mcangle_it1.872
X-RAY DIFFRACTIONc_scbond_it2.962
X-RAY DIFFRACTIONc_scangle_it4.242.5
LS refinement shellResolution: 1.47→1.56 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.341 132 4.9 %
Rwork0.329 2535 -
obs-2535 72.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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