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- PDB-1c8c: CRYSTAL STRUCTURES OF THE CHROMOSOMAL PROTEINS SSO7D/SAC7D BOUND ... -

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Basic information

Entry
Database: PDB / ID: 1c8c
TitleCRYSTAL STRUCTURES OF THE CHROMOSOMAL PROTEINS SSO7D/SAC7D BOUND TO DNA CONTAINING T-G MISMATCHED BASE PAIRS
Components
  • 5'-D(*GP*TP*GP*AP*TP*CP*GP*C)-3'
  • DNA-BINDING PROTEIN 7A
KeywordsDNA BINDING PROTEIN/DNA / DNA BINDING PROTEIN / PROTEIN-DNA INTERACTION / PROTEIN STABILITY / HYPERTHERMOPHILE / ACHAEABACTERIA / ELECTROSTATICS / MOLECULAR MODELING / T-G MISMATCH / DNA BINDING PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


RNA endonuclease activity / DNA binding / cytoplasm
Similarity search - Function
DNA-binding 7kDa protein / 7kD DNA-binding domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / Chromo-like domain superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DNA / DNA-binding protein 7d
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsSu, S. / Gao, Y.-G. / Robinson, H. / Liaw, Y.-C. / Edmondson, S.P. / Shriver, J.W. / Wang, A.H.-J.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Crystal structures of the chromosomal proteins Sso7d/Sac7d bound to DNA containing T-G mismatched base-pairs.
Authors: Su, S. / Gao, Y.G. / Robinson, H. / Liaw, Y.C. / Edmondson, S.P. / Shriver, J.W. / Wang, A.H.
History
DepositionMay 4, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 5'-D(*GP*TP*GP*AP*TP*CP*GP*C)-3'
C: 5'-D(*GP*TP*GP*AP*TP*CP*GP*C)-3'
A: DNA-BINDING PROTEIN 7A


Theoretical massNumber of molelcules
Total (without water)12,1223
Polymers12,1223
Non-polymers00
Water2,828157
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.475, 49.800, 37.681
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: DNA chain 5'-D(*GP*TP*GP*AP*TP*CP*GP*C)-3'


Mass: 2442.616 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein DNA-BINDING PROTEIN 7A / SSO7D / 7 KDA DNA-BINDING PROTEIN D


Mass: 7236.563 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: GERMAN COLLECTION OF MICROORGANISMS (DSM) 1617, #1616
Source: (natural) Sulfolobus solfataricus (archaea) / References: UniProt: P39476
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 1.8 Å3/Da / Density % sol: 39 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: PROTEIN WAS CRYSTALLIZED FROM 1.3MM SSO7D, 1.3MM DUPLEX DNA, 2.5 MM TRIS (PH 6.5), 2.5% PEG 400, EQUILIBRATED AGAINST 15% PEG 400 at pH 6.5, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1TRIS11
2PEG 40011
3PEG 40012
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.3 mMSso7d1drop
21.3 mMDNA duplex1drop
32.5 mMTris-HCl1drop
42.5 %PEG4001drop
515 %PEG4001reservoir

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Aug 15, 1998
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.38→20 Å / Num. obs: 14498 / % possible obs: 89.1 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.054
Reflection shell
*PLUS
Highest resolution: 1.45 Å / Lowest resolution: 1.52 Å / % possible obs: 63 %

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Processing

Software
NameClassification
AMoREphasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AZP

1azp


Resolution: 1.45→8 Å / Cross valid method: THROUGHOUT / σ(F): 4
RfactorNum. reflection% reflectionSelection details
Rfree0.2868 884 5 %EVERY 20TH REFLECTION
all0.229 17583 --
obs0.229 -72.2 %-
Refinement stepCycle: LAST / Resolution: 1.45→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms636 362 0 471 1469
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
σ(F): 4 / % reflection Rfree: 5 % / Rfactor Rwork: 0.229
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.009
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg2.3

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