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- PDB-1bnz: SSO7D HYPERTHERMOPHILE PROTEIN/DNA COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1bnz
TitleSSO7D HYPERTHERMOPHILE PROTEIN/DNA COMPLEX
Components
  • 5'-D(*GP*TP*AP*AP*TP*TP*AP*C)-3'
  • DNA-BINDING PROTEIN 7A
KeywordsDNA BINDING PROTEIN/DNA / PROTEIN-DNA INTERACTION / 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 / DNA-binding protein 7a
Similarity search - Component
Biological speciesSulfolobus acidocaldarius (acidophilic)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2 Å
AuthorsGao, Y.-G. / Su, S.-Y. / Robinson, H. / Padmanabhan, S. / Lim, L. / Mccrary, B.S. / Edmondos, S.P. / Shrive, J.W. / Wang, A.H.-J.
CitationJournal: Nat.Struct.Biol. / Year: 1998
Title: The crystal structure of the hyperthermophile chromosomal protein Sso7d bound to DNA.
Authors: Gao, Y.G. / Su, S.Y. / Robinson, H. / Padmanabhan, S. / Lim, L. / McCrary, B.S. / Edmondson, S.P. / Shriver, J.W. / Wang, A.H.
History
DepositionJul 31, 1998Deposition site: BNL / Processing site: NDB
Revision 1.0Nov 11, 1998Provider: repository / Type: Initial release
Revision 1.1May 9, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Other
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software
Revision 1.5Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)12,1473
Polymers12,1473
Non-polymers00
Water1,78399
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.600, 50.770, 42.060
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*AP*AP*TP*TP*AP*C)-3'


Mass: 2425.629 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein DNA-BINDING PROTEIN 7A


Mass: 7295.584 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius (acidophilic)
References: UniProt: P80170, UniProt: P39476*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.12 Å3/Da / Density % sol: 42 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.3 mMSso7d1drop
21.3 mMDNA duplex1drop
32 mMTris-Cl1drop
42.6 %PEG4001drop
515 %PEG4001reservoir

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: May 15, 1997
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.9→10 Å / Num. obs: 7607 / % possible obs: 94.1 % / Observed criterion σ(I): 1 / Redundancy: 3 % / Biso Wilson estimate: 32 Å2 / Rmerge(I) obs: 0.075
Reflection
*PLUS
Lowest resolution: 10 Å / Observed criterion σ(F): 1 / Rmerge(I) obs: 0.0753
Reflection shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.1 Å / % possible obs: 83 %

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Processing

Software
NameVersionClassification
PHASITmodel building
X-PLOR3.1refinement
PHASITphasing
RefinementMethod to determine structure: MIR / Resolution: 2→6 Å / σ(F): 4
RfactorNum. reflection% reflectionSelection details
Rfree0.268 --RANDOM
Rwork0.168 ---
obs0.168 5682 76 %-
Refinement stepCycle: LAST / Resolution: 2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms510 322 0 99 931
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.37
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM_NDBX_HIGH.DNATOP_NDBX.DNA
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 6 Å / σ(I): 2 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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