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- PDB-1azp: HYPERTHERMOPHILE CHROMOSOMAL PROTEIN SAC7D BOUND WITH KINKED DNA ... -

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Basic information

Entry
Database: PDB / ID: 1azp
TitleHYPERTHERMOPHILE CHROMOSOMAL PROTEIN SAC7D BOUND WITH KINKED DNA DUPLEX
Components
  • DNA (5'-D(*GP*CP*GP*AP*TP*CP*GP*C)-3')
  • PROTEIN (HYPERTHERMOPHILE CHROMOSOMAL PROTEIN SAC7D)
KeywordsDNA BINDING PROTEIN/DNA / COMPLEX (CHROMATIN PROTEIN-DNA) / DNA-BINDING / ARCHEA KINKED-DNA / MINOR-GROOVE BINDING / INTERCALATION / 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 acidocaldarius (acidophilic)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.6 Å
AuthorsRobinson, H. / Gao, Y.-G. / Mccrary, B.S. / Edmondson, S.P. / Shriver, J.W. / Wang, A.H.-J.
CitationJournal: Nature / Year: 1998
Title: The hyperthermophile chromosomal protein Sac7d sharply kinks DNA.
Authors: Robinson, H. / Gao, Y.G. / McCrary, B.S. / Edmondson, S.P. / Shriver, J.W. / Wang, A.H.
History
DepositionNov 19, 1997Processing site: NDB
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA (5'-D(*GP*CP*GP*AP*TP*CP*GP*C)-3')
C: DNA (5'-D(*GP*CP*GP*AP*TP*CP*GP*C)-3')
A: PROTEIN (HYPERTHERMOPHILE CHROMOSOMAL PROTEIN SAC7D)


Theoretical massNumber of molelcules
Total (without water)12,4823
Polymers12,4823
Non-polymers00
Water2,378132
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.108, 77.173, 35.480
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 DNA (5'-D(*GP*CP*GP*AP*TP*CP*GP*C)-3')


Mass: 2427.605 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein PROTEIN (HYPERTHERMOPHILE CHROMOSOMAL PROTEIN SAC7D) / 7 KD HYPERTHERMOPHILE DNA-BINDING PROTEIN


Mass: 7626.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius (acidophilic)
Production host: Escherichia coli (E. coli) / References: UniProt: P13123
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.81 Å3/Da / Density % sol: 56 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5 / Details: pH 6.5, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2TRIS BUFFER11
3MPD12
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.3 mMprotein1drop
21.3 mMDNA duplex1drop
32 mMTris-HCl1drop
45 %MPD1drop
520 %MPD1reservoir

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.540598
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jul 15, 1997
RadiationMonochromator: GRAPHITE / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.540598 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 18497 / % possible obs: 95 % / Observed criterion σ(I): 1 / Redundancy: 6.6 % / Biso Wilson estimate: 19.4 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.1
Reflection shellResolution: 1.6→1.65 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 1.5 / % possible all: 95.2
Reflection shell
*PLUS
% possible obs: 95.2 %

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Processing

Software
NameVersionClassification
PHASESphasing
X-PLOR3.843refinement
bioteXdata reduction
bioteXdata scaling
RefinementMethod to determine structure: MIR / Resolution: 1.6→6 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.001 / Cross valid method: A POSTERIORI / σ(F): 3
RfactorNum. reflection% reflectionSelection details
Rfree0.252 729 5 %RANDOM
Rwork0.211 ---
obs0.211 14584 79.3 %-
Refinement stepCycle: LAST / Resolution: 1.6→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms533 322 0 132 987
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.39
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 DIFFRACTION2PARAM11.WATTOPH19.PEP
X-RAY DIFFRACTION3PARAM_NDBX_HIGH.DNATOPH11.WAT
X-RAY DIFFRACTION4TOP_NDBX.DNA
Software
*PLUS
Name: X-PLOR / Version: 3.84 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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