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- PDB-1wd1: Crystal structures of the hyperthermophilic chromosomal protein S... -

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Basic information

Entry
Database: PDB / ID: 1wd1
TitleCrystal structures of the hyperthermophilic chromosomal protein Sac7d in complex with DNA decamers
Components
  • 5'-D(*CP*CP*TP*AP*CP*GP*TP*AP*GP*G)-3'
  • DNA-binding proteins 7a/7b/7d
Keywordsstructural protein/DNA / PROTEIN-DNA COMPLEX / structural 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 / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKo, T.-P. / Chu, H.-M. / Chen, C.-Y. / Chou, C.-C. / Wang, A.H.-J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Structures of the hyperthermophilic chromosomal protein Sac7d in complex with DNA decamers.
Authors: Ko, T.P. / Chu, H.M. / Chen, C.Y. / Chou, C.C. / Wang, A.H.
History
DepositionMay 10, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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

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Assembly

Deposited unit
B: 5'-D(*CP*CP*TP*AP*CP*GP*TP*AP*GP*G)-3'
C: 5'-D(*CP*CP*TP*AP*CP*GP*TP*AP*GP*G)-3'
A: DNA-binding proteins 7a/7b/7d


Theoretical massNumber of molelcules
Total (without water)13,7173
Polymers13,7173
Non-polymers00
Water1,60389
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.634, 46.841, 53.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsmonomer Sac7d is bound to DNA, DNA forms virtual double helices

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Components

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


Mass: 3045.004 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein DNA-binding proteins 7a/7b/7d / Sac7d chromosomal protein / 7 kDa DNA-binding proteins a/b/d / Sac7a / Sac7b / Sac7d


Mass: 7626.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius (acidophilic)
Plasmid: pET-3B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P13123
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 30 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: potassium phosphate, PEG8000, pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1potassium phosphate11
2PEG800011
3H2O11
4potassium phosphate12
5PEG800012
6H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 18, 2003
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 5271 / Num. obs: 5166 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 25
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2 / Num. unique all: 453 / % possible all: 88.5

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb 1azp

1azp


Resolution: 2.2→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.29 257 -RANDOM
Rwork0.248 ---
all0.254 5243 --
obs0.25 4798 91.5 %-
Displacement parametersBiso mean: 33.5 Å2
Baniso -1Baniso -2Baniso -3
1-8.512 Å20 Å20 Å2
2---16.839 Å20 Å2
3---8.327 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms515 372 0 89 976
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg2.17
X-RAY DIFFRACTIONc_bond_d0.02
LS refinement shellResolution: 2.2→2.28 Å / Rfactor Rfree error: 0.087
RfactorNum. reflection% reflection
Rfree0.476 17 -
Rwork0.389 --
obs--75 %

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