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- PDB-1sgs: Crystal structure of a free kB DNA -

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Basic information

Entry
Database: PDB / ID: 1sgs
TitleCrystal structure of a free kB DNA
ComponentskB DNA
KeywordsDNA / free kB DNA / Calcium binding / NF-kB binding
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsHuang, D.B. / Phelps, C.B. / Fusco, A.J. / Ghosh, G.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Crystal structure of a free kappaB DNA: insights into DNA recognition by transcription factor NF-kappaB.
Authors: Huang, D.B. / Phelps, C.B. / Fusco, A.J. / Ghosh, G.
History
DepositionFeb 24, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: kB DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,4287
Polymers5,1871
Non-polymers2406
Water1,928107
1
A: kB DNA
hetero molecules

A: kB DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,85614
Polymers10,3752
Non-polymers48112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation17_435x-y-2/3,-y-4/3,-z+2/31
Unit cell
Length a, b, c (Å)38.916, 38.916, 158.910
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-201-

CA

21A-202-

CA

31A-203-

CA

41A-204-

CA

51A-247-

HOH

61A-273-

HOH

DetailsThe second part of the biological assembly is generated by a two fold axis in R32 space group

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Components

#1: DNA chain kB DNA


Mass: 5187.373 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The protein was chemically synthesized. The sequence of the protein naturally occurs in Homo sapiens (human).
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.23 Å3/Da / Density % sol: 44.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 3350, BOG, CaCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
112 mg/mlDNA complex1drop
215-20 %(w/v)PEG33501reservoir
30.05 %(w/v)beta-octylglucopyranoside1reservoir
45 mMspermine1reservoir
50.1 MTris-HCl1reservoirpH7.5
60.2-0.4 M1reservoirCaCl2

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Jul 1, 2003 / Details: mirrors
RadiationMonochromator: osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. all: 6411 / Num. obs: 6341 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 37 % / Biso Wilson estimate: 16.5 Å2 / Rmerge(I) obs: 0.39 / Net I/σ(I): 29.4
Reflection shellResolution: 1.6→1.66 Å / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 12 / % possible all: 91.3
Reflection
*PLUS
% possible obs: 99 % / Num. measured all: 242967 / Rmerge(I) obs: 0.039
Reflection shell
*PLUS
% possible obs: 91 % / Rmerge(I) obs: 0.256 / Mean I/σ(I) obs: 12

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1RAM

1ram


Resolution: 1.6→14.37 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1003948.67 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.218 612 9.7 %RANDOM
Rwork0.207 ---
obs0.207 6341 98.5 %-
all-6341 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.4827 Å2 / ksol: 0.380301 e/Å3
Displacement parametersBiso mean: 24.9 Å2
Baniso -1Baniso -2Baniso -3
1-1.59 Å2-0.07 Å20 Å2
2--1.59 Å20 Å2
3----3.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.6→14.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 344 6 107 457
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d20.4
X-RAY DIFFRACTIONc_improper_angle_d1.75
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.359 87 9 %
Rwork0.333 880 -
obs--91.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Refinement
*PLUS
Lowest resolution: 30 Å / Num. reflection obs: 6340 / % reflection Rfree: 10 % / Rfactor Rfree: 0.215
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0076
X-RAY DIFFRACTIONc_angle_deg1.54
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.75

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