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- PDB-9bdz: TA-centric NF-kappaB RelA binding DNA -

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Basic information

Entry
Database: PDB / ID: 9bdz
TitleTA-centric NF-kappaB RelA binding DNA
Components(double-stranded DNA) x 2
KeywordsDNA / kappaB DNA / Promoter / Transcription / RelA
Function / homologyACETATE ION / DNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsBiswas, T. / Shahabi, S. / Tsodikov, O.V. / Wang, V. / Ghosh, G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM085490-11 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: Transient interactions modulate the affinity of NF-kappa B transcription factors for DNA.
Authors: Li, T. / Shahabi, S. / Biswas, T. / Tsodikov, O.V. / Pan, W. / Huang, D.B. / Wang, V.Y. / Wang, Y. / Ghosh, G.
History
DepositionApr 13, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2024Group: Derived calculations / Category: pdbx_struct_assembly / pdbx_struct_assembly_gen

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: double-stranded DNA
O: double-stranded DNA
E: double-stranded DNA
R: double-stranded DNA
G: double-stranded DNA
V: double-stranded DNA
I: double-stranded DNA
Z: double-stranded DNA
K: double-stranded DNA
c: double-stranded DNA
N: double-stranded DNA
e: double-stranded DNA
Y: double-stranded DNA
g: double-stranded DNA
W: double-stranded DNA
i: double-stranded DNA
U: double-stranded DNA
k: double-stranded DNA
S: double-stranded DNA
m: double-stranded DNA
Q: double-stranded DNA
o: double-stranded DNA
M: double-stranded DNA
q: double-stranded DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,936132
Polymers87,91024
Non-polymers7,026108
Water8,323462
1
A: double-stranded DNA
O: double-stranded DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,84310
Polymers7,3262
Non-polymers5178
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: double-stranded DNA
R: double-stranded DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,96712
Polymers7,3262
Non-polymers64110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: double-stranded DNA
V: double-stranded DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,97412
Polymers7,3262
Non-polymers64810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
I: double-stranded DNA
Z: double-stranded DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,91411
Polymers7,3262
Non-polymers5899
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
K: double-stranded DNA
c: double-stranded DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,90811
Polymers7,3262
Non-polymers5829
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
N: double-stranded DNA
e: double-stranded DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,91411
Polymers7,3262
Non-polymers5899
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
Y: double-stranded DNA
g: double-stranded DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,91411
Polymers7,3262
Non-polymers5899
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
W: double-stranded DNA
i: double-stranded DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,91411
Polymers7,3262
Non-polymers5899
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
U: double-stranded DNA
k: double-stranded DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,91411
Polymers7,3262
Non-polymers5899
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
S: double-stranded DNA
m: double-stranded DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,91411
Polymers7,3262
Non-polymers5899
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
Q: double-stranded DNA
o: double-stranded DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,91411
Polymers7,3262
Non-polymers5899
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
M: double-stranded DNA
q: double-stranded DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,84310
Polymers7,3262
Non-polymers5178
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.078, 46.233, 98.646
Angle α, β, γ (deg.)89.90, 89.86, 60.10
Int Tables number1
Space group name H-MP1

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Components

#1: DNA chain
double-stranded DNA


Mass: 3678.403 Da / Num. of mol.: 12 / Source method: obtained synthetically
Details: Each chain is two separate complementary DNA oligomers: CGGGAATTTCCG and CGGAAATTCCCG
Source: (synth.) Homo sapiens (human)
#2: DNA chain
double-stranded DNA


Mass: 3647.393 Da / Num. of mol.: 12 / Source method: obtained synthetically
Details: Each chain is two separate complementary DNA oligomers: CGGGAATTTCCG and CGGAAATTCCCG
Source: (synth.) Homo sapiens (human)
#3: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 102 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 462 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.06 Å3/Da / Density % sol: 40.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: PEG3350 8%, Sodium Acetate pH 3.5 100 mM, 50 mM Zinc Acetate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 12092 / % possible obs: 88.9 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 12.2
Reflection shellResolution: 3→3.1 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.625 / Num. unique obs: 1100 / % possible all: 94.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→30 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.894 / SU B: 24.401 / SU ML: 0.452 / Cross valid method: THROUGHOUT / ESU R Free: 0.759 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.33907 515 4.1 %RANDOM
Rwork0.25843 ---
obs0.26197 12083 88.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.472 Å2
Baniso -1Baniso -2Baniso -3
1-2.1 Å2-0.97 Å20.63 Å2
2---0.48 Å2-0.25 Å2
3----2.41 Å2
Refinement stepCycle: 1 / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 5451 126 462 6039
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0116392
X-RAY DIFFRACTIONr_bond_other_d0.0010.022982
X-RAY DIFFRACTIONr_angle_refined_deg0.8181.1749387
X-RAY DIFFRACTIONr_angle_other_deg1.4862.9927080
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0520.2792
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023240
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021344
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.2815.5866
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.964.616386
X-RAY DIFFRACTIONr_scbond_other1.964.616385
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4176.9089388
X-RAY DIFFRACTIONr_long_range_B_refined5.47540.3097880
X-RAY DIFFRACTIONr_long_range_B_other5.47540.3087881
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.508 23 -
Rwork0.33 1062 -
obs--94.59 %

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