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- PDB-3nm9: HMGD(M13A)-DNA complex -

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Basic information

Entry
Database: PDB / ID: 3nm9
TitleHMGD(M13A)-DNA complex
Components
  • DNA 5'-D(*G*GP*CP*GP*AP*TP*AP*TP*CP*GP*C)-3'
  • High mobility group protein DHigh-mobility group
KeywordsGENE REGULATION/DNA / High mobility group / DNA bending / non-sequence-specific / HMG domain / chromosomal protein / DNA / GENE REGULATION-DNA complex
Function / homology
Function and homology information


DNA binding, bending / minor groove of adenine-thymine-rich DNA binding / chromatin organization / transcription cis-regulatory region binding / chromatin / DNA binding / nucleus
Similarity search - Function
High mobility group box domain / DNA Binding (I), subunit A / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / High mobility group protein D
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsChurchill, M.E.A. / Klass, J. / Zoetewey, D.L.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Structural analysis of HMGD-DNA complexes reveals influence of intercalation on sequence selectivity and DNA bending.
Authors: Churchill, M.E. / Klass, J. / Zoetewey, D.L.
History
DepositionJun 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / 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
A: High mobility group protein D
D: High mobility group protein D
G: High mobility group protein D
J: High mobility group protein D
M: High mobility group protein D
P: High mobility group protein D
B: DNA 5'-D(*G*GP*CP*GP*AP*TP*AP*TP*CP*GP*C)-3'
C: DNA 5'-D(*G*GP*CP*GP*AP*TP*AP*TP*CP*GP*C)-3'
E: DNA 5'-D(*G*GP*CP*GP*AP*TP*AP*TP*CP*GP*C)-3'
F: DNA 5'-D(*G*GP*CP*GP*AP*TP*AP*TP*CP*GP*C)-3'
H: DNA 5'-D(*G*GP*CP*GP*AP*TP*AP*TP*CP*GP*C)-3'
I: DNA 5'-D(*G*GP*CP*GP*AP*TP*AP*TP*CP*GP*C)-3'
K: DNA 5'-D(*G*GP*CP*GP*AP*TP*AP*TP*CP*GP*C)-3'
L: DNA 5'-D(*G*GP*CP*GP*AP*TP*AP*TP*CP*GP*C)-3'
N: DNA 5'-D(*G*GP*CP*GP*AP*TP*AP*TP*CP*GP*C)-3'
O: DNA 5'-D(*G*GP*CP*GP*AP*TP*AP*TP*CP*GP*C)-3'


Theoretical massNumber of molelcules
Total (without water)83,60416
Polymers83,60416
Non-polymers00
Water724
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.750, 71.700, 89.020
Angle α, β, γ (deg.)92.49, 91.12, 107.10
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
High mobility group protein D / High-mobility group / HMG-D


Mass: 8310.396 Da / Num. of mol.: 6 / Mutation: M13A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG17950, HmgD / Plasmid: pET-D74-M13A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q05783
#2: DNA chain
DNA 5'-D(*G*GP*CP*GP*AP*TP*AP*TP*CP*GP*C)-3'


Mass: 3374.210 Da / Num. of mol.: 10 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 3.26 Å3/Da / Density % sol: 62.27 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5.25
Details: 1.2 mM HMGDM13A protein, 1.18 mM duplex DNA fragment (GCGATATCGC), 5 mM MES-Na pH 5.25, 10 mM NaCl, and 7.6% PEG 3350 equilibrated against 0.5 mL 32% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 1, 2001 / Details: Blue Optics
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 23992 / % possible obs: 92.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Rsym value: 0.06 / Net I/σ(I): 21.9
Reflection shellResolution: 2.8→2.91 Å / Mean I/σ(I) obs: 4.6 / Rsym value: 0.208 / % possible all: 82.1

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1qrv

1qrv


Resolution: 2.85→20 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.855 / SU B: 12.834 / SU ML: 0.251 / Cross valid method: THROUGHOUT / ESU R Free: 0.444 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29556 1179 5.2 %RANDOM
Rwork0.24499 ---
obs0.24763 21700 93.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.037 Å2
Baniso -1Baniso -2Baniso -3
1--4.41 Å2-0.6 Å2-1.28 Å2
2--0.4 Å2-4.37 Å2
3---3.22 Å2
Refinement stepCycle: LAST / Resolution: 2.85→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3510 2042 0 4 5556
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0225861
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3342.4028297
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9735432
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.76323.571168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.87715696
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2771536
X-RAY DIFFRACTIONr_chiral_restr0.070.2868
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023748
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2090.252129
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.253569
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.25230
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.2580
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3460.2516
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.68122241
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.8212.53450
X-RAY DIFFRACTIONr_scbond_it3.0783.54847
X-RAY DIFFRACTIONr_scangle_it4.2794.54847
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.85→2.923 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.449 71 -
Rwork0.422 1429 -
obs--84.89 %

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