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- PDB-2ht0: IHF bound to doubly nicked DNA -

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Basic information

Entry
Database: PDB / ID: 2ht0
TitleIHF bound to doubly nicked DNA
Components
  • (Integration host factor ...) x 2
  • 5'-D(*CP*GP*GP*TP*GP*CP*AP*AP*CP*AP*AP*AP*T)-3'
  • 5'-D(*GP*CP*TP*TP*AP*TP*CP*AP*AP*TP*TP*TP*GP*TP*TP*GP*CP*AP*CP*C)-3'
  • 5'-D(*GP*GP*CP*CP*AP*AP*AP*AP*AP*AP*GP*CP*AP*TP*T)-3'
  • 5'-D(*TP*GP*AP*TP*AP*AP*GP*CP*AP*AP*TP*GP*CP*TP*TP*TP*TP*TP*TP*GP*GP*C)-3'
KeywordsTRANSCRIPTION/DNA / DNA bending / kink / nick / protein-DNA complex / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


IHF-DNA complex / DNA-binding transcription activator activity / protein-DNA complex / structural constituent of chromatin / regulation of translation / chromosome / DNA recombination / transcription cis-regulatory region binding / DNA-templated transcription / regulation of DNA-templated transcription ...IHF-DNA complex / DNA-binding transcription activator activity / protein-DNA complex / structural constituent of chromatin / regulation of translation / chromosome / DNA recombination / transcription cis-regulatory region binding / DNA-templated transcription / regulation of DNA-templated transcription / DNA binding / cytosol
Similarity search - Function
Integration host factor, alpha subunit / Integration host factor, beta subunit / HU Protein; Chain A / IHF-like DNA-binding proteins / Histone-like DNA-binding protein, conserved site / Bacterial histone-like DNA-binding proteins signature. / Histone-like DNA-binding protein / Bacterial DNA-binding protein / bacterial (prokaryotic) histone like domain / Integration host factor (IHF)-like DNA-binding domain superfamily ...Integration host factor, alpha subunit / Integration host factor, beta subunit / HU Protein; Chain A / IHF-like DNA-binding proteins / Histone-like DNA-binding protein, conserved site / Bacterial histone-like DNA-binding proteins signature. / Histone-like DNA-binding protein / Bacterial DNA-binding protein / bacterial (prokaryotic) histone like domain / Integration host factor (IHF)-like DNA-binding domain superfamily / Few Secondary Structures / Irregular
Similarity search - Domain/homology
: / DNA / DNA (> 10) / Integration host factor subunit alpha / Integration host factor subunit beta / Integration host factor subunit beta
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2 Å
AuthorsSwinger, K.K. / Rice, P.A.
Citation
Journal: J.Mol.Biol. / Year: 2007
Title: Structure-based Analysis of HU-DNA Binding.
Authors: Swinger, K.K. / Rice, P.A.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1996
Title: Crystal structure of an IHF-DNA complex: a protein-induced DNA U-turn.
Authors: Rice, P.A. / Yang, S.-W. / Nash, H. / Mizuuchi, K.
History
DepositionJul 24, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_asym_id / _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.ptnr3_auth_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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _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_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
C: 5'-D(*CP*GP*GP*TP*GP*CP*AP*AP*CP*AP*AP*AP*T)-3'
D: 5'-D(*TP*GP*AP*TP*AP*AP*GP*CP*AP*AP*TP*GP*CP*TP*TP*TP*TP*TP*TP*GP*GP*C)-3'
E: 5'-D(*GP*GP*CP*CP*AP*AP*AP*AP*AP*AP*GP*CP*AP*TP*T)-3'
F: 5'-D(*GP*CP*TP*TP*AP*TP*CP*AP*AP*TP*TP*TP*GP*TP*TP*GP*CP*AP*CP*C)-3'
A: Integration host factor alpha-subunit
B: Integration host factor beta-subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6017
Polymers43,4886
Non-polymers1121
Water4,684260
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.942, 58.944, 181.676
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is the heterodimer found in the asymmetric unit.

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Components

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DNA chain , 4 types, 4 molecules CDEF

#1: DNA chain 5'-D(*CP*GP*GP*TP*GP*CP*AP*AP*CP*AP*AP*AP*T)-3'


Mass: 3984.624 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*TP*GP*AP*TP*AP*AP*GP*CP*AP*AP*TP*GP*CP*TP*TP*TP*TP*TP*TP*GP*GP*C)-3'


Mass: 6772.386 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain 5'-D(*GP*GP*CP*CP*AP*AP*AP*AP*AP*AP*GP*CP*AP*TP*T)-3'


Mass: 4611.039 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: DNA chain 5'-D(*GP*CP*TP*TP*AP*TP*CP*AP*AP*TP*TP*TP*GP*TP*TP*GP*CP*AP*CP*C)-3'


Mass: 6074.938 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Integration host factor ... , 2 types, 2 molecules AB

#5: Protein Integration host factor alpha-subunit / IHF-alpha


Mass: 11373.952 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A6X7
#6: Protein Integration host factor beta-subunit / IHF-beta


Mass: 10671.178 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A6Y1, UniProt: Q14F22*PLUS

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Non-polymers , 2 types, 261 molecules

#7: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.84 Å3/Da / Density % sol: 56.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1mM protein, 1.5 molar excess DNA, ~22%PEG4000, 50mM KCl, 1mM spermine, 5-15% glycerol, 15mM Cd++, 0.3% NaN3, 50mM Tris-HCl soaked in cryoprotectant with more glycerol, more PEG, and Mg++ ...Details: 1mM protein, 1.5 molar excess DNA, ~22%PEG4000, 50mM KCl, 1mM spermine, 5-15% glycerol, 15mM Cd++, 0.3% NaN3, 50mM Tris-HCl soaked in cryoprotectant with more glycerol, more PEG, and Mg++ replacing Cd++, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG400011
2KCl11
3spermine11
4glycerol11
5Cd++11
6NaN311
7Tris-HCl11
8H2O11
9PEG400012
10KCl12
11glycerol12
12Cd++12
13NaN312
14Tris-HCl12
15H2O12

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Jun 1, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2→15 Å / Num. all: 35004 / Num. obs: 33359 / % possible obs: 95.3 % / Observed criterion σ(F): -999 / Observed criterion σ(I): -3 / Biso Wilson estimate: 11.2 Å2
Reflection shellResolution: 2→2.03 Å / % possible all: 83.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MIR / Resolution: 2→14.81 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 819957.77 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.278 1266 4.8 %RANDOM, same indices as for 1IHF
Rwork0.235 ---
all0.237 34955 --
obs0.235 26426 75.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 67.7761 Å2 / ksol: 0.375388 e/Å3
Displacement parametersBiso mean: 60.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å20 Å20 Å2
2--33.68 Å20 Å2
3----33.39 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2→14.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1540 1423 1 260 3224
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.13
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.421.5
X-RAY DIFFRACTIONc_mcangle_it2.182
X-RAY DIFFRACTIONc_scbond_it3.152
X-RAY DIFFRACTIONc_scangle_it4.082.5
LS refinement shellResolution: 2→2.12 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.363 105 4.8 %
Rwork0.315 2101 -
obs--38.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3dna-rna_rep_nopuckers2.paramdna-rna.top
X-RAY DIFFRACTION4ion.paramion.top

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