› 2ht0

X-ray diffraction
2Å resolution

IHF bound to doubly nicked DNA

Released:
DOI: 10.2210/pdb2ht0/pdb
PDB entry 2ht0 coloured by chain, front view.
PDB entry 2ht0 coloured by chain, side view.
PDB entry 2ht0 coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Structure-based analysis of HU-DNA binding.
Swinger KK, Rice PA
J Mol Biol 365 1005-16 (2007)
PMID: 17097674

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-115366 (preferred)
Entry contents:
2 distinct polypeptide molecules
4 distinct DNA molecules
Macromolecules (6 distinct):
Integration host factor subunit alpha Chain: A
Molecule details ›
Chain: A
Length: 99 amino acids
Theoretical weight: 11.37 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A6X7 (Residues: 1-99; Coverage: 100%)
Gene names: JW1702, b1712, hid, himA, ihfA
Sequence domains: Bacterial DNA-binding protein
Structure domains: IHF-like DNA-binding proteins
Integration host factor subunit beta Chain: B
Molecule details ›
Chain: B
Length: 94 amino acids
Theoretical weight: 10.67 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: Q14F22 (Residues: 1-94; Coverage: 100%)
Gene names: A5U30_001526, A8502_001643, ACN81_15370, ACU57_24975, AW118_05710, AWP47_29690, B6R15_004117, B6R31_003516, BANRA_01427, BANRA_04734, BE932_28810, BER14_06950, BG944_003081, BGM66_002804, BGZ_00286, BGZ_00643, BJI68_12015, BK292_06350, BK383_04110, BKL28_000571, BTB68_001156, BTQ06_17235, BXT93_13720, BvCmsKKP061_04587, BvCmsSIP010_00904, C1Q91_002779, C2M16_00665, C2R31_002417, C3F40_07730, C9Z68_12540, CF22_002557, CG704_09085, CG831_002274, CIG67_23390, CTR35_002698, CV83915_00692, D3G36_04095, D4M65_10395, D4N09_10160, D9D43_06680, D9E49_14705, D9J61_20550, DD762_16185, DIV22_10825, DNQ45_10930, DNX30_10415, DS732_09560, DTL43_10185, DU321_00110, E4K51_09750, E5H86_16435, E6D34_03025, EAI46_02325, ECs0995, EIA08_02090, EIZ93_00585, EN85_000477, EPS76_10665, EPS97_02585, EWK56_13420, ExPECSC038_03332, F7F11_21915, F7N46_01450, F9413_08295, F9461_02085, F9B07_02065, FGAF848_13170, FIJ20_09845, FJQ40_00060, FKO60_07830, FOI11_008375, FOI11_11670, FORC44_3860, FPI65_05465, FPS11_01030, FTV93_09340, FVB16_16590, FWK02_28325, FZU14_07525, G3V95_07250, G3W53_07710, G5603_01425, GAI89_09285, GAJ12_12195, GKF66_13195, GNW61_20130, GP711_00170, GP954_09480, GP965_08025, GP975_07500, GP979_00625, GQA06_11345, GQE86_18445, GQM04_13350, GQM13_15280, GQM21_05265, GQN34_21155, GQW07_02395, GRC73_05485, GRO95_00700, GRW05_05260, GRW24_12270, GRW56_06815, GRW57_15115, GUC01_02515, H0O72_02115, HEP30_004685, HEP34_002346, HHH44_001079, HI055_004342, HIE29_000209, HJQ60_004514, HLX92_02860, HLZ50_00835, HMV95_03065, HV109_15500, HV209_05925, HVV39_21530, HVW04_06420, HVW43_07770, HVY77_17170, I6H00_09450, I6H02_23375, IFB95_003036, J0541_002915, J5U05_000507, JNP96_09495, KV499_000445, NCTC10082_05175, NCTC10089_03319, NCTC10418_04891, NCTC10429_05599, NCTC10764_04608, NCTC10767_04811, NCTC10974_03684, NCTC11112_04713, NCTC11126_01174, NCTC11181_00393, NCTC11341_04666, NCTC13148_05930, NCTC7922_00328, NCTC7927_03633, NCTC7928_00752, NCTC8009_06023, NCTC8179_02433, NCTC8333_03850, NCTC8500_03574, NCTC8621_03404, NCTC8622_06245, NCTC8959_00518, NCTC8960_00593, NCTC8985_01998, NCTC9001_01213, NCTC9044_04218, NCTC9073_02215, NCTC9077_03963, NCTC9117_04055, NCTC9702_03761, NCTC9706_00594, NEP60_21975, OGM49_08560, RZR61_03160, SAMEA3472112_03036, SAMEA3752557_03337, WR15_11925, himD, ihfB
Sequence domains: Bacterial DNA-binding protein
Structure domains: IHF-like DNA-binding proteins
5'-D(*CP*GP*GP*TP*GP*CP*AP*AP*CP*AP*AP*AP*T)-3' Chain: C
Molecule details ›
Chain: C
Length: 13 nucleotides
Theoretical weight: 3.98 KDa
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' Chain: D
Molecule details ›
Chain: D
Length: 22 nucleotides
Theoretical weight: 6.77 KDa
5'-D(*GP*GP*CP*CP*AP*AP*AP*AP*AP*AP*GP*CP*AP*TP*T)-3' Chain: E
Molecule details ›
Chain: E
Length: 15 nucleotides
Theoretical weight: 4.61 KDa
5'-D(*GP*CP*TP*TP*AP*TP*CP*AP*AP*TP*TP*TP*GP*TP*TP*GP*CP*AP*CP*C)-3' Chain: F
Molecule details ›
Chain: F
Length: 20 nucleotides
Theoretical weight: 6.07 KDa

Ligands and Environments

1 bound ligand:
Ligand CD 1 x CD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X4A
Spacegroup: P212121
Unit cell:
a: 46.942Å b: 58.944Å c: 181.676Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.237 0.235 0.278

Quick links

Citations

14 review citations

Inorganic polyphosphate: essential for growth and survival.
Rao et al. (2009)
13 more

1 mention without citation

Structure-based analysis of HU-DNA binding.
Swinger et al. (2007)