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- PDB-1ouz: Crystal structure of a mutant IHF (BetaE44A) complexed with a var... -

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Basic information

Entry
Database: PDB / ID: 1ouz
TitleCrystal structure of a mutant IHF (BetaE44A) complexed with a variant H' Site (T44A)
Components
  • (Integration Host Factor ...) x 2
  • 5'-D(*GP*CP*TP*TP*AP*TP*CP*AP*AP*TP*TP*TP*GP*TP*AP*GP*CP*AP*CP*C)-3'
  • 5'-D(*GP*GP*CP*CP*AP*AP*AP*AP*AP*AP*GP*CP*AP*TP*T)-3'
  • Phage lambda H' site
KeywordsTRANSCRIPTION/DNA / protein-DNA recognition / indirect readout / IHF / DNA bending / 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 / DNA replication / transcription cis-regulatory region binding / DNA-templated transcription ...IHF-DNA complex / DNA-binding transcription activator activity / protein-DNA complex / structural constituent of chromatin / regulation of translation / chromosome / DNA recombination / DNA replication / 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
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.41 Å
AuthorsLynch, T.W. / Read, E.K. / Mattis, A.N. / Gardner, J.F. / Rice, P.A.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Integration Host Factor: putting a twist on protein-DNA recognition
Authors: Lynch, T.W. / Read, E.K. / Mattis, A.N. / Gardner, J.F. / Rice, P.A.
History
DepositionMar 25, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Phage lambda H' site
D: 5'-D(*GP*GP*CP*CP*AP*AP*AP*AP*AP*AP*GP*CP*AP*TP*T)-3'
E: 5'-D(*GP*CP*TP*TP*AP*TP*CP*AP*AP*TP*TP*TP*GP*TP*AP*GP*CP*AP*CP*C)-3'
A: Integration Host Factor Alpha-subunit
B: Integration Host Factor Beta-subunit


Theoretical massNumber of molelcules
Total (without water)43,4755
Polymers43,4755
Non-polymers00
Water2,918162
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.799, 60.107, 181.179
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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DNA chain , 3 types, 3 molecules CDE

#1: DNA chain Phage lambda H' site


Mass: 10792.955 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: 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
#3: DNA chain 5'-D(*GP*CP*TP*TP*AP*TP*CP*AP*AP*TP*TP*TP*GP*TP*AP*GP*CP*AP*CP*C)-3'


Mass: 6083.953 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Integration Host Factor ... , 2 types, 2 molecules AB

#4: Protein Integration Host Factor Alpha-subunit / IHF-alpha


Mass: 11373.952 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6X7
#5: Protein Integration Host Factor Beta-subunit / IHF-beta


Mass: 10613.142 Da / Num. of mol.: 1 / Mutation: E44A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6Y1

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Non-polymers , 1 types, 162 molecules

#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.9 Å3/Da / Density % sol: 57.22 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG5000-MME, glycerol, Tris-HCl, magnesium chloride, sodium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG5000-MME11
2glycerol11
3Tris-HCl11
4magnesium chloride11
5sodium chloride11
6PEG5000-MME12
7magnesium chloride12
8sodium chloride12
Crystal grow
*PLUS
Temperature: 19 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
16.7 mg/mlprotein1drop
210 mMHEPES1droppH7.0
30.1 M1dropNaCl
40.1 mMEDTA1drop
58 %glycerol1drop
615 %glycerol1reservoir
725 %PEG5000 MME1reservoir
850 mMTris-HCl1reservoirpH7.5
910 mM1reservoirMgCl2
1050 mM1reservoirNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 23, 2001
RadiationMonochromator: Ge(111) single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.4→100 Å / Num. all: 15710 / Num. obs: 13356 / % possible obs: 85 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1IHF

1ihf


Resolution: 2.41→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.271 614 Random
Rwork0.2412 --
all0.2426 15710 -
obs0.2426 13356 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.327 Å20 Å20 Å2
2---20.604 Å20 Å2
3---23.931 Å2
Refinement stepCycle: LAST / Resolution: 2.41→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1513 1426 0 162 3101
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2dna-rna_rep_nopuckers2.param
X-RAY DIFFRACTION3water_rep.param
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rwork: 0.241
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.003
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg0.69

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