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- PDB-4hf1: Crystal Structure of IscR bound to its promoter -

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Basic information

Entry
Database: PDB / ID: 4hf1
TitleCrystal Structure of IscR bound to its promoter
Components
  • (DNA (29-MER)) x 2
  • HTH-type transcriptional regulator IscR
KeywordsTranscription/DNA / wHTH / Protein-DNA Complex / Iron-Sulfur Cluster / winged Helix-turn-Helix / Transcriptional Regulator / Redox sensor / DNA Binding / Transcription-DNA complex
Function / homology
Function and homology information


2 iron, 2 sulfur cluster binding / double-stranded DNA binding / iron ion binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / identical protein binding / cytosol
Similarity search - Function
Transcription factor HTH, IscR / Transcription regulator Rrf2-type, conserved site / Rrf2-type HTH domain signature. / Transcription regulator Rrf2 / Iron-dependent Transcriptional regulator / Rrf2-type HTH domain profile. / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily ...Transcription factor HTH, IscR / Transcription regulator Rrf2-type, conserved site / Rrf2-type HTH domain signature. / Transcription regulator Rrf2 / Iron-dependent Transcriptional regulator / Rrf2-type HTH domain profile. / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / HTH-type transcriptional regulator IscR
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.222 Å
AuthorsRajagopalan, S.R. / Phillips, K.J.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: Studies of IscR reveal a unique mechanism for metal-dependent regulation of DNA binding specificity.
Authors: Rajagopalan, S. / Teter, S.J. / Zwart, P.H. / Brennan, R.G. / Phillips, K.J. / Kiley, P.J.
History
DepositionOct 4, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1May 29, 2013Group: Database references
Revision 1.2Jul 3, 2013Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: HTH-type transcriptional regulator IscR
B: HTH-type transcriptional regulator IscR
C: DNA (29-MER)
D: DNA (29-MER)


Theoretical massNumber of molelcules
Total (without water)54,2334
Polymers54,2334
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10060 Å2
ΔGint-65 kcal/mol
Surface area19440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.124, 75.320, 187.394
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HTH-type transcriptional regulator IscR


Mass: 18205.348 Da / Num. of mol.: 2 / Mutation: C92A, C98A, C104A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: iscR, yfhP, b2531, JW2515 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AGK8
#2: DNA chain DNA (29-MER)


Mass: 8888.754 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#3: DNA chain DNA (29-MER)


Mass: 8933.824 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)

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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: 3.2 Å3/Da / Density % sol: 61.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2-0.3M Ammonium Phosphate, 20% glycerol, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 24, 2009
RadiationMonochromator: Asymmetric curved crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.22→50 Å / Num. obs: 33154 / % possible obs: 94 % / Redundancy: 7 % / Rsym value: 0.071 / Net I/σ(I): 10.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
PHENIX(phenix.refine: 1.8.1_1161)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.222→48.081 Å / SU ML: 0.23 / σ(F): 1.34 / Phase error: 28.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2277 2377 7.42 %RANDOM
Rwork0.2028 ---
obs0.2047 27065 48.43 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 69.2135 Å2
Refinement stepCycle: LAST / Resolution: 2.222→48.081 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1913 1183 0 0 3096
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053258
X-RAY DIFFRACTIONf_angle_d1.0344650
X-RAY DIFFRACTIONf_dihedral_angle_d23.9491279
X-RAY DIFFRACTIONf_chiral_restr0.062536
X-RAY DIFFRACTIONf_plane_restr0.003398
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2222-2.26760.2189440.2338541X-RAY DIFFRACTION15
2.2676-2.31690.3017570.2322706X-RAY DIFFRACTION20
2.3169-2.37080.2294630.2477794X-RAY DIFFRACTION22
2.3708-2.43010.2791770.2436966X-RAY DIFFRACTION26
2.4301-2.49580.2698850.24281078X-RAY DIFFRACTION30
2.4958-2.56920.3223970.27371211X-RAY DIFFRACTION34
2.5692-2.65210.24321060.26141322X-RAY DIFFRACTION37
2.6521-2.74690.27721180.2861476X-RAY DIFFRACTION41
2.7469-2.85690.28231270.2971601X-RAY DIFFRACTION44
2.8569-2.98690.36941430.29671775X-RAY DIFFRACTION50
2.9869-3.14430.34591580.26711962X-RAY DIFFRACTION55
3.1443-3.34130.24531660.2432026X-RAY DIFFRACTION56
3.3413-3.59920.22881880.21082246X-RAY DIFFRACTION62
3.5992-3.96120.2342020.18692584X-RAY DIFFRACTION72
3.9612-4.53410.17612260.15972807X-RAY DIFFRACTION78
4.5341-5.7110.21952530.17523176X-RAY DIFFRACTION88
5.711-48.09260.1822670.17263387X-RAY DIFFRACTION94

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