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- PDB-4chu: E. coli IscR-DNA complex -

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Basic information

Entry
Database: PDB / ID: 4chu
TitleE. coli IscR-DNA complex
Components
  • (HYA PROMOTER FRAGMENT) x 2
  • HTH-TYPE TRANSCRIPTIONAL REGULATOR ISCR
KeywordsTRANSCRIPTION / TRANSCRIPTION REGULATION / DNA RECOGNITION / HELIX-TURN-HELIX MOTIF / RRF2-LIKE REGULATOR
Function / homology
Function and homology information


2 iron, 2 sulfur cluster binding / double-stranded DNA binding / iron ion binding / DNA-binding transcription factor activity
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 K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.489 Å
AuthorsSantos, J.A. / Macedo-Ribeiro, S. / Pereira, P.J.B.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: The Unique Regulation of Iron-Sulfur Cluster Biogenesis in a Gram-Positive Bacterium.
Authors: Santos, J.A. / Alonso-Garcia, N. / Macedo-Ribeiro, S. / Pereira, P.J.B.
History
DepositionDec 4, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 4, 2014Group: Database references
Revision 1.2Jun 25, 2014Group: Database references
Revision 1.3May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HTH-TYPE TRANSCRIPTIONAL REGULATOR ISCR
B: HTH-TYPE TRANSCRIPTIONAL REGULATOR ISCR
C: HYA PROMOTER FRAGMENT
D: HYA PROMOTER FRAGMENT


Theoretical massNumber of molelcules
Total (without water)51,3244
Polymers51,3244
Non-polymers00
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9870 Å2
ΔGint-63.4 kcal/mol
Surface area18650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.015, 75.835, 173.421
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.906403, 0.421922, -0.020374), (0.420988, 0.898331, -0.125578), (-0.034682, -0.122402, -0.991874)
Vector: -8.4702, 3.3643, 29.7306)

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Components

#1: Protein HTH-TYPE TRANSCRIPTIONAL REGULATOR ISCR / ISCR


Mass: 17367.414 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI K-12 (bacteria) / Plasmid: PETZ2_1A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: C3SZN7
#2: DNA chain HYA PROMOTER FRAGMENT


Mass: 8296.367 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ESCHERICHIA COLI K-12 (bacteria) / References: GenBank: 557270520
#3: DNA chain HYA PROMOTER FRAGMENT


Mass: 8292.399 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ESCHERICHIA COLI K-12 (bacteria) / References: GenBank: 557270520
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsINSERTION OF G BETWEEN RESIDUES 1 AND 2. MUTATIONS C92S, C98S, C104S. ADDITIONAL 5' G ADDITIONAL 5' C

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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: 3.13 Å3/Da / Density % sol: 60.7 % / Description: NONE
Crystal growpH: 4
Details: 0.1M CITRIC ACID PH 4.0, 0.1M LICL, 20% (W/V) PEG6K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARRESEARCH / Detector: CCD / Date: May 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.49→46 Å / Num. obs: 23387 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 49.27 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.6
Reflection shellResolution: 2.49→2.62 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 1.5 / % possible all: 96.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: T. POTENS ISCR

Resolution: 2.489→45.973 Å / SU ML: 0.33 / σ(F): 1.34 / Phase error: 29.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2508 1193 5.1 %
Rwork0.2067 --
obs0.209 23250 98.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.489→45.973 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1841 1101 0 15 2957
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083136
X-RAY DIFFRACTIONf_angle_d1.3814468
X-RAY DIFFRACTIONf_dihedral_angle_d26.6281233
X-RAY DIFFRACTIONf_chiral_restr0.055515
X-RAY DIFFRACTIONf_plane_restr0.005389
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4888-2.58850.38261410.33952313X-RAY DIFFRACTION95
2.5885-2.70630.361280.30852426X-RAY DIFFRACTION100
2.7063-2.84890.26791230.27292416X-RAY DIFFRACTION100
2.8489-3.02740.29021150.26542461X-RAY DIFFRACTION100
3.0274-3.26110.31191460.23462410X-RAY DIFFRACTION99
3.2611-3.58910.24251460.2112389X-RAY DIFFRACTION98
3.5891-4.10820.23031360.18252485X-RAY DIFFRACTION100
4.1082-5.17480.21931240.16492505X-RAY DIFFRACTION100
5.1748-45.98120.21321340.17952652X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.48640.13451.26796.12950.35636.4923-0.14560.0591-0.21680.2311-0.0928-0.16740.03350.26590.20840.1741-0.0292-0.0110.2368-0.06930.341217.721985.2081-8.7488
22.1606-0.2634-0.51892.46562.48884.4913-0.0733-0.15030.0198-0.0529-0.13790.1881-0.0761-0.70790.17560.2224-0.02650.01090.45920.00030.3348.367990.1005-0.9307
35.8361-0.95460.28892.5726-3.78885.80430.1296-0.07951.24040.8012-0.3695-0.4654-1.5880.33740.35450.5588-0.11290.02550.6843-0.13870.499719.9515102.539-1.3346
45.8833-0.3042-4.32310.898-0.42034.0804-0.11150.1943-0.3803-0.35520.0219-0.04490.7984-0.09970.04380.6593-0.0985-0.00410.8230.0160.427313.590989.92621.8908
52.37630.36460.29993.2643-0.52757.29450.1067-0.8752-0.1780.6019-0.1394-0.01131.29740.7566-0.01330.79780.04850.00081.06270.07190.395517.749987.706229.736
63.8907-0.5887-0.16622.50971.77963.9252-0.0633-0.62390.02170.25160.3421-0.18590.20090.8123-0.26160.3398-0.0497-0.01760.5280.0390.416622.2694.08115.9066
72.15140.6716-0.97380.2294-0.52132.38880.0884-0.3236-0.8429-0.08770.5228-0.09051.9946-0.2722-0.24771.95170.0984-0.17761.48370.26620.567415.23172.578733.5475
84.32420.33782.61124.14840.22672.65380.3045-0.0516-0.6968-0.1134-0.05670.43381.4618-0.5672-0.34310.6693-0.05090.01580.7227-0.11880.58767.546871.6309-9.2071
92.3097-0.18051.20433.6019-2.22616.47950.35440.1629-0.8488-0.02590.39580.27081.28290.4251-0.68740.71810.008-0.11840.7043-0.10530.5529.105270.5847-10.4697
101.44340.39162.87780.67391.25796.1284-0.0438-0.8536-0.767-0.07320.28640.09742.44280.59230.04131.8305-0.00960.08571.52110.32660.716114.874672.302232.5085
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 0 THROUGH 38 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 39 THROUGH 122 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 123 THROUGH 139 )
4X-RAY DIFFRACTION4CHAIN B AND (RESID 1 THROUGH 20 )
5X-RAY DIFFRACTION5CHAIN B AND (RESID 21 THROUGH 83 )
6X-RAY DIFFRACTION6CHAIN B AND (RESID 84 THROUGH 135 )
7X-RAY DIFFRACTION7CHAIN C AND (RESID 1 THROUGH 12 )
8X-RAY DIFFRACTION8CHAIN C AND (RESID 13 THROUGH 27 )
9X-RAY DIFFRACTION9CHAIN D AND (RESID 1 THROUGH 16 )
10X-RAY DIFFRACTION10CHAIN D AND (RESID 17 THROUGH 27 )

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