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- PDB-3ikt: Crystal structure of a Rex-family repressor/DNA/NAD+ complex from... -

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Basic information

Entry
Database: PDB / ID: 3ikt
TitleCrystal structure of a Rex-family repressor/DNA/NAD+ complex from Thermus aquaticus
Components
  • Redox-sensing transcriptional repressor rex
  • Rex operator DNA
KeywordsDNA BINDING PROTEIN/DNA / redox-sensing / winged helix / Rossmann fold / Nicotinamide Adenine Dinucleotide / NAD / Rex / Thermus aquaticus / DNA BINDING PROTEIN / Cytoplasm / DNA-binding / Repressor / Transcription / Transcription regulation / DNA BINDING PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


response to redox state / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA binding / cytoplasm
Similarity search - Function
Rex DNA-binding, C-terminal domain / Redox-sensing transcriptional repressor Rex / Putative DNA-binding protein N-terminus / CoA binding domain / CoA binding domain / CoA-binding / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / NAD(P)-binding Rossmann-like Domain / Winged helix DNA-binding domain superfamily ...Rex DNA-binding, C-terminal domain / Redox-sensing transcriptional repressor Rex / Putative DNA-binding protein N-terminus / CoA binding domain / CoA binding domain / CoA-binding / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / NAD(P)-binding Rossmann-like Domain / Winged helix DNA-binding domain superfamily / NAD(P)-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / DNA / DNA (> 10) / Redox-sensing transcriptional repressor Rex
Similarity search - Component
Biological speciesThermus thermophilus HB27 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsMcLaughlin, K.J. / Kielkopf, C.L.
CitationJournal: Mol.Cell / Year: 2010
Title: Structural basis for NADH/NAD+ redox sensing by a Rex family repressor.
Authors: McLaughlin, K.J. / Strain-Damerell, C.M. / Xie, K. / Brekasis, D. / Soares, A.S. / Paget, M.S. / Kielkopf, C.L.
History
DepositionAug 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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
A: Redox-sensing transcriptional repressor rex
B: Redox-sensing transcriptional repressor rex
C: Rex operator DNA
D: Rex operator DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6315
Polymers58,9684
Non-polymers6631
Water6,810378
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10710 Å2
ΔGint-69.2 kcal/mol
Surface area24190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.150, 63.150, 299.260
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsBIOLOGICAL UNIT IS THE SAME AS ASYMMETRIC UNIT.

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Components

#1: Protein Redox-sensing transcriptional repressor rex


Mass: 22730.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB27 (bacteria) / Strain: HB27 / DSM 7039 / Gene: rex, TT_C1293 / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q72I39
#2: DNA chain Rex operator DNA


Mass: 6753.354 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic 22bp dsDNA obtained from IDT
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / 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: 2.93 Å3/Da / Density % sol: 57.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20-30% PEG 400, 0.1M Na Cacodylate pH 6.0, 0.2M CaCl2, 5-10% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 40011
2Na Cacodylate11
3CaCl211
4Glycerol11
5PEG 40012
6Na Cacodylate12
7CaCl212
8Glycerol12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
Details: Vertically collimating mirror followed by a channel-cut Si(111) crystal monochromator and a double focusing toroidal mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.26→50 Å / Num. obs: 40822 / % possible obs: 97.6 % / Redundancy: 10.7 % / Rsym value: 0.086 / Net I/σ(I): 21.3
Reflection shellResolution: 2.26→2.37 Å / Redundancy: 11.5 % / Mean I/σ(I) obs: 7.2 / Rsym value: 0.401 / % possible all: 99.8

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Processing

Software
NameClassification
HKL-2000data collection
PHASERphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1XCB

1xcb


Resolution: 2.26→20 Å / Cross valid method: MAXIMUM LIKELIHOOD / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.268 3315 -Random
Rwork0.234 ---
all0.234 33165 --
obs0.234 33165 98.6 %-
Refinement stepCycle: LAST / Resolution: 2.26→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3166 896 44 378 4484
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.48
X-RAY DIFFRACTIONc_bond_d0.007

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