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- PDB-3ikv: Crystal structure of a Rex-family repressor R90D mutant from Ther... -

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Basic information

Entry
Database: PDB / ID: 3ikv
TitleCrystal structure of a Rex-family repressor R90D mutant from Thermus aquaticus
ComponentsRedox-sensing transcriptional repressor rex
KeywordsDNA BINDING PROTEIN / redox-sensing / winged helix / Rossmann fold / Nicotinamide Adenine Dinucleotide / NAD / Rex / Thermus aquaticus / Mutant / Cytoplasm / DNA-binding / Repressor / Transcription / Transcription regulation
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
Redox-sensing transcriptional repressor Rex
Similarity search - Component
Biological speciesThermus thermophilus HB27 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 1.2Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 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

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Assembly

Deposited unit
A: Redox-sensing transcriptional repressor rex
B: Redox-sensing transcriptional repressor rex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4173
Polymers45,3772
Non-polymers401
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-41.6 kcal/mol
Surface area19930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.995, 88.222, 99.576
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsBIOLOGICAL UNIT IS THE SAME AS ASYMMETRIC UNIT.

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Components

#1: Protein Redox-sensing transcriptional repressor rex


Mass: 22688.332 Da / Num. of mol.: 2 / Mutation: R90D
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: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 2.76 Å3/Da / Density % sol: 55.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20-30% PEG 400, 0.1M Na Cacodylate pH 6.0, 5-10% Glycerol, 0.1-0.2M CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 15, 2006
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: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 20539 / % possible obs: 98.5 % / Redundancy: 7.1 % / Rsym value: 0.143 / Net I/σ(I): 13.9
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 1.9 / Rsym value: 0.251 / % possible all: 92.2

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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: 2.4→20 Å / Cross valid method: MAXIMUM LIKELIHOOD / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1571 -Random
Rwork0.218 ---
all0.218 17691 --
obs0.218 17691 90.1 %-
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3178 0 1 217 3396
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.53
X-RAY DIFFRACTIONc_bond_d0.008

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