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- PDB-5zz5: Redox-sensing transcriptional repressor Rex -

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Basic information

Entry
Database: PDB / ID: 5zz5
TitleRedox-sensing transcriptional repressor Rex
ComponentsRedox-sensing transcriptional repressor Rex
KeywordsGENE REGULATION / Redox sensing / transcription factor
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 / Winged helix-like DNA-binding domain superfamily / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Redox-sensing transcriptional repressor Rex 1
Similarity search - Component
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPark, Y.W. / Jang, Y.Y. / Joo, H.K. / Lee, J.Y.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (Korea)NRF- 2017-R1D1A1B03032109 Korea, Republic Of
CitationJournal: Sci Rep / Year: 2018
Title: Structural Analysis of Redox-sensing Transcriptional Repressor Rex from Thermotoga maritima
Authors: Park, Y.W. / Jang, Y.Y. / Joo, H.K. / Lee, J.Y.
History
DepositionMay 30, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: Redox-sensing transcriptional repressor Rex
D: Redox-sensing transcriptional repressor Rex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,3158
Polymers91,9474
Non-polymers3684
Water5,368298
1
A: Redox-sensing transcriptional repressor Rex
B: Redox-sensing transcriptional repressor Rex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1574
Polymers45,9732
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5790 Å2
ΔGint-48 kcal/mol
Surface area18890 Å2
MethodPISA
2
C: Redox-sensing transcriptional repressor Rex
D: Redox-sensing transcriptional repressor Rex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1574
Polymers45,9732
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint-47 kcal/mol
Surface area15980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.577, 88.464, 87.967
Angle α, β, γ (deg.)90.000, 96.810, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Redox-sensing transcriptional repressor Rex


Mass: 22986.643 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Gene: rex1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9WY16
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 2.25 Å3/Da / Density % sol: 45.36 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / Details: potassium chloride, PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Apr 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 55075 / % possible obs: 99.6 % / Redundancy: 3.8 % / Biso Wilson estimate: 39.09 Å2 / Net I/σ(I): 18.21
Reflection shellResolution: 2→2.03 Å / Rmerge(I) obs: 0.559

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→29.115 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.47
RfactorNum. reflection% reflection
Rfree0.2583 2790 5.08 %
Rwork0.204 --
obs0.2068 54885 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 124.57 Å2 / Biso mean: 48.56 Å2 / Biso min: 21.48 Å2
Refinement stepCycle: final / Resolution: 2→29.115 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5531 0 24 298 5853
Biso mean--56.76 49.25 -
Num. residues----745
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085644
X-RAY DIFFRACTIONf_angle_d1.0387638
X-RAY DIFFRACTIONf_chiral_restr0.044910
X-RAY DIFFRACTIONf_plane_restr0.005978
X-RAY DIFFRACTIONf_dihedral_angle_d13.1352033
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.03450.34421440.28392593273799
2.0345-2.07150.31261480.2642593274199
2.0715-2.11130.29971200.248825852705100
2.1113-2.15440.30451330.246226352768100
2.1544-2.20120.29291160.241525812697100
2.2012-2.25240.29311270.23212623275099
2.2524-2.30870.27771410.228425732714100
2.3087-2.37110.34031430.226925812724100
2.3711-2.44090.29731270.221126582785100
2.4409-2.51960.25181360.221825932729100
2.5196-2.60960.27961560.216925582714100
2.6096-2.7140.2531380.215326262764100
2.714-2.83740.29531570.216326032760100
2.8374-2.98690.26851410.222825902731100
2.9869-3.17380.29731550.214326072762100
3.1738-3.41850.26521360.208426112747100
3.4185-3.76190.25771540.19926192773100
3.7619-4.30480.22541300.175226232753100
4.3048-5.41780.21241440.17326552799100
5.4178-29.11850.23951440.19472588273297
Refinement TLS params.Method: refined / Origin x: 74.515 Å / Origin y: 118.18 Å / Origin z: -68.359 Å
111213212223313233
T0.2225 Å20.0253 Å20.0058 Å2-0.232 Å20.002 Å2--0.2015 Å2
L0.4002 °20.3163 °20.1377 °2-0.7467 °20.3849 °2--0.3745 °2
S0.0562 Å °-0.0453 Å °-0.0146 Å °0.0665 Å °-0.0469 Å °0.0667 Å °0.0157 Å °-0.0258 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA9 - 208
2X-RAY DIFFRACTION1allA301
3X-RAY DIFFRACTION1allA401 - 495
4X-RAY DIFFRACTION1allC13 - 207
5X-RAY DIFFRACTION1allC301
6X-RAY DIFFRACTION1allC401 - 454
7X-RAY DIFFRACTION1allB3 - 208
8X-RAY DIFFRACTION1allB301
9X-RAY DIFFRACTION1allB401 - 501
10X-RAY DIFFRACTION1allD8 - 206
11X-RAY DIFFRACTION1allD301
12X-RAY DIFFRACTION1allD401 - 448

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