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- PDB-3wgi: Crystal structure of RSP in complex with beta-NAD+ and operator DNA -

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Basic information

Entry
Database: PDB / ID: 3wgi
TitleCrystal structure of RSP in complex with beta-NAD+ and operator DNA
Components
  • DNA (5'-D(*TP*AP*GP*AP*TP*TP*GP*TP*TP*AP*AP*TP*CP*GP*AP*TP*TP*AP*AP*CP*AP*AP*TP*C)-3')
  • Redox-sensing transcriptional repressor rex
KeywordsTRANSCRIPTION/DNA / winged helix / Rossmann fold / transcription repressor / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


response to redox state / DNA-binding transcription factor activity / nucleotide binding / negative regulation of DNA-templated transcription / DNA binding / metal ion 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE (ACIDIC FORM) / DNA / DNA (> 10) / Redox-sensing transcriptional repressor Rex
Similarity search - Component
Biological speciesThermoanaerobacter ethanolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsZheng, Y. / Ko, T.-P. / Guo, R.-T.
CitationJournal: J.Struct.Biol. / Year: 2014
Title: Distinct structural features of Rex-family repressors to sense redox levels in anaerobes and aerobes.
Authors: Zheng, Y. / Ko, T.-P. / Sun, H. / Huang, C.-H. / Pei, J. / Qiu, R. / Wang, A.H.-J. / Wiegel, J. / Shao, W. / Guo, R.-T.
History
DepositionAug 5, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 8, 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_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: Redox-sensing transcriptional repressor rex
D: Redox-sensing transcriptional repressor rex
E: DNA (5'-D(*TP*AP*GP*AP*TP*TP*GP*TP*TP*AP*AP*TP*CP*GP*AP*TP*TP*AP*AP*CP*AP*AP*TP*C)-3')
F: DNA (5'-D(*TP*AP*GP*AP*TP*TP*GP*TP*TP*AP*AP*TP*CP*GP*AP*TP*TP*AP*AP*CP*AP*AP*TP*C)-3')
G: DNA (5'-D(*TP*AP*GP*AP*TP*TP*GP*TP*TP*AP*AP*TP*CP*GP*AP*TP*TP*AP*AP*CP*AP*AP*TP*C)-3')
H: DNA (5'-D(*TP*AP*GP*AP*TP*TP*GP*TP*TP*AP*AP*TP*CP*GP*AP*TP*TP*AP*AP*CP*AP*AP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,01812
Polymers131,3648
Non-polymers2,6544
Water00
1
A: Redox-sensing transcriptional repressor rex
B: Redox-sensing transcriptional repressor rex
E: DNA (5'-D(*TP*AP*GP*AP*TP*TP*GP*TP*TP*AP*AP*TP*CP*GP*AP*TP*TP*AP*AP*CP*AP*AP*TP*C)-3')
F: DNA (5'-D(*TP*AP*GP*AP*TP*TP*GP*TP*TP*AP*AP*TP*CP*GP*AP*TP*TP*AP*AP*CP*AP*AP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0096
Polymers65,6824
Non-polymers1,3272
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13890 Å2
ΔGint-88 kcal/mol
Surface area26280 Å2
MethodPISA
2
C: Redox-sensing transcriptional repressor rex
D: Redox-sensing transcriptional repressor rex
G: DNA (5'-D(*TP*AP*GP*AP*TP*TP*GP*TP*TP*AP*AP*TP*CP*GP*AP*TP*TP*AP*AP*CP*AP*AP*TP*C)-3')
H: DNA (5'-D(*TP*AP*GP*AP*TP*TP*GP*TP*TP*AP*AP*TP*CP*GP*AP*TP*TP*AP*AP*CP*AP*AP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0096
Polymers65,6824
Non-polymers1,3272
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13940 Å2
ΔGint-88 kcal/mol
Surface area26250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.990, 116.439, 132.887
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12E
22F
32G
42H

NCS domain segments:

Refine code: 1

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LYSLYSPROPROAA4 - 1204 - 120
211LYSLYSPROPROBB4 - 1204 - 120
311LYSLYSPROPROCC4 - 1204 - 120
411LYSLYSPROPRODD4 - 1204 - 120
121LEULEUNAJNAJAA - I122 - 900122
221LEULEUNAJNAJBB - J122 - 900122
321LEULEUNAJNAJCC - K122 - 900122
421LEULEUNAJNAJDD - L122 - 900122
112DTDTDCDCEE299 - 3221 - 24
212DTDTDCDCFF299 - 3221 - 24
312DTDTDCDCGG299 - 3221 - 24
412DTDTDCDCHH299 - 3221 - 24

NCS ensembles :
ID
1
2

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Components

#1: Protein
Redox-sensing transcriptional repressor rex / RSP repressor


Mass: 25474.279 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacter ethanolicus (bacteria)
Strain: JW200 / Gene: rex, rsp / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D5KM69
#2: DNA chain
DNA (5'-D(*TP*AP*GP*AP*TP*TP*GP*TP*TP*AP*AP*TP*CP*GP*AP*TP*TP*AP*AP*CP*AP*AP*TP*C)-3')


Mass: 7366.802 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: operator DNA
#3: Chemical
ChemComp-NAJ / NICOTINAMIDE-ADENINE-DINUCLEOTIDE (ACIDIC FORM)


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2
Sequence detailsSEQUENCE OF THE DNA IS AN AVERAGE OF THE REAL SEQUENCE OF TAGATTGTTAAATGAATAACAATC AND ...SEQUENCE OF THE DNA IS AN AVERAGE OF THE REAL SEQUENCE OF TAGATTGTTAAATGAATAACAATC AND TAGATTGTTATTCATTTAACAATC USED IN CRYSTALLIZATION.

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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: 2.83 Å3/Da / Density % sol: 56.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.39mM RSP protein, 0.21mM of each DNA oligonucleotide, 1mM beta-NAD+, 0.2M sodium malonate, 20% w/v PEG3350, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 16, 2012 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.25→25 Å / Num. all: 24010 / Num. obs: 23962 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 20.9
Reflection shellResolution: 3.25→3.37 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.543 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceControl Softwaredata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
REFMAC5.5.0109refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 3WGH

3wgh


Resolution: 3.25→25 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.926 / Occupancy max: 1 / Occupancy min: 1 / SU B: 57.161 / SU ML: 0.404 / Cross valid method: THROUGHOUT / ESU R Free: 0.49 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22833 1105 4.9 %RANDOM
Rwork0.19337 ---
obs0.19508 22664 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 126.468 Å2
Baniso -1Baniso -2Baniso -3
1--6.85 Å20 Å20 Å2
2--6 Å20 Å2
3---0.85 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.52 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.81 Å0.61 Å
Refinement stepCycle: LAST / Resolution: 3.25→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6960 1956 176 0 9092
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0229452
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5832.25813196
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6165864
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.92824.419344
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.561151324
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7091552
X-RAY DIFFRACTIONr_chiral_restr0.0920.21492
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026368
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0851.54292
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.11326936
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.11835160
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.6174.56260
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1773tight positional0.090.05
12B1773tight positional0.10.05
13C1773tight positional0.090.05
14D1773tight positional0.090.05
21E489tight positional0.070.05
22F489tight positional0.060.05
23G489tight positional0.050.05
24H489tight positional0.050.05
11A1773tight thermal0.170.5
12B1773tight thermal0.160.5
13C1773tight thermal0.160.5
14D1773tight thermal0.150.5
21E489tight thermal0.10.5
22F489tight thermal0.110.5
23G489tight thermal0.080.5
24H489tight thermal0.080.5
LS refinement shellResolution: 3.253→3.426 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.343 158 -
Rwork0.309 2789 -
obs--100 %
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)
10.97590.81320.18160.60060.388-0.0584-0.00320.06770.0934-0.13330.03690.2970.1071-0.1596-0.03370.13640.0313-0.00090.18190.0110.14566.3839-12.584314.2149
21.4619-0.22340.32610.6219-0.11150.6566-0.00680.23930.0691-0.18160.00010.05760.03390.07230.00670.18750.0343-0.00360.16860.02180.109171.3103-6.22031.1399
31.60330.17280.13030.56010.1310.6558-0.0342-0.2876-0.14180.1569-0.0218-0.3737-0.02720.11190.0560.19850.0186-0.07920.25330.03980.2718.2773-14.964924.9021
40.64230.0138-0.63250.89730.40981.34350.0317-0.127-0.0947-0.0218-0.0552-0.3844-0.1940.00020.02350.22740.0102-0.02120.1869-0.02440.294321.3716-4.677313.885
50.3683-0.15190.0327-0.0223-0.6433-1.5220.27650.11430.3316-0.11920.08880.2708-0.4039-0.0235-0.36540.31070.4034-0.11140.1096-0.16150.071565.961415.262820.851
60.3553-0.87350.1733-1.04660.27060.9529-0.09130.04320.68030.28160.15820.3237-0.4148-0.5192-0.06680.37050.2512-0.23960.0122-0.09420.256260.617516.450214.9198
72.1624-1.97130.25142.7517-0.5647-0.0002-0.0327-0.84980.19980.37220.2338-0.5091-0.70390.2456-0.20110.4797-0.0471-0.31080.4825-0.30730.145227.62347.297540.3006
85.431-2.35973.88980.106-2.31244.3194-0.0368-0.81310.54280.6909-0.0719-0.4259-0.7352-0.14760.10870.53840.0719-0.31750.3615-0.30490.224521.513411.683637.366
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 220
2X-RAY DIFFRACTION1A900
3X-RAY DIFFRACTION2B4 - 220
4X-RAY DIFFRACTION2B900
5X-RAY DIFFRACTION3C4 - 220
6X-RAY DIFFRACTION3C900
7X-RAY DIFFRACTION4D4 - 220
8X-RAY DIFFRACTION4D900
9X-RAY DIFFRACTION5E299 - 322
10X-RAY DIFFRACTION6F299 - 322
11X-RAY DIFFRACTION7G299 - 322
12X-RAY DIFFRACTION8H299 - 322

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