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- PDB-3wgg: Crystal structure of RSP in complex with alpha-NAD+ -

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Basic information

Entry
Database: PDB / ID: 3wgg
TitleCrystal structure of RSP in complex with alpha-NAD+
ComponentsRedox-sensing transcriptional repressor rex
KeywordsTRANSCRIPTION / winged helix / Rossmann fold / transcription repressor
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 / 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
alpha-Diphosphopyridine nucleotide / Redox-sensing transcriptional repressor Rex
Similarity search - Component
Biological speciesThermoanaerobacter ethanolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsZheng, Y. / Ko, T.-P. / Guo, R.-T.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2015
Title: Binding mode of the oxidized alpha-anomer of NAD(+) to RSP, a Rex-family repressor
Authors: Zheng, Y. / Ko, T.-P. / Yang, Y. / Shao, W. / Guo, R.-T.
History
DepositionAug 5, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 28, 2015Group: Database references
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,85210
Polymers50,9492
Non-polymers1,9038
Water7,530418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6330 Å2
ΔGint-43 kcal/mol
Surface area20870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.816, 74.137, 54.764
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-437-

HOH

21A-475-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B
14A
24B
15A
25B

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PHEPHETYRTYR5AA56 - 6456 - 64
21PHEPHETYRTYR5BB56 - 6456 - 64
12GLUGLULYSLYS5AA210 - 216210 - 216
22GLUGLULYSLYS5BB210 - 216210 - 216
13PROPROGLNGLN5AA155 - 160155 - 160
23PROPROGLNGLN5BB155 - 160155 - 160
14LEULEUVALVAL5AA26 - 3026 - 30
24LEULEUVALVAL5BB26 - 3026 - 30
15LYSLYSLYSLYS6AA4 - 2164 - 216
25LYSLYSLYSLYS6BB4 - 2164 - 216

NCS ensembles :
ID
1
2
3
4
5

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Components

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


Mass: 25474.279 Da / Num. of mol.: 2
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: Chemical ChemComp-8NA / alpha-Diphosphopyridine nucleotide / alpha-NAD


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 418 / 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: 2.79 Å3/Da / Density % sol: 55.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 20% w/v PEG 3350, 0.4M ammonium sulfate, 0.1M Bis-Tris, plus 5mM alpha-NAD+, pH 5.5, 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: Nov 9, 2010
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→25 Å / Num. all: 34128 / Num. obs: 33930 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 5 % / Biso Wilson estimate: 31.3 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 20.7
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.456 / Mean I/σ(I) obs: 2.5 / % possible all: 96.6

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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 3WG9

3wg9


Resolution: 2.1→24.9 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.931 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 10.167 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.199 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23124 1596 5 %RANDOM
Rwork0.17934 ---
obs0.18198 32146 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: 44.519 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å20 Å20 Å2
2---1.45 Å20 Å2
3---1.98 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.1→24.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3430 0 118 418 3966
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223604
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8182.0114878
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9545424
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.59724.353170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.21815656
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3951526
X-RAY DIFFRACTIONr_chiral_restr0.1240.2548
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022640
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_it1.41.52108
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.44723410
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.63331496
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.6134.51468
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

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
136medium positional0.380.5
228medium positional0.420.5
324medium positional0.130.5
420medium positional0.090.5
132loose positional0.885
235loose positional1.255
322loose positional0.915
420loose positional0.495
51715loose positional0.655
136medium thermal1.982
228medium thermal3.232
324medium thermal4.832
420medium thermal1.482
132loose thermal1.8710
235loose thermal2.5210
322loose thermal3.8910
420loose thermal1.4710
51715loose thermal5.710
LS refinement shellResolution: 2.1→2.213 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.284 222 -
Rwork0.218 3920 -
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)
10.0996-0.07250.14330.57590.07980.4733-0.01370.0635-0.09140.10440.03090.132-0.00610.1052-0.01710.02070.00490.01640.0601-0.05080.134219.96813.73579.754
20.527-0.2135-0.01290.7893-0.19740.0642-0.0435-0.0328-0.05010.07690.0590.0642-0.0352-0.0066-0.01540.09870.01510.00010.0573-0.00180.047323.475723.602221.0583
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 216
2X-RAY DIFFRACTION2B4 - 216

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