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- PDB-7b0c: [4Fe-4S]-NsrR complexed to 23-bp HmpA1 operator fragment -

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Basic information

Entry
Database: PDB / ID: 7b0c
Title[4Fe-4S]-NsrR complexed to 23-bp HmpA1 operator fragment
Components
  • DNA (5'-D(P*AP*AP*CP*AP*CP*GP*AP*AP*TP*AP*TP*CP*AP*TP*CP*TP*AP*CP*CP*AP*AP*TP*T)-3')
  • DNA (5'-D(P*AP*AP*TP*TP*GP*GP*TP*AP*GP*AP*TP*GP*AP*TP*AP*TP*TP*CP*GP*TP*GP*TP*T)-3')
  • HTH-type transcriptional repressor NsrR
KeywordsDNA BINDING PROTEIN / NO SENSOR / IRON SULFUR CLUSTER / TRANSCRIPTION / DNA COMPLEX
Function / homology
Function and homology information


2 iron, 2 sulfur cluster binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / DNA binding / metal ion binding / cytosol
Similarity search - Function
Transcription regulator Rrf2 / Iron-dependent Transcriptional regulator / Rrf2-type HTH domain profile. / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / DNA / DNA (> 10) / HTH-type transcriptional repressor NsrR
Similarity search - Component
Biological speciesStreptomyces coelicolor A3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsRohac, R. / Fontecilla-Camps, J.C. / Volbeda, A.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-18-CE11-0010 France
Citation
Journal: Commun Biol / Year: 2022
Title: Structural determinants of DNA recognition by the NO sensor NsrR and related Rrf2-type [FeS]-transcription factors.
Authors: Rohac, R. / Crack, J.C. / de Rosny, E. / Gigarel, O. / Le Brun, N.E. / Fontecilla-Camps, J.C. / Volbeda, A.
#1: Journal: Nat Commun / Year: 2017
Title: Crystal structures of the NO sensor NsrR reveal how its iron-sulfur cluster modulates DNA binding.
Authors: Volbeda, A. / Dodd, E.L. / Darnault, C. / Crack, J.C. / Renoux, O. / Hutchings, M.I. / Le Brun, N.E. / Fontecilla-Camps, J.C.
History
DepositionNov 19, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2022Group: Database references / Structure summary / Category: citation / citation_author / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct.title
Revision 1.2Jan 31, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: HTH-type transcriptional repressor NsrR
B: HTH-type transcriptional repressor NsrR
C: DNA (5'-D(P*AP*AP*CP*AP*CP*GP*AP*AP*TP*AP*TP*CP*AP*TP*CP*TP*AP*CP*CP*AP*AP*TP*T)-3')
D: DNA (5'-D(P*AP*AP*TP*TP*GP*GP*TP*AP*GP*AP*TP*GP*AP*TP*AP*TP*TP*CP*GP*TP*GP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8276
Polymers49,1234
Non-polymers7032
Water724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10710 Å2
ΔGint-119 kcal/mol
Surface area18600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.810, 118.810, 89.530
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1(chain "B" and (resid 1 through 143 or (resid 144...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1METASPA1 - 144
d_12ens_1FS4FS4B
d_21ens_1METASPC1 - 144
d_22ens_1FS4FS4D

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Components

#1: Protein HTH-type transcriptional repressor NsrR


Mass: 17503.107 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor A3(2) (bacteria)
Gene: nsrR, SCO7427, SC6D11.23 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9L132
#2: DNA chain DNA (5'-D(P*AP*AP*CP*AP*CP*GP*AP*AP*TP*AP*TP*CP*AP*TP*CP*TP*AP*CP*CP*AP*AP*TP*T)-3')


Mass: 6976.563 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Streptomyces coelicolor A3(2) (bacteria)
#3: DNA chain DNA (5'-D(P*AP*AP*TP*TP*GP*GP*TP*AP*GP*AP*TP*GP*AP*TP*AP*TP*TP*CP*GP*TP*GP*TP*T)-3')


Mass: 7140.628 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Streptomyces coelicolor A3(2) (bacteria)
#4: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.72 Å3/Da / Density % sol: 66.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: PEG 550 MME, PEG 20000, magnesium chloride, calcium chloride, MOPS/HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00001 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 3→67.54 Å / Num. obs: 14398 / % possible obs: 99.3 % / Redundancy: 3.5 % / Biso Wilson estimate: 131.22 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Net I/σ(I): 9.6
Reflection shellResolution: 3→3.18 Å / Rmerge(I) obs: 1.9 / Num. unique obs: 2320 / CC1/2: 0.332 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N07

5n07


Resolution: 3→51.45 Å / SU ML: 0.5348 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.624
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2362 716 4.98 %
Rwork0.2194 13648 -
obs0.2202 14364 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 148.19 Å2
Refinement stepCycle: LAST / Resolution: 3→51.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2147 943 16 4 3110
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00353255
X-RAY DIFFRACTIONf_angle_d0.7044631
X-RAY DIFFRACTIONf_chiral_restr0.0374552
X-RAY DIFFRACTIONf_plane_restr0.0041433
X-RAY DIFFRACTIONf_dihedral_angle_d33.15891274
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.28779804623 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.230.41031600.36732725X-RAY DIFFRACTION99.86
3.23-3.560.3251420.28742710X-RAY DIFFRACTION99.06
3.56-4.070.26531370.26232744X-RAY DIFFRACTION99.52
4.07-5.130.23181380.19932729X-RAY DIFFRACTION99.17
5.13-51.450.1991390.19762740X-RAY DIFFRACTION97.83
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)
14.05052009640.593037078839-0.8431157024465.31531669702-2.411095624885.83309251667-0.138207477495-0.392538503249-0.3969386458811.04895259548-0.130104578310.0425549063198-0.0113813096905-0.222463031090.001195665693741.50498463457-0.1092843113640.001837039634221.199411024150.124275166031.28135910364-17.3583072796-20.10315605057.31219466839
27.07498649347-0.713761843172.472737814773.1103172294-0.3729834277156.096915144870.1870372923670.9575008763260.226778172832-0.593313576345-0.4966974938090.4235150467120.175347351932-0.02378577190380.001176527058271.190334138390.108693669476-0.1246454215661.501776988540.01853175644461.31145677042-26.0971189722-4.98147099794-22.2652635943
30.8755200562020.717144683823-0.6077991117430.8055952437280.2762832730612.994069761630.31370677589-0.158257749516-1.00539414108-0.1785608071540.4854427907931.937320772540.673054412823-1.38448627683-3.01712182159E-81.65336439162-0.409035510373-0.1223231206952.023349488440.1460633161972.12126496991-37.5883947694-21.6813876757-7.45222729355
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and ((resid 1 through 85) or (resid 124 through 144))) or (chain 'B' and ((resid 86 through 123) or resid 150))A - BA - D1 - 2011
22(chain 'A' and ((resid 86 through 123) or resid 150)) or (chain 'B' and ((resid 1 through 85) or (resid 124 through 144)))A - BA - C86 - 14486 - 144
33(chain 'C' and (resid 1 through 23)) or (chain 'D' and (resid 1 through 23))C - DE - F1 - 23

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