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- PDB-5n08: Structure of the apo form of the NO response regulator NsrR -

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Basic information

Entry
Database: PDB / ID: 5n08
TitleStructure of the apo form of the NO response regulator NsrR
ComponentsHTH-type transcriptional repressor NsrR
KeywordsTRANSCRIPTION / NO SENSOR / APO FORM
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
HTH-type transcriptional repressor NsrR
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.90095480392 Å
AuthorsVolbeda, A. / Fontecilla-Camps, J.C.
CitationJournal: 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
DepositionFeb 2, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
Revision 1.1May 3, 2017Group: Database references
Revision 1.2Aug 16, 2017Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type
Revision 1.3May 1, 2024Group: Data collection / Database references / 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
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

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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: HTH-type transcriptional repressor NsrR
D: HTH-type transcriptional repressor NsrR
E: HTH-type transcriptional repressor NsrR


Theoretical massNumber of molelcules
Total (without water)87,0355
Polymers87,0355
Non-polymers00
Water00
1
A: HTH-type transcriptional repressor NsrR

A: HTH-type transcriptional repressor NsrR


Theoretical massNumber of molelcules
Total (without water)34,8142
Polymers34,8142
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+1/31
Buried area2800 Å2
ΔGint-21 kcal/mol
Surface area13090 Å2
MethodPISA
2
B: HTH-type transcriptional repressor NsrR
D: HTH-type transcriptional repressor NsrR


Theoretical massNumber of molelcules
Total (without water)34,8142
Polymers34,8142
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-20 kcal/mol
Surface area13410 Å2
MethodPISA
3
C: HTH-type transcriptional repressor NsrR
E: HTH-type transcriptional repressor NsrR


Theoretical massNumber of molelcules
Total (without water)34,8142
Polymers34,8142
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-19 kcal/mol
Surface area13330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.530, 159.530, 76.560
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGARGARG(chain A and (resseq 2 or (resid 3 and (name...AA2 - 592 - 59
12LEULEUPROPRO(chain A and (resseq 2 or (resid 3 and (name...AA66 - 13466 - 134
23ARGARGARGARG(chain B and (resseq 2 or (resid 3 and (name...BB2 - 592 - 59
24LEULEUPROPRO(chain B and (resseq 2 or (resid 3 and (name...BB66 - 13466 - 134
35ARGARGARGARG(chain C and (resseq 2 or (resid 3 and (name...CC2 - 592 - 59
36LEULEUPROPRO(chain C and (resseq 2 or (resid 3 and (name...CC66 - 13466 - 134
47ARGARGARGARG(chain D and (resseq 2 or (resid 3 and (name...DD2 - 592 - 59
48LEULEUPROPRO(chain D and (resseq 2 or (resid 3 and (name...DD66 - 13466 - 134
51ARGARGARGARG(chain E and (resseq 2:18 or (resid 19 and (name...EE2 - 592 - 59
59LEULEUPROPRO(chain E and (resseq 2:18 or (resid 19 and (name...EE66 - 13466 - 134

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Components

#1: Protein
HTH-type transcriptional repressor NsrR


Mass: 17406.910 Da / Num. of mol.: 5 / Mutation: C93A, C99A, C105A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145) (bacteria)
Gene: nsrR, SCO7427, SC6D11.23 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9L132

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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: 3.23 Å3/Da / Density % sol: 61.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.6 / Details: MPD, Tris, anaerobic

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Dec 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.14
ReflectionResolution: 3.9→43.14 Å / Num. obs: 10293 / % possible obs: 98.2 % / Redundancy: 7.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.18 / Rpim(I) all: 0.063 / Net I/σ(I): 9.7
Reflection shellResolution: 3.9→4.04 Å / Redundancy: 7.8 % / Rmerge(I) obs: 2.274 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 984 / CC1/2: 0.164 / Rpim(I) all: 0.907 / % possible all: 96.8

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: holo-NsrR

Resolution: 3.90095480392→43.1394718379 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34218458775 / Phase error: 39.6275402404
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: USE OF TORSION NCS RESTRAINTS
RfactorNum. reflection% reflection
Rfree0.276728442014 554 5.38491446345 %
Rwork0.26984705262 9734 -
obs0.269802059181 10288 98.2617000955 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 214.70875756 Å2
Refinement stepCycle: LAST / Resolution: 3.90095480392→43.1394718379 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4364 0 0 0 4364
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004708363529584417
X-RAY DIFFRACTIONf_angle_d0.8685046708216044
X-RAY DIFFRACTIONf_chiral_restr0.0404552879778779
X-RAY DIFFRACTIONf_plane_restr0.0081370579761776
X-RAY DIFFRACTIONf_dihedral_angle_d13.42459768112664
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.9028-4.2940.395536933211440.3853976123452385X-RAY DIFFRACTION92.5854037267
4.294-4.91180.3307788886611300.3131038722042417X-RAY DIFFRACTION93.7912301125
4.9118-6.17480.2858100124151540.2847000460522394X-RAY DIFFRACTION92.7547462224
6.1748-26.10980.2223370887941210.2211226816512504X-RAY DIFFRACTION93.1547619048
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)
13.773611910240.885503070052-3.682707838225.05883052762-1.263907010237.96451721585-0.632273751496-0.2921068555230.1951804427060.961503526733-0.08786517378351.532620043841.008879341641.457615799290.8810087003371.52438070484-0.0049281618445-0.1998254502191.102677743930.1886766983491.6653776236215.028632128135.43580923525.5196903252
23.466358424790.0102926618173-2.730150121772.97142193429-2.096992242663.068377486450.3591577045160.01191258739030.4160694191820.6899550416620.1488686527131.201870838160.414683741101-0.08831057497610.02822250286152.016048580040.2433272436880.2085492070711.53899934909-0.00288467444122.5339131195620.2819446809108.25936239121.0178584295
33.897108768190.420226459274-0.2776664433772.74948620047-1.10140334534.0417103458-0.4525412011610.00737567664842-1.820770815350.8639215088750.1767674845221.094270801690.561275829637-0.00624582382862-0.1379186889081.791416543220.4569278553120.113053399511.36735454569-0.05321210610592.4727739593936.862396289986.116393444615.0676414729
42.509313025-3.591341695722.55948077782.608519638510.3439582829284.4564824689-0.0385063181221-0.25583601403-1.58897272959-0.05733536332840.4348279747071.256199159580.4661456419970.08328596897350.4456247825532.238155191560.3620888048340.4120725288061.91436646321-0.09264796999751.8835476551117.82745077113.544566033-4.65685426916
52.75028141122-0.18797823853.050251699593.180041435881.533791289947.587743308171.203272632150.766348082498-0.604342912565-0.579992617040.4674257153650.58608919308-0.415522251718-0.941985811547-1.004210312861.908437830470.5101112123920.00477873526131.62947462576-0.2500944157532.417656171332.689279878389.9276330036-10.0606707632
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 134 )
2X-RAY DIFFRACTION2chain 'B' and (resid 2 through 134 )
3X-RAY DIFFRACTION3chain 'C' and (resid 2 through 134 )
4X-RAY DIFFRACTION4chain 'D' and (resid 2 through 134 )
5X-RAY DIFFRACTION5chain 'E' and (resid 2 through 134 )

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