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- PDB-8qto: CRYSTAL STRUCTURE OF HOLO-L28H-FNR OF A. FISCHERI -

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Basic information

Entry
Database: PDB / ID: 8qto
TitleCRYSTAL STRUCTURE OF HOLO-L28H-FNR OF A. FISCHERI
ComponentsFNR type regulator
KeywordsTRANSCRIPTION / oxygen sensor / labile dimer / O2 resistance / NO sensitive
Function / homology
Function and homology information


2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / DNA-binding transcription factor activity / DNA binding / metal ion binding / cytosol
Similarity search - Function
helix_turn_helix, cAMP Regulatory protein / Transcription regulator HTH, Crp-type, conserved site / Crp-type HTH domain signature. / : / Crp-like helix-turn-helix domain / Crp-type HTH domain profile. / Crp-type HTH domain / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. ...helix_turn_helix, cAMP Regulatory protein / Transcription regulator HTH, Crp-type, conserved site / Crp-type HTH domain signature. / : / Crp-like helix-turn-helix domain / Crp-type HTH domain profile. / Crp-type HTH domain / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / RmlC-like jelly roll fold / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / FNR type regulator
Similarity search - Component
Biological speciesAliivibrio fischeri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsVolbeda, A. / Fontecilla-Camps, J.C.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-18-CE11-0010 France
Citation
Journal: Inorganics (Basel) / Year: 2023
Title: Probing the Reactivity of [4Fe-4S] Fumarate and Nitrate Reduction (FNR) Regulator with O2 and NO: Increased O2 Resistance and Relative Specificity for NO of the [4Fe-4S] L28H FNR Cluster
Authors: Crack, J.C. / Amara, P. / de Rosny, E. / Darnault, C. / Stapleton, M.R. / Green, J. / Volbeda, A. / Fontecilla-Camps, J.C. / Le Brun, N.E.
#1: Journal: Sci Adv / Year: 2015
Title: The crystal structure of the global anaerobic transcriptional regulator FNR explains its extremely fine-tuned monomer-dimer equilibrium.
Authors: Volbeda, A. / Darnault, C. / Renoux, O. / Nicolet, Y. / Fontecilla-Camps, J.C.
History
DepositionOct 13, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FNR type regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0736
Polymers29,2481
Non-polymers8245
Water1,49583
1
A: FNR type regulator
hetero molecules

A: FNR type regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,14512
Polymers58,4972
Non-polymers1,64910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area7370 Å2
ΔGint-150 kcal/mol
Surface area20060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.200, 75.200, 217.470
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Space group name HallI42
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1/2,x+1/2,z+1/2
#11: y+1/2,-x+1/2,z+1/2
#12: x+1/2,-y+1/2,-z+1/2
#13: -x+1/2,y+1/2,-z+1/2
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2

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Components

#1: Protein FNR type regulator


Mass: 29248.387 Da / Num. of mol.: 1 / Mutation: L28H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aliivibrio fischeri (bacteria) / Gene: fnr / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q70ET4
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.63 Å3/Da / Density % sol: 53.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.1 / Details: MPD, HEPES, anaerobic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.984 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 2.4→47.77 Å / Num. obs: 12709 / % possible obs: 99.9 % / Redundancy: 11.6 % / Biso Wilson estimate: 76.49 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.071 / Net I/σ(I): 18.6
Reflection shellResolution: 2.4→2.48 Å / Rmerge(I) obs: 3.408 / Num. unique obs: 1205 / CC1/2: 0.449

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→47.77 Å / SU ML: 0.5477 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.7886
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2274 568 4.49 %
Rwork0.198 12078 -
obs0.1993 12646 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 85.67 Å2
Refinement stepCycle: LAST / Resolution: 2.4→47.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1835 0 40 83 1958
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00341907
X-RAY DIFFRACTIONf_angle_d0.57252579
X-RAY DIFFRACTIONf_chiral_restr0.041296
X-RAY DIFFRACTIONf_plane_restr0.0027326
X-RAY DIFFRACTIONf_dihedral_angle_d24.4072717
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.640.45321570.41462877X-RAY DIFFRACTION97.81
2.64-3.020.34061280.2843001X-RAY DIFFRACTION99.9
3.02-3.810.25111460.21882997X-RAY DIFFRACTION99.97
3.81-47.770.17851370.16173203X-RAY DIFFRACTION100
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)
11.51398686626-0.460501479704-0.4016670423890.455423630650.7534196964621.17681166012-0.743804687509-1.70697103668-0.01925677636211.158286829940.931562091497-1.22920326993-0.5754025982410.6873531205740.001969664314141.105901278660.233971005115-0.1454498791251.668724750990.06805390977040.948206106602-20.4574853673-5.53561079306-11.7122467862
23.7745575303-0.924054104011-3.323098975132.965271348680.9384097412444.13164762461-0.338025038377-0.37562366512-1.15633063330.510743015840.02483128860750.0845853677820.5217734278120.0263110522608-0.000341294287510.7031746853850.03665772785730.03964566088960.7469033943620.1068877398770.875861243558-29.7642359952-13.562382601-27.606054605
34.20366899671-1.519901757680.3235789782811.306377903141.219900104831.67210268084-0.566981579781-1.042956707760.2380529613760.5753748784390.341138005271-0.0321974692872-0.382532285828-0.1557450929870.0001175417622070.6715925632890.0599154012221-0.09139177331671.03268787756-0.01606268074610.670001834853-33.5590968060.315366086977-21.1541372852
48.59669610371.09065804621-0.6282725991426.64925838628-0.04915184817654.372340410230.02234095202650.3403503081680.406027419386-0.333400776978-0.277342316255-0.07449224781320.035087646751-0.299673971394-0.0001129174957740.6069232929570.0406577628418-0.02770537738410.616879901096-0.006641067887830.639166738124-19.70253328991.4774027746-42.5612033495
Refinement TLS group

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

IDRefine TLS-IDSelection detailsLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and ((resid 17 through 48 )A - B17 - 481
22chain 'A' and (resid 49 through 125 )A49 - 12533 - 109
33chain 'A' and (resid 126 through 164 )A126 - 164110 - 148
44chain 'A' and (resid 165 through 250 )A165 - 250149 - 234

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