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- PDB-5e44: Crystal structure of holo-FNR of A. fischeri -

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Basic information

Entry
Database: PDB / ID: 5.0E+44
TitleCrystal structure of holo-FNR of A. fischeri
ComponentsFNR regulator
KeywordsTRANSCRIPTION / labile dimer
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
Similarity search - Function
Transcription regulator HTH, Crp-type, conserved site / Crp-type HTH domain signature. / helix_turn_helix, cAMP Regulatory protein / Crp-type HTH domain profile. / Crp-like helix-turn-helix domain / Crp-type HTH domain / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain ...Transcription regulator HTH, Crp-type, conserved site / Crp-type HTH domain signature. / helix_turn_helix, cAMP Regulatory protein / Crp-type HTH domain profile. / Crp-like helix-turn-helix domain / 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 / Jelly Rolls / RmlC-like jelly roll fold / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Jelly Rolls / Winged helix-like DNA-binding domain superfamily / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / FNR type regulator
Similarity search - Component
Biological speciesAliivibrio fischeri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsVolbeda, A. / Fontecilla-Camps, J.C.
CitationJournal: 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 5, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2015Group: Database references
Revision 1.2Jan 10, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FNR regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8114
Polymers29,2231
Non-polymers5883
Water0
1
A: FNR regulator
hetero molecules

A: FNR regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6238
Polymers58,4472
Non-polymers1,1766
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area6160 Å2
ΔGint-108 kcal/mol
Surface area20540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.500, 75.500, 218.100
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422

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Components

#1: Protein FNR regulator / Fumarate and nitrate reduction regulatory protein


Mass: 29223.398 Da / Num. of mol.: 1 / Fragment: UNP residues 3-250
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aliivibrio fischeri (bacteria) / Gene: fnr / Plasmid: pET-15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q70ET4
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / 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 / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM

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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: 2.66 Å3/Da / Density % sol: 53.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.4 / Details: MPD, MES, dithionite, anaerobic

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.65→47.95 Å / Num. all: 9630 / Num. obs: 9607 / % possible obs: 99.78 % / Redundancy: 25.4 % / Biso Wilson estimate: 82.7 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.172 / Rpim(I) all: 0.036 / Net I/σ(I): 14.2 / Num. measured all: 244255 / Scaling rejects: 6
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.65-2.7425.84.3891232289180.3760.91197.9
10.26-47.95210.07845.343852090.9950.01898.8

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Processing

Software
NameVersionClassification
PHENIX1.9-1692refinement
Aimless0.5.2data scaling
PDB_EXTRACT3.15data extraction
XDSNovember 3, 2014data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4i20

4i20


Resolution: 2.65→47.949 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.08 / Stereochemistry target values: ML
Details: BIJVOET PAIRS WERE TREATED AS INDEPENDENT OBSERVATIONS ALLOWING TO MODEL ANOMALOUS CONTRIBUTIONS OF FE AND S ATOMS, AS THIS GAVE SIGNIFICANTLY IMPROVED REFINEMENT STATISTICS
RfactorNum. reflection% reflection
Rfree0.2424 746 4.27 %
Rwork0.1879 16738 -
obs0.1902 9607 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 178.32 Å2 / Biso mean: 96.0049 Å2 / Biso min: 53.41 Å2
Refinement stepCycle: final / Resolution: 2.65→47.949 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1771 0 24 0 1795
Biso mean--100.13 --
Num. residues----230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131826
X-RAY DIFFRACTIONf_angle_d1.4632463
X-RAY DIFFRACTIONf_chiral_restr0.054283
X-RAY DIFFRACTIONf_plane_restr0.005315
X-RAY DIFFRACTIONf_dihedral_angle_d17.527685
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6503-2.8550.42081380.3563331346999
2.855-3.14220.32741420.294333603502100
3.1422-3.59680.32081600.235533343494100
3.5968-4.5310.23321570.168833413498100
4.531-47.95680.18991490.149133723521100
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)
14.701-3.88590.12857.78073.33452.5968-0.2081-0.18230.91390.10920.6033-1.5107-1.5386-0.160.50581.19820.3731-0.13692.61890.00840.9196-19.9106-3.0083-14.5527
20.30461.00040.31233.71791.97392.36690.1459-1.3018-0.5876-0.71450.17740.0043-0.7406-0.11290.05251.45360.1093-0.19671.92870.55910.9046-21.2793-12.0771-12.6261
35.0281-0.5617-0.8081.39580.0833.1563-0.4611-0.9883-0.76770.28290.20970.0970.22860.13690.00090.59650.0579-0.00910.98110.17790.6889-31.8969-8.3699-25.4697
45.6820.20430.28054.1673-0.57961.41160.10050.03770.2911-0.5101-0.2932-0.25140.2392-0.33910.00020.65870.0512-0.06830.6774-0.00010.6559-19.65461.3523-42.7423
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 19 through 35 or resid 301 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 36 through 53 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 54 through 163 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 164 through 248 )A0

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