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- PDB-5cvr: Crystal structure of FNR of A. fischeri in a partially degraded form -

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Basic information

Entry
Database: PDB / ID: 5cvr
TitleCrystal structure of FNR of A. fischeri in a partially degraded form
ComponentsFNR type regulator
KeywordsTRANSCRIPTION
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
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
FE2/S2 (INORGANIC) CLUSTER / FNR type regulator
Similarity search - Component
Biological speciesAliivibrio fischeri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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
DepositionJul 27, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2015Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / 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 type regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7545
Polymers29,2231
Non-polymers5304
Water1448
1
A: FNR type regulator
hetero molecules

A: FNR type regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,50710
Polymers58,4472
Non-polymers1,0618
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area6470 Å2
ΔGint-98 kcal/mol
Surface area19540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.270, 75.270, 212.430
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 type regulator


Mass: 29223.398 Da / Num. of mol.: 1
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-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.56 Å3/Da / Density % sol: 61.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.4 / Details: MPD, MES, LiCL, anaerobic

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 2.6→47.58 Å / Num. obs: 9847 / % possible obs: 99.9 % / Redundancy: 12.8 % / Biso Wilson estimate: 72.29 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.027 / Net I/σ(I): 21.1 / Num. measured all: 126067
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.6-2.6913.62.4071.3127229380.5860.69999.9
10.07-47.5810.70.023100.1227321310.00798.9

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Processing

Software
NameVersionClassification
Aimless0.5.2data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
PHENIXphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: FIXK2

Resolution: 2.6→37.635 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / Phase error: 30.47 / 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% reflectionSelection details
Rfree0.2373 775 4.32 %Random selection
Rwork0.1911 17173 --
obs0.193 9845 99.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 244.33 Å2 / Biso mean: 101.1447 Å2 / Biso min: 48.05 Å2
Refinement stepCycle: final / Resolution: 2.6→37.635 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1590 0 28 8 1626
Biso mean--116.66 85.29 -
Num. residues----206
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091639
X-RAY DIFFRACTIONf_angle_d1.1522205
X-RAY DIFFRACTIONf_chiral_restr0.047251
X-RAY DIFFRACTIONf_plane_restr0.004281
X-RAY DIFFRACTIONf_dihedral_angle_d17.343613
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.6-2.76290.3611150.390628732988
2.7629-2.97610.40331380.331328482986
2.9761-3.27550.2911200.258428612981
3.2755-3.74910.25791440.196328422986
3.7491-4.7220.18951260.151528732999
4.722-37.63890.20911320.157128763008
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)
10.3353-0.4403-0.07880.30060.08740.01230.1351-0.07640.41710.3811-0.0759-0.4273-0.0967-0.40090.00091.8948-0.36410.36331.20830.05321.3015-15.080822.7476-11.6019
20.08910.17230.01770.1355-0.27290.43990.257-0.1935-0.07760.4416-0.59711.41260.0211-0.6747-0.00070.9974-0.07790.22090.8804-0.2071.1153-15.664630.1936-26.8018
31.09870.57050.44780.35570.54330.4189-0.0031-0.29540.74720.457-0.40510.97730.0174-0.38600.8831-0.02890.17670.8053-0.07411.0003-11.429733.4029-30.2413
40.04880.0640.04130.3156-0.060.20230.0947-0.7826-1.48021.6836-0.3209-0.21430.5021-0.73840.00111.7487-0.25480.36781.36350.02931.1134-9.791830.3328-12.2199
5-0.32140.1003-0.17190.3303-0.06230.16720.32030.0957-0.12290.4765-0.2239-0.2547-0.08520.3242-0.00051.0934-0.0604-0.06560.67720.10450.58222.992233.2276-25.2537
60.75850.18050.18340.23830.36750.4321-0.20650.0036-0.24750.0304-0.2502-0.9388-0.32430.06830.00390.6736-0.013-0.02680.5740.07840.66723.54123.1005-38.1141
71.1014-0.3098-0.66121.21710.64090.5901-0.29490.1398-1.27891.0010.06310.5399-0.5946-0.1175-0.00130.6678-0.00090.04960.6390.01660.7576-3.831119.8778-37.2685
81.19281.8563-0.66672.9705-1.08790.4995-0.67380.9269-1.0251-1.2302-0.3793-0.46730.0907-1.2745-0.24760.81160.053-0.07810.7362-0.23270.532-0.615218.5692-50.1943
90.26120.20710.21110.2042-0.08140.3621-0.0085-0.0078-0.4947-0.0297-0.142-0.06650.42960.1901-0.00050.6432-0.03310.16490.6946-0.02051.0411.764511.3725-42.109
100.04480.20870.27710.78950.7010.61250.2519-0.19810.6419-0.26250.7403-0.814-0.32871.19820.12740.7027-0.16230.08790.5960.16881.121311.821623.4375-42.6079
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 43 through 52 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 53 through 81 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 82 through 118 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 119 through 136 or resid 301 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 137 through 163 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 164 through 182 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 183 through 207 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 208 through 220 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 221 through 235 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 236 through 248 )A0

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