[English] 日本語
Yorodumi
- PDB-8qto: CRYSTAL STRUCTURE OF HOLO-L28H-FNR OF A. FISCHERI -

+
Open data


ID or keywords:

Loading...

-
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
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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more