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- PDB-7yl8: Neutron structure of Bacillus thermoproteolyticus Ferredoxin at r... -

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Basic information

Entry
Database: PDB / ID: 7yl8
TitleNeutron structure of Bacillus thermoproteolyticus Ferredoxin at room temperature
ComponentsFerredoxin
KeywordsELECTRON TRANSPORT / ferredoxin / hydrogen / hydrogen-bonding / hydrogen-bonding network / redox potential / iron-sulfur cluster
Function / homology4Fe-4S single cluster domain of Ferredoxin I / 3Fe-4S ferredoxin / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / 4 iron, 4 sulfur cluster binding / electron transfer activity / iron ion binding / IRON/SULFUR CLUSTER / Ferredoxin
Function and homology information
Biological speciesBacillus thermoproteolyticus (bacteria)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsUnno, M. / Wada, K. / Kobayashi, K.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)24570122 Japan
Japan Society for the Promotion of Science (JSPS)20H03196 Japan
CitationJournal: To Be Published
Title: Protonation/deprotonation-driven switch for the redox stability of the low-potential [4Fe-4S] ferredoxin
Authors: Wada, K. / Kobayashi, K. / Era, I. / Isobe, Y. / Kamimura, T. / Murakawa, M. / Sugishima, M. / Kusaka, K. / Yano, N. / Fukuyama, K. / Mishima, M. / Kitagawa, Y. / Unno, M.
History
DepositionJul 25, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ferredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1252
Polymers8,7741
Non-polymers3521
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area360 Å2
ΔGint-21 kcal/mol
Surface area4350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.430, 37.910, 33.010
Angle α, β, γ (deg.)90.000, 105.960, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-253-

HOH

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Components

#1: Protein Ferredoxin


Mass: 8773.595 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thermoproteolyticus (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: P10245
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 49.06 %
Crystal growTemperature: 277 K / Method: microdialysis / Details: MES, ammonium sulfate

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
12971N
22971N
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONPhoton Factory AR-NW12A11
SPALLATION SOURCEJPARC MLF BL-03J-PARC MLF BEAMLINE BL-0321.5-4.5
Detector
TypeIDDetectorDate
ADSC QUANTUM 2701CCDDec 10, 2018
iBIX2DIFFRACTOMETERNov 2, 2018
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2LAUELneutron2
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.51
34.51
Reflection

Biso Wilson estimate: 16.15 Å2 / Entry-ID: 7YL8

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)CC1/2Diffraction-IDNet I/σ(I)Rmerge(I) obsRsym value
1.45-50150071006.70.999125.2
1.6-15.878404199.67.561725.150.19760.0685
Reflection shell
Resolution (Å)Num. unique obsCC1/2Diffraction-IDRmerge(I) obsRpim(I) all
1.45-1.487480.8941
1.6-1.66688820.46020.1926

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
Refinement

SU ML: 0.1464 / Cross valid method: FREE R-VALUE / Method to determine structure: MOLECULAR REPLACEMENT / Phase error: 15.5429 / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Starting model: 1IQZ

1iqz

/ Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 / Solvent model: FLAT BULK SOLVENT MODEL

Resolution (Å)Refine-IDBiso mean (Å2)Rfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection RworkNum. reflection obs% reflection Rfree (%)% reflection obs (%)Diffraction-IDσ(F)
1.45-33.08X-RAY DIFFRACTION25.520.15720.1390.139977114090148615.1998.8711.38
1.6-15.12NEUTRON DIFFRACTION0.18420.16241050094.132
Refinement stepCycle: LAST / Resolution: 1.45→33.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms608 0 8 66 682
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0107698
X-RAY DIFFRACTIONf_angle_d1.0652972
X-RAY DIFFRACTIONf_chiral_restr0.1093108
X-RAY DIFFRACTIONf_plane_restr0.0081139
X-RAY DIFFRACTIONf_dihedral_angle_d17.2996262
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.540.23441300.19432300X-RAY DIFFRACTION97.94
1.54-1.660.17961310.15952344X-RAY DIFFRACTION99.24
1.66-1.820.15221280.14592343X-RAY DIFFRACTION99.44
1.82-2.090.15821210.12812371X-RAY DIFFRACTION99.92
2.09-2.630.14871320.13752370X-RAY DIFFRACTION99.52
2.63-33.080.15071290.13312362X-RAY DIFFRACTION97.23

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