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Basic information

Entry
Database: PDB / ID: 7vos
TitleHigh-resolution neutron and X-ray joint refined structure of high-potential iron-sulfur protein in the oxidized state
ComponentsHigh-potential iron-sulfur protein
KeywordsMETAL BINDING PROTEIN / IRON-SULFUR PROTEIN
Function / homology
Function and homology information


aerobic electron transport chain / 4 iron, 4 sulfur cluster binding / electron transfer activity / metal ion binding
Similarity search - Function
High potential iron-sulfur protein / High potential iron-sulphur protein / High potential iron-sulphur protein superfamily / High potential iron-sulfur proteins family profile.
Similarity search - Domain/homology
trideuteriooxidanium / DEUTERATED WATER / AMMONIUM ION / IRON/SULFUR CLUSTER / High-potential iron-sulfur protein
Similarity search - Component
Biological speciesThermochromatium tepidum (bacteria)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.66 Å
AuthorsHanazono, Y. / Hirano, Y. / Takeda, K. / Kusaka, K. / Tamada, T. / Miki, K.
Funding support Japan, 3items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan) Japan
Japan Science and Technology Japan
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Sci Adv / Year: 2022
Title: Revisiting the concept of peptide bond planarity in an iron-sulfur protein by neutron structure analysis.
Authors: Hanazono, Y. / Hirano, Y. / Takeda, K. / Kusaka, K. / Tamada, T. / Miki, K.
History
DepositionOct 14, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: High-potential iron-sulfur protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,18017
Polymers8,7941
Non-polymers1,38716
Water2,324129
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.334, 58.855, 23.548
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein High-potential iron-sulfur protein / HiPIP


Mass: 8793.851 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochromatium tepidum (bacteria) / References: UniProt: P80176

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Non-polymers , 6 types, 145 molecules

#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-NH4 / AMMONIUM ION / Ammonium


Mass: 18.038 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H4N
#6: Chemical ChemComp-D3O / trideuteriooxidanium / perdeuterated oxonium


Mass: 22.042 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: D3O
#7: Chemical ChemComp-DOD / water / Heavy water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: D2O

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Details

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: 1.83 Å3/Da / Density % sol: 32.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 1.8M ammonium sulfate, 0.1M Na citrate buffer

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-5A10.75
SPALLATION SOURCEJPARC MLF BL-03J-PARC MLF BEAMLINE BL-0322.00-4.40
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDJun 10, 2014
iBIX2DIFFRACTOMETERMay 13, 2014
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2LAUELneutron2
Radiation wavelength
IDWavelength (Å)Relative weight
10.751
221
34.41
Reflection

Biso Wilson estimate: 3.81 Å2 / Entry-ID: 7VOS

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Rmerge(I) obsDiffraction-IDNet I/σ(I)
0.66-5011710796.37.40.059145.4
1.2-201966994.94.80.2126
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsDiffraction-ID% possible all
0.66-0.674.80.2724.55461191
1.2-1.242.50.42.14383284.4

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
SCALAdata scaling
MOLREPphasing
HKL-2000data collection
Refinement

SU ML: 0.044 / Cross valid method: FREE R-VALUE / Method to determine structure: MOLECULAR REPLACEMENT / Phase error: 4.924 / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Starting model: 5WQQ

5wqq

/ Stereochemistry target values: GEOSTD + MONOMER LIBRARY + CDL V1.2 / Solvent model: FLAT BULK SOLVENT MODEL

Resolution (Å)Refine-IDRfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection obs% reflection Rfree (%)% reflection obs (%)σ(F)
0.66-36.41X-RAY DIFFRACTION0.0820.0740.07457991170204.9696.31.51
1.2-15.07NEUTRON DIFFRACTION0.1680.1540.1541966794.6
Refinement stepCycle: LAST / Resolution: 0.66→36.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms616 0 68 129 813
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.66-0.670.20492030.18983390X-RAY DIFFRACTION90
0.67-0.680.16821840.1533495X-RAY DIFFRACTION92
0.68-0.690.1151750.11873564X-RAY DIFFRACTION92
0.69-0.70.10731870.1063519X-RAY DIFFRACTION94
0.7-0.710.11531940.10163536X-RAY DIFFRACTION93
0.71-0.720.10831850.09373557X-RAY DIFFRACTION94
0.72-0.730.10071940.09053587X-RAY DIFFRACTION94
0.73-0.740.09751770.08433605X-RAY DIFFRACTION94
0.74-0.760.0872190.08733597X-RAY DIFFRACTION95
0.76-0.770.08871920.08333593X-RAY DIFFRACTION95
0.77-0.780.08721970.08273628X-RAY DIFFRACTION95
0.78-0.80.09761850.07913687X-RAY DIFFRACTION96
0.8-0.810.08252130.0783644X-RAY DIFFRACTION95
0.81-0.830.07741730.07753679X-RAY DIFFRACTION96
0.83-0.850.08542000.07363714X-RAY DIFFRACTION97
0.85-0.870.06961920.07193702X-RAY DIFFRACTION96
0.87-0.90.071900.06543742X-RAY DIFFRACTION98
0.9-0.920.071940.06283740X-RAY DIFFRACTION98
0.92-0.950.0681820.063777X-RAY DIFFRACTION98
0.95-0.990.07481990.05693793X-RAY DIFFRACTION98
0.99-1.030.06181800.05773790X-RAY DIFFRACTION98
1.03-1.070.06032120.05623823X-RAY DIFFRACTION99
1.07-1.130.06291950.05153838X-RAY DIFFRACTION100
1.13-1.20.06031920.05113870X-RAY DIFFRACTION100
1.2-1.290.06452160.05723896X-RAY DIFFRACTION100
1.29-1.420.06611950.06263884X-RAY DIFFRACTION100
1.42-1.630.0611950.05873945X-RAY DIFFRACTION100
1.63-2.050.07271810.06943994X-RAY DIFFRACTION100
2.05-36.410.10162120.09194151X-RAY DIFFRACTION0
1.2-1.260.22181120.21682303NEUTRON DIFFRACTION83
1.26-1.340.19171450.18642504NEUTRON DIFFRACTION91
1.34-1.450.19271260.1692646NEUTRON DIFFRACTION94
1.45-1.590.1661360.13832723NEUTRON DIFFRACTION97
1.59-1.820.15031270.13292798NEUTRON DIFFRACTION99
1.82-2.290.13021390.12522843NEUTRON DIFFRACTION100
2.3-15.070.15041480.13922917NEUTRON DIFFRACTION98

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