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- PDB-5d8v: Ultra-high resolution structure of high-potential iron-sulfur protein -

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Basic information

Entry
Database: PDB / ID: 5d8v
TitleUltra-high resolution structure of high-potential iron-sulfur protein
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-sulphur protein / High-Potential Iron-Sulfur Protein; Chain A / High potential iron-sulfur protein / High potential iron-sulphur protein / High potential iron-sulphur protein superfamily / High potential iron-sulfur proteins family profile. / Few Secondary Structures / Irregular
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / High-potential iron-sulfur protein
Similarity search - Component
Biological speciesThermochromatium tepidum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.48 Å
AuthorsHirano, Y. / Takeda, K. / Miki, K.
CitationJournal: Nature / Year: 2016
Title: Charge-density analysis of an iron-sulfur protein at an ultra-high resolution of 0.48 angstrom
Authors: Hirano, Y. / Takeda, K. / Miki, K.
History
DepositionAug 18, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2016Group: Database references
Revision 1.2Feb 22, 2017Group: Database references
Revision 1.3Feb 19, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Nov 8, 2023Group: 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)9,90210
Polymers8,7941
Non-polymers1,1089
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area370 Å2
ΔGint-22 kcal/mol
Surface area4790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.478, 58.905, 23.436
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#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
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


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


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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 1.82 Å3/Da / Density % sol: 32.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 1.6 M ammonium sulfate, 0.1 M sodium-citrate, 5 mM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.45086 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Feb 23, 2009 / Details: fiber-optic taper
RadiationMonochromator: Double-crystal Si(111) liquid-nitrogen-cooled
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.45086 Å / Relative weight: 1
ReflectionResolution: 0.48→20 Å / Num. obs: 301119 / % possible obs: 96.3 % / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 61.1
Reflection shellResolution: 0.48→0.5 Å / Redundancy: 3 % / Rmerge(I) obs: 0.339 / Mean I/σ(I) obs: 2.7 / % possible all: 89

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Processing

Software
NameVersionClassification
MOPRO11.1refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3A39

3a39


Resolution: 0.48→20 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.078 -5 %
Rwork0.072 --
obs-301119 96.3 %
Displacement parametersBiso mean: 6.19 Å2
Refinement stepCycle: LAST / Resolution: 0.48→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms616 0 51 180 847
LS refinement shellResolution: 0.48→0.48 Å / Rfactor Rfree: 0.41 / Rfactor Rwork: 0.397

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