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- PDB-1iua: Ultra-high resolution structure of HiPIP from Thermochromatium tepidum -

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Basic information

Entry
Database: PDB / ID: 1iua
TitleUltra-high resolution structure of HiPIP from Thermochromatium tepidum
ComponentsHigh-potential iron-sulfur protein
KeywordsELECTRON TRANSPORT / HiPIP
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: 0.8 Å
AuthorsLiu, L. / Nogi, T. / Kobayashi, M. / Nozawa, T. / Miki, K.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Ultrahigh-resolution structure of high-potential iron-sulfur protein from Thermochromatium tepidum.
Authors: Liu, L. / Nogi, T. / Kobayashi, M. / Nozawa, T. / Miki, K.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: CRYSTAL STRUCTURES OF PHOTOSYNTHETIC REACTION CENTER AND HIGH-POTENTIAL IRON-SULFUR PROTEIN FROM THERMOCHROMATIUM TEPIDUM: THERMOSTABILITY AND ELECTRON TRANSFER
Authors: Nogi, T. / Fathir, I. / Kobayashi, M. / Nozawa, T. / Miki, K.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: CRYSTALLIZATION AND PRELIMINARY CRYSTALLOGRAPHIC ANALYSIS OF HIGH-POTENTIAL IRON-SULFUR PROTEIN FROM THERMOCHROMATIUM TEPIDUM
Authors: Nogi, T. / Kobayashi, M. / Nozawa, T. / Miki, K.
History
DepositionMar 1, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jan 23, 2019Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop / pdbx_struct_conn_angle
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _pdbx_struct_conn_angle.value
Revision 2.1Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)9,4345
Polymers8,7941
Non-polymers6404
Water1,67593
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.697, 58.272, 23.454
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


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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 1.74 Å3/Da / Density % sol: 29.17 %
Crystal growTemperature: 293.2 K / Method: vapor diffusion, sitting drop / pH: 3.5
Details: 0.7M A/S, 0.05M Sodium Citrate, pH 3.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.2K
Crystal grow
*PLUS
Temperature: 293 K / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
150 mMTris-HCl1droppH8.0
21.4 Mammonium sulfate1reservoir
30.1 Msodium citrate1reservoirpH3.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 0.7293 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 25, 2000
RadiationMonochromator: undulator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7293 Å / Relative weight: 1
ReflectionResolution: 0.8→50 Å / Num. all: 65310 / Num. obs: 64373 / % possible obs: 98.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 0.8→0.81 Å / % possible all: 95.5
Reflection
*PLUS
Lowest resolution: 5 Å / Num. measured all: 823255 / Rmerge(I) obs: 0.052
Reflection shell
*PLUS
% possible obs: 95.5 % / Num. unique obs: 3094 / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 2.74

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Processing

Software
NameClassification
AMoREphasing
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.8→20 Å / σ(F): 4 / Stereochemistry target values: Engh & Huber / Details: No restraint for the last full-matrix refinement
RfactorNum. reflectionSelection details
Rfree0.1141 2842 random
all0.1011 60959 -
obs0.0916 52278 -
Refinement stepCycle: LAST / Resolution: 0.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms642 0 23 100 765
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONrmsd bonds0.016
X-RAY DIFFRACTIONrmsd angles2
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor Rwork: 0.101
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg2

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