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- PDB-1hpi: MOLECULAR STRUCTURE OF THE OXIDIZED HIGH-POTENTIAL IRON-SULFUR PR... -

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Basic information

Entry
Database: PDB / ID: 1hpi
TitleMOLECULAR STRUCTURE OF THE OXIDIZED HIGH-POTENTIAL IRON-SULFUR PROTEIN ISOLATED FROM ECTOTHIORHODOSPIRA VACUOLATA
ComponentsHIGH POTENTIAL IRON SULFUR PROTEIN
KeywordsELECTRON TRANSFER(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 isozyme 2
Similarity search - Component
Biological speciesEctothiorhodospira shaposhnikovii (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsBenning, M.M. / Meyer, T.E. / Rayment, I. / Holden, H.M.
CitationJournal: Biochemistry / Year: 1994
Title: Molecular structure of the oxidized high-potential iron-sulfur protein isolated from Ectothiorhodospira vacuolata.
Authors: Benning, M.M. / Meyer, T.E. / Rayment, I. / Holden, H.M.
History
DepositionDec 9, 1993Processing site: BNL
Revision 1.0Apr 30, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 7, 2024Group: 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)8,1762
Polymers7,8251
Non-polymers3521
Water1,02757
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.400, 64.700, 39.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein HIGH POTENTIAL IRON SULFUR PROTEIN


Mass: 7824.582 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ectothiorhodospira shaposhnikovii (bacteria)
References: UniProt: P38524
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


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


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.12 %
Crystal grow
*PLUS
Method: vapor diffusion / Details: in the presence of atmospheric oxygen
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12.2 Mammonium sulfate1reservoir
250 mMsodium/potassium phosphate1reservoir
35 mM1reservoirNaN3
420-40 mg/mlprotein1drop

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 29.2 Å / Num. obs: 7028 / % possible obs: 98 % / Num. measured all: 19816 / Rmerge(I) obs: 0.049
Reflection shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 1.92 Å / Num. unique obs: 1134 / Num. measured obs: 1918 / Rmerge(I) obs: 0.095

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Processing

SoftwareName: TNT / Classification: refinement
RefinementRfactor obs: 0.163 / Highest resolution: 1.8 Å
Refinement stepCycle: LAST / Highest resolution: 1.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms548 0 8 57 613
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.007
X-RAY DIFFRACTIONt_angle_deg2.2
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å / Num. reflection obs: 6973 / Rfactor obs: 0.163
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg
X-RAY DIFFRACTIONt_dihedral_angle_d15.6
X-RAY DIFFRACTIONt_dihedral_angle_deg

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