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- PDB-2hip: THE MOLECULAR STRUCTURE OF THE HIGH POTENTIAL IRON-SULFUR PROTEIN... -

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Basic information

Entry
Database: PDB / ID: 2hip
TitleTHE MOLECULAR STRUCTURE OF THE HIGH POTENTIAL IRON-SULFUR PROTEIN ISOLATED FROM ECTOTHIORHODOSPIRA HALOPHILA DETERMINED AT 2.5-ANGSTROMS RESOLUTION
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 1
Similarity search - Component
Biological speciesHalorhodospira halophila (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsBreiter, D.R. / Meyer, T.E. / Rayment, I. / Holden, H.M.
CitationJournal: J.Biol.Chem. / Year: 1991
Title: The molecular structure of the high potential iron-sulfur protein isolated from Ectothiorhodospira halophila determined at 2.5-A resolution.
Authors: Breiter, D.R. / Meyer, T.E. / Rayment, I. / Holden, H.M.
History
DepositionJun 24, 1991Processing site: BNL
Revision 1.0Jul 15, 1992Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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
B: HIGH POTENTIAL IRON SULFUR PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5684
Polymers15,8652
Non-polymers7032
Water1,874104
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.000, 31.940, 40.270
Angle α, β, γ (deg.)90.00, 100.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HIGH POTENTIAL IRON SULFUR PROTEIN


Mass: 7932.446 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halorhodospira halophila (bacteria) / References: UniProt: P04168
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.39 Å3/Da / Density % sol: 48.54 %
Crystal grow
*PLUS
Method: vapor diffusion / Details: macro-seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
23.2 Mammonium sulfate1drop
350 mMsodium pottassium phosphate1drop
45 mMsodium azide1drop
550 mMsodium pottassium phosphate1reservoir
63.2 Mammonium sulfate1reservoir
75 mMsodium azide1reservoir
1protein1drop

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Data collection

Reflection
*PLUS
Highest resolution: 2.5 Å

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Processing

SoftwareName: TNT / Classification: refinement
RefinementRfactor obs: 0.184 / Highest resolution: 2.5 Å
Refinement stepCycle: LAST / Highest resolution: 2.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1104 0 16 104 1224
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.014
X-RAY DIFFRACTIONt_angle_deg2.221
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
Refinement
*PLUS
Lowest resolution: 30 Å / Num. reflection obs: 5333 / Rfactor obs: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg
X-RAY DIFFRACTIONt_dihedral_angle_d19.4370

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