3H31 | pdb_00003h31

Structure of Rhodothermus marinus HiPIP at 1.0 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3H31/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Rhodothermus marinus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-04-15 Released: 2009-12-15 
• Deposition Author(s): Stelter, M., Melo, A.M.P., Saraiva, L., Teixeira, M., Archer, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free: 
  0.144 (Depositor) 
• R-Value Work: 
  0.104 (Depositor), 0.112 (DCC) 
• R-Value Observed: 
  0.104 (Depositor) 

Literature

Structure at 1.0 A resolution of a high-potential iron-sulfur protein involved in the aerobic respiratory chain of Rhodothermus marinus

Stelter, M., Melo, A.M.P., Hreggvidsson, G.O., Hjorleifsdottir, S., Saraiva, L.M., Teixeira, M., Archer, M.

(2010) J Biol Inorg Chem 15: 303-313

• PubMed: 20225399 
• DOI: https://doi.org/10.1007/s00775-009-0603-8
• Primary Citation Related Structures: 
  3H31


• PubMed Abstract: 
  

  The aerobic respiratory chain of the thermohalophilic bacterium Rhodothermus marinus, a nonphotosynthetic organism from the Bacteroidetes/Chlorobi group, contains a high-potential iron-sulfur protein (HiPIP) that transfers electrons from a bc 1 analog complex to a caa 3 oxygen reductase. Here, we describe the crystal structure of the reduced form of R. marinus HiPIP, solved by the single-wavelength anomalous diffraction method, based on the anomalous scattering of the iron atoms from the [4Fe-4S]3+/2+ cluster and refined to 1.0 A resolution. This is the first structure of a HiPIP isolated from a nonphotosynthetic bacterium involved in an aerobic respiratory chain. The structure shows a similar environment around the cluster as the other HiPIPs from phototrophic bacteria, but reveals several features distinct from those of the other HiPIPs of phototrophic bacteria, such as a different fold of the N-terminal region of the polypeptide due to a disulfide bridge and a ten-residue-long insertion.

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Organizational Affiliation: 
• Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República (EAN), 2780-157 Oeiras, Portugal.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 8.45 kDa 
• Atom Count: 808 
• Modeled Residue Count: 74 
• Deposited Residue Count: 74 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
High potential iron-sulfur protein	A	74	Rhodothermus marinus	Mutation(s): 0  Gene Names: hip
UniProt
Find proteins for C4P582 (Rhodothermus marinus) Explore C4P582  Go to UniProtKB:  C4P582

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SF4	B [auth A]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free:  0.144 (Depositor) 
• R-Value Work:  0.104 (Depositor), 0.112 (DCC) 
• R-Value Observed: 0.104 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 27.267	α = 90
b = 43.343	β = 90
c = 46.787	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
SHELX	model building
SHELXL-97	refinement
MOSFLM	data reduction
SCALA	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-12-15 
Deposition Author(s): Stelter, M., Melo, A.M.P., Saraiva, L., Teixeira, M., Archer, M.

Revision History  

• Version 1.0: 2009-12-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-08-24
  Changes: Database references
• Version 1.3: 2018-01-24
  Changes: Experimental preparation
• Version 1.4: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Structure summary