3BB5

CRYSTAL STRUCTURE OF A DIMERIC FERREDOXIN-LIKE PROTEIN OF UNKNOWN FUNCTION (JANN_3925) FROM JANNASCHIA SP. CCS1 AT 2.30 A RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb3BB5/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Jannaschia sp. CCS1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-11-09 Released: 2007-11-20 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.222 
• R-Value Work: 0.179 
• R-Value Observed: 0.181 

Literature

Crystal structure of dimeric ferredoxin-like protein of unknown function (YP_511867.1) from Jannaschia sp. CCS1 at 2.30 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration, light scattering

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration, light scattering

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration, light scattering

Macromolecule Content

• Total Structure Weight: 84.65 kDa 
• Atom Count: 5,027 
• Modelled Residue Count: 624 
• Deposited Residue Count: 726 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Stress responsive alpha-beta protein	A, B, C, D, E, F	121	Jannaschia sp. CCS1	Mutation(s): 0  Gene Names: YP_511867.1, Jann_3925
UniProt
Find proteins for Q28KC0 (Jannaschia sp. (strain CCS1)) Explore Q28KC0  Go to UniProtKB:  Q28KC0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	H [auth B], J [auth C], K [auth D], M [auth E], O [auth F]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
EDO	G [auth A], I [auth C], L [auth E], N [auth F]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D, E, F	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.222 
• R-Value Work: 0.179 
• R-Value Observed: 0.181 
• Space Group: C 1 2 1
• Diffraction Data: https://doi.org/10.18430/M33BB5

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 147.721	α = 90
b = 66.323	β = 93.41
c = 110.452	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
ADSC	data collection
MOSFLM	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-11-20 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2007-11-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence, Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.5: 2024-10-30
  Changes: Data collection, Refinement description, Structure summary