2QCB | pdb_00002qcb

T7-tagged full-length streptavidin complexed with ruthenium ligand

• PDB DOI: https://doi.org/10.2210/pdb2QCB/pdb

• Classification: BIOTIN BINDING PROTEIN
• Organism(s): Streptomyces avidinii
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-06-19 Released: 2008-04-29 
• Deposition Author(s): Le Trong, I., Creus, M., Pordea, A., Ward, T.R., Stenkamp, R.E.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.187 (Depositor), 0.193 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Literature

X-ray structure and designed evolution of an artificial transfer hydrogenase

Creus, M., Pordea, A., Rossel, T., Sardo, A., Letondor, C., Ivanova, A., Letrong, I., Stenkamp, R.E., Ward, T.R.

(2008) Angew Chem Int Ed Engl 47: 1400-1404

• PubMed: 18176932 
• DOI: https://doi.org/10.1002/anie.200704865
• Primary Citation Related Structures: 
  2QCB

---

Organizational Affiliation: 
• Institute of Chemistry, University of Neuchâtel, Av. Bellevaux 51, CP 158, 2009 Neuchâtel, Switzerland.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 17.27 kDa 
• Atom Count: 1,089 
• Modeled Residue Count: 122 
• Deposited Residue Count: 159 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Streptavidin	A	159	Streptomyces avidinii	Mutation(s): 1
UniProt
Find proteins for P22629 (Streptomyces avidinii) Explore P22629  Go to UniProtKB:  P22629

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
KYS	B [auth A]	N-(4-{[(2-AMINOETHYL)AMINO]SULFONYL}PHENYL)-5-[(3AS,4S,6AR)-2-OXOHEXAHYDRO-1H-THIENO[3,4-D]IMIDAZOL-4-YL]PENTANAMIDE-(1,2,3,4,5,6-ETA)-BENZENE-CHLORO-RUTHENIUM(III) C24 H31 Cl N5 O4 Ru S2 SBEKQEIQNPKQAM-CRZSKOOBSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.187 (Depositor), 0.193 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.651	α = 90
b = 57.651	β = 90
c = 183.823	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-04-29 
Deposition Author(s): Le Trong, I., Creus, M., Pordea, A., Ward, T.R., Stenkamp, R.E.

Revision History  

• Version 1.0: 2008-04-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.2: 2017-10-18
  Changes: Refinement description
• Version 1.3: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.4: 2024-02-21
  Changes: Data collection
• Version 1.5: 2026-08-12
  Type: Remediation
  Reason: Metalloprotein remediation
  Changes: Derived calculations, Structure summary