2ZKI | pdb_00002zki

Crystal structure of hypothetical Trp repressor binding protein from Sul folobus tokodaii (ST0872)

• PDB DOI: https://doi.org/10.2210/pdb2ZKI/pdb

• Classification: TRANSCRIPTION
• Organism(s): Sulfurisphaera tokodaii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-03-21 Released: 2008-04-22 
• Deposition Author(s): Kawano, T., Teshima, N., Suzuki, A., Kuramitsu, S., Yamane, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.257 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of hypothetical Trp repressor binding protein from Sul folobus tokodaii (ST0872)

Kawano, T., Teshima, N., Suzuki, A., Kuramitsu, S., Yamane, T.

To be published.

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 (software)

Biological Assembly 2  

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

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

Biological Assembly 3  

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

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

Macromolecule Content 

• Total Structure Weight: 180.86 kDa 
• Atom Count: 12,553 
• Modeled Residue Count: 1,555 
• Deposited Residue Count: 1,592 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
199aa long hypothetical Trp repressor binding protein	A, B, C, D, E, F, G, H	199	Sulfurisphaera tokodaii	Mutation(s): 0  EC: 1.6.5.2
UniProt
Find proteins for F9VNA8 (Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)) Explore F9VNA8  Go to UniProtKB:  F9VNA8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	AA [auth C], AB [auth H], BA [auth D], BB [auth H], CA [auth D], CB [auth H], DA [auth D], DB [auth H], EA [auth D], EB [auth H], FA [auth D], GA [auth D], HA [auth E], I [auth A], IA [auth E], J [auth A], JA [auth E], K [auth A], KA [auth E], L [auth A], LA [auth E], M [auth A], MA [auth E], N [auth A], NA [auth F], O [auth B], OA [auth F], P [auth B], PA [auth F], Q [auth B], QA [auth F], R [auth B], RA [auth F], S [auth B], SA [auth F], T [auth B], TA [auth G], U [auth B], UA [auth G], V [auth C], VA [auth G], W [auth C], WA [auth G], X [auth C], XA [auth G], Y [auth C], YA [auth H], Z [auth C], ZA [auth H]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.257 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.624	α = 90
b = 194.995	β = 90
c = 100.851	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data collection
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-04-22 
Deposition Author(s): Kawano, T., Teshima, N., Suzuki, A., Kuramitsu, S., Yamane, T.

Revision History  

• Version 1.0: 2008-04-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-06
  Changes: Structure summary