2ZKI

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.257
R-Value Work: 0.202
R-Value Observed: 0.205

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
199aa long hypothetical Trp repressor binding protein	A, B, C, D, E A, B, C, D, E, F, G, H	199	Sulfurisphaera tokodaii	Mutation(s): 0
UniProt
Find proteins for F9VNA8 (Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)) Explore F9VNA8 Go to UniProtKB: F9VNA8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	F9VNA8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain AB [auth H] SDF format, chain BA [auth D] SDF format, chain BB [auth H] SDF format, chain CA [auth D] SDF format, chain CB [auth H] SDF format, chain DA [auth D] SDF format, chain DB [auth H] SDF format, chain EA [auth D] SDF format, chain EB [auth H] SDF format, chain FA [auth D] SDF format, chain GA [auth D] SDF format, chain HA [auth E] SDF format, chain I [auth A] SDF format, chain IA [auth E] SDF format, chain J [auth A] SDF format, chain JA [auth E] SDF format, chain K [auth A] SDF format, chain KA [auth E] SDF format, chain L [auth A] SDF format, chain LA [auth E] SDF format, chain M [auth A] SDF format, chain MA [auth E] SDF format, chain N [auth A] SDF format, chain NA [auth F] SDF format, chain O [auth B] SDF format, chain OA [auth F] SDF format, chain P [auth B] SDF format, chain PA [auth F] SDF format, chain Q [auth B] SDF format, chain QA [auth F] SDF format, chain R [auth B] SDF format, chain RA [auth F] SDF format, chain S [auth B] SDF format, chain SA [auth F] SDF format, chain T [auth B] SDF format, chain TA [auth G] SDF format, chain U [auth B] SDF format, chain UA [auth G] SDF format, chain V [auth C] SDF format, chain VA [auth G] SDF format, chain W [auth C] SDF format, chain WA [auth G] SDF format, chain X [auth C] SDF format, chain XA [auth G] SDF format, chain Y [auth C] SDF format, chain YA [auth H] SDF format, chain Z [auth C] SDF format, chain ZA [auth H] MOL2 format, chain AA [auth C] MOL2 format, chain AB [auth H] MOL2 format, chain BA [auth D] MOL2 format, chain BB [auth H] MOL2 format, chain CA [auth D] MOL2 format, chain CB [auth H] MOL2 format, chain DA [auth D] MOL2 format, chain DB [auth H] MOL2 format, chain EA [auth D] MOL2 format, chain EB [auth H] MOL2 format, chain FA [auth D] MOL2 format, chain GA [auth D] MOL2 format, chain HA [auth E] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth E] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth E] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth E] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth E] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth E] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth F] MOL2 format, chain O [auth B] MOL2 format, chain OA [auth F] MOL2 format, chain P [auth B] MOL2 format, chain PA [auth F] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth F] MOL2 format, chain R [auth B] MOL2 format, chain RA [auth F] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth F] MOL2 format, chain T [auth B] MOL2 format, chain TA [auth G] MOL2 format, chain U [auth B] MOL2 format, chain UA [auth G] MOL2 format, chain V [auth C] MOL2 format, chain VA [auth G] MOL2 format, chain W [auth C] MOL2 format, chain WA [auth G] MOL2 format, chain X [auth C] MOL2 format, chain XA [auth G] MOL2 format, chain Y [auth C] MOL2 format, chain YA [auth H] MOL2 format, chain Z [auth C] MOL2 format, chain ZA [auth H]	AA [auth C] AB [auth H] BA [auth D] BB [auth H] CA [auth D] 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		Interactions Focus chain AA [auth C] Focus chain AB [auth H] Focus chain BA [auth D] Focus chain BB [auth H] Focus chain CA [auth D] Focus chain CB [auth H] Focus chain DA [auth D] Focus chain DB [auth H] Focus chain EA [auth D] Focus chain EB [auth H] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain HA [auth E] Focus chain I [auth A] Focus chain IA [auth E] Focus chain J [auth A] Focus chain JA [auth E] Focus chain K [auth A] Focus chain KA [auth E] Focus chain L [auth A] Focus chain LA [auth E] Focus chain M [auth A] Focus chain MA [auth E] Focus chain N [auth A] Focus chain NA [auth F] Focus chain O [auth B] Focus chain OA [auth F] Focus chain P [auth B] Focus chain PA [auth F] Focus chain Q [auth B] Focus chain QA [auth F] Focus chain R [auth B] Focus chain RA [auth F] Focus chain S [auth B] Focus chain SA [auth F] Focus chain T [auth B] Focus chain TA [auth G] Focus chain U [auth B] Focus chain UA [auth G] Focus chain V [auth C] Focus chain VA [auth G] Focus chain W [auth C] Focus chain WA [auth G] Focus chain X [auth C] Focus chain XA [auth G] Focus chain Y [auth C] Focus chain YA [auth H] Focus chain Z [auth C] Focus chain ZA [auth H] Interactions & Density Focus chain AA [auth C] Focus chain AB [auth H] Focus chain BA [auth D] Focus chain BB [auth H] Focus chain CA [auth D] Focus chain CB [auth H] Focus chain DA [auth D] Focus chain DB [auth H] Focus chain EA [auth D] Focus chain EB [auth H] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain HA [auth E] Focus chain I [auth A] Focus chain IA [auth E] Focus chain J [auth A] Focus chain JA [auth E] Focus chain K [auth A] Focus chain KA [auth E] Focus chain L [auth A] Focus chain LA [auth E] Focus chain M [auth A] Focus chain MA [auth E] Focus chain N [auth A] Focus chain NA [auth F] Focus chain O [auth B] Focus chain OA [auth F] Focus chain P [auth B] Focus chain PA [auth F] Focus chain Q [auth B] Focus chain QA [auth F] Focus chain R [auth B] Focus chain RA [auth F] Focus chain S [auth B] Focus chain SA [auth F] Focus chain T [auth B] Focus chain TA [auth G] Focus chain U [auth B] Focus chain UA [auth G] Focus chain V [auth C] Focus chain VA [auth G] Focus chain W [auth C] Focus chain WA [auth G] Focus chain X [auth C] Focus chain XA [auth G] Focus chain Y [auth C] Focus chain YA [auth H] Focus chain Z [auth C] Focus chain ZA [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.257
R-Value Work: 0.202
R-Value Observed: 0.205
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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2008-04-22

Deposition Author(s):

Revision History (Full details and data files)

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