5X7L | pdb_00005x7l

Structure of TsrD from Streptomyces laurentii

• PDB DOI: https://doi.org/10.2210/pdb5X7L/pdb

• Classification: ISOMERASE
• Organism(s): Streptomyces laurentii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-02-27 Released: 2018-03-07 
• Deposition Author(s): Song, Y., Lin, Z., Deng, W., Liu, W.
• Funding Organization(s): NSFC, STCSM, CAS

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.22 Å
• R-Value Free: 
  0.166 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.151 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.151 (Depositor) 

Literature

Structure of TsrD from Streptomyces laurentii

Song, Y., Lin, Z., Deng, W., Liu, W.

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: light scattering

Macromolecule Content 

• Total Structure Weight: 31.52 kDa 
• Atom Count: 2,451 
• Modeled Residue Count: 269 
• Deposited Residue Count: 276 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TsrD	A, B	138	Streptomyces laurentii	Mutation(s): 0  Gene Names: tsrD
UniProt
Find proteins for C0JRY3 (Streptomyces laurentii) Explore C0JRY3  Go to UniProtKB:  C0JRY3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IPA	C [auth A], D [auth A], E [auth A], F [auth B], G [auth B]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.22 Å
• R-Value Free:  0.166 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.151 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.151 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.232	α = 90
b = 54.232	β = 90
c = 199.952	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data processing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-03-07 
Deposition Author(s): Song, Y., Lin, Z., Deng, W., Liu, W.

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Funding Organization	Location	Grant Number
NSFC	China	31430005, 21520102004, 21472231 and 21621002
STCSM	China	14JC1407700 and 15JC1400400
CAS	China	XDB20020200

Revision History  

• Version 1.0: 2018-03-07
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Data collection, Database references, Structure summary