5FHP | pdb_00005fhp

SeMet regulator of nicotine degradation

• PDB DOI: https://doi.org/10.2210/pdb5FHP/pdb

• Classification: APOPTOSIS
• Organism(s): Pseudomonas putida S16
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-12-22 Released: 2016-12-21 
• Deposition Author(s): Zhang, K., Tang, H., Wu, G., Wang, W., Hu, H., Xu, P.
• Funding Organization(s): Chinese National Natural Science Foundation, Chinese National Science Foundation for Excellent Young Scholars

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 
  0.251 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Literature

Co-crystal Structure of NicR2_Hsp

Zhang, K., Tang, H., Wu, G., Wang, W., Hu, H., Xu, P.

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 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 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)

Macromolecule Content 

• Total Structure Weight: 148.11 kDa 
• Atom Count: 10,162 
• Modeled Residue Count: 1,229 
• Deposited Residue Count: 1,254 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NicR	A, B, C, D, E, F	209	Pseudomonas putida S16	Mutation(s): 0  Gene Names: nicR
UniProt
Find proteins for A0A0B4KIF6 (Pseudomonas putida (strain DSM 28022 / S16)) Explore A0A0B4KIF6  Go to UniProtKB:  A0A0B4KIF6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MLA	H [auth B], J [auth E]	MALONIC ACID C3 H4 O4 OFOBLEOULBTSOW-UHFFFAOYSA-N
GOL	G [auth A], I [auth D], K [auth E], L [auth F]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-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: 2.65 Å
• R-Value Free:  0.251 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 150.011	α = 90
b = 150.011	β = 90
c = 156.689	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-12-21 
Deposition Author(s): Zhang, K., Tang, H., Wu, G., Wang, W., Hu, H., Xu, P.

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Funding Organization	Location	Grant Number
Chinese National Natural Science Foundation	China	31230002
Chinese National Natural Science Foundation	China	31270154
Chinese National Science Foundation for Excellent Young Scholars	China	31422004

Revision History  

• Version 1.0: 2016-12-21
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Data collection, Database references, Structure summary