5FHP

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.251
R-Value Work: 0.197
R-Value Observed: 0.200

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Co-crystal Structure of NicR2_Hsp

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

To be published.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NicR	A, B, C, D, E 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0B4KIF6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MLA Query on MLA Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain J [auth E] MOL2 format, chain H [auth B] MOL2 format, chain J [auth E]	H [auth B], J [auth E]	MALONIC ACID C₃ H₄ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain J [auth E] Interactions & Density Focus chain H [auth B] Focus chain J [auth E]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth D] SDF format, chain K [auth E] SDF format, chain L [auth F] MOL2 format, chain G [auth A] MOL2 format, chain I [auth D] MOL2 format, chain K [auth E] MOL2 format, chain L [auth F]	G [auth A], I [auth D], K [auth E], L [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth D] Focus chain K [auth E] Focus chain L [auth F] Interactions & Density Focus chain G [auth A] Focus chain I [auth D] Focus chain K [auth E] Focus chain L [auth F]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E 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
R-Value Work: 0.197
R-Value Observed: 0.200
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

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2016-12-21

Deposition Author(s):

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 (Full details and data files)

Version 1.0: 2016-12-21
Type: Initial release

Prepare Data

Validate Data

Deposit Data

Help and Resources

5FHP

SeMet regulator of nicotine degradation

Co-crystal Structure of NicR2_Hsp

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)