7YLR | pdb_00007ylr

Structure of a bacteria protein

• PDB DOI: https://doi.org/10.2210/pdb7YLR/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Variovorax paradoxus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-07-26 Released: 2023-06-14 
• Deposition Author(s): Zhang, H., Ma, Y.J., Yu, G.M., Li, X.Z.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free: 
  0.209 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: in silico

Literature

Structure of a bacteria protein

Zhang, H., Ma, Y.J., Yu, G.M., Li, X.Z.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 36.39 kDa 
• Atom Count: 2,902 
• Modeled Residue Count: 326 
• Deposited Residue Count: 330 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferredoxin	A	330	Variovorax paradoxus	Mutation(s): 0  Gene Names: Vapar_1492
UniProt
Find proteins for C5CSP5 (Variovorax paradoxus (strain S110)) Explore C5CSP5  Go to UniProtKB:  C5CSP5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN (Subject of Investigation/LOI)	B [auth A]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
FES (Subject of Investigation/LOI)	C [auth A]	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free:  0.209 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.217	α = 90
b = 84.042	β = 90
c = 87.864	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
autoPROC	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-06-14 
Deposition Author(s): Zhang, H., Ma, Y.J., Yu, G.M., Li, X.Z.

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Funding Organization	Location	Grant Number
Other government	China	--

Revision History  

• Version 1.0: 2023-06-14
  Type: Initial release
  
• Version 1.1: 2024-04-03
  Changes: Data collection, Refinement description