6DZD | pdb_00006dzd

Crystal structure of Bacillus licheniformis hypothetical protein YfiH

• PDB DOI: https://doi.org/10.2210/pdb6DZD/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Bacillus licheniformis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-07-03 Released: 2019-09-11 
• Deposition Author(s): Almeida, L.R., Grejo, M.P., Mulinari, E.J., Santos, J.C., Camargo, S., Bernardes, A., Muniz, J.R.C.
• Funding Organization(s): Sao Paulo Research Foundation (FAPESP), Brazilian National Council for Scientific and Technological Development (CNPq)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.66 Å
• R-Value Free: 
  0.248 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Bacillus licheniformis hypothetical protein YfiH

Almeida, L.R., Grejo, M.P., Mulinari, E.J., Santos, J.C., Camargo, S., Bernardes, A., Muniz, J.R.C.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 62.78 kDa 
• Atom Count: 4,357 
• Modeled Residue Count: 536 
• Deposited Residue Count: 558 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein YfiH	A, B	279	Bacillus licheniformis	Mutation(s): 0
UniProt
Find proteins for A5A677 (Bacillus licheniformis (strain ATCC 14580 / DSM 13 / JCM 2505 / CCUG 7422 / NBRC 12200 / NCIMB 9375 / NCTC 10341 / NRRL NRS-1264 / Gibson 46)) Explore A5A677  Go to UniProtKB:  A5A677

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
K	D [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	G [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.66 Å
• R-Value Free:  0.248 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.567	α = 90
b = 69.464	β = 90
c = 179.589	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SAINT	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-09-11 
Deposition Author(s): Almeida, L.R., Grejo, M.P., Mulinari, E.J., Santos, J.C., Camargo, S., Bernardes, A., Muniz, J.R.C.

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Funding Organization	Location	Grant Number
Sao Paulo Research Foundation (FAPESP)	Brazil	2017/16291-5
Brazilian National Council for Scientific and Technological Development (CNPq)	Brazil	309767/2015-6

Revision History  

• Version 1.0: 2019-09-11
  Type: Initial release
  
• Version 1.1: 2020-01-01
  Changes: Author supporting evidence
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description