1D9Y | pdb_00001d9y

NEISSERIA GONORRHOEAE FERRIC BINDING PROTEIN

• PDB DOI: https://doi.org/10.2210/pdb1D9Y/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Neisseria gonorrhoeae
• Mutation(s): No 


• Deposited: 1999-10-30 Released: 1999-11-17 
• Deposition Author(s): McRee, D.E., Bruns, C.M., Williams, P.A., Mietzner, T.A., Nunn, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.377 (Depositor) 
• R-Value Work: 
  0.231 (Depositor) 
• R-Value Observed: 
  0.185 (Depositor) 

Literature

Structural Basis of Iron Uptake in the Pathogen Neisseria gonorrhoeae

McRee, D.E., Bruns, C.M., Williams, P.A., Mietzner, T.A., Nunn, R.

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: 33.86 kDa 
• Atom Count: 2,756 
• Modeled Residue Count: 309 
• Deposited Residue Count: 309 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (PERIPLASMIC IRON-BINDING PROTEIN)	A	309	Neisseria gonorrhoeae	Mutation(s): 0
UniProt
Find proteins for Q50964 (Neisseria gonorrhoeae) Explore Q50964  Go to UniProtKB:  Q50964

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
FE	B [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.377 (Depositor) 
• R-Value Work:  0.231 (Depositor) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.583	α = 90
b = 111.009	β = 90
c = 140.423	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
SHELXL-97	refinement
MAR345	data collection
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-11-17 
Deposition Author(s): McRee, D.E., Bruns, C.M., Williams, P.A., Mietzner, T.A., Nunn, R.

Revision History  

• Version 1.0: 1999-11-17
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-04
  Changes: Advisory, Refinement description
• Version 1.4: 2024-02-07
  Changes: Advisory, Data collection, Database references, Derived calculations