6FU3 | pdb_00006fu3

Structure of the mixed-valence, active form, of cytochrome c peroxidase from obligate human pathogenic bacterium Neisseria gonorrhoeae

• PDB DOI: https://doi.org/10.2210/pdb6FU3/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Neisseria gonorrhoeae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-02-26 Released: 2019-03-13 
• Deposition Author(s): Carvalho, A.L., Romao, M.J., Pauleta, S., Nobrega, C.
• Funding Organization(s): Fundacao para a Ciencia e a Tecnologia

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.244 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

Literature

Structure of the mixed-valence, active form, of cytochrome c peroxidase from obligate human pathogenic bacterium Neisseria gonorrhoeae

Carvalho, A.L., Romao, M.J., Pauleta, S., Nobrega, C.

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.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 77.79 kDa 
• Atom Count: 5,776 
• Modeled Residue Count: 653 
• Deposited Residue Count: 678 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein CcpR	A, B	339	Neisseria gonorrhoeae	Mutation(s): 0  Gene Names:  ccpA, WHOF_00612, WHOF_02054, WHOG_00329, WHOG_02247C, WHOK_00254, WHOK_02247C, WHOL_00503, WHOL_01944C, WHOM_00704, WHOM_02256C, WHON_00634, WHON_02251C, WHOO_00344, WHOO_01926, WHOP_00646, WHOP_02256C, WHOU_00764, WHOU_02329C, WHOV_00550, WHOV_02317C, WHOW_00232, WHOW_02310C, WHOX_00887, WHOX_02246C, WHOY_00586, WHOY_02329C, WHOZ_00270, WHOZ_02318C EC: 1.11.1.5
UniProt
Find proteins for Q5F5Z9 (Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090)) Explore Q5F5Z9  Go to UniProtKB:  Q5F5Z9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEC (Subject of Investigation/LOI)	D [auth A], E [auth A], G [auth B], H [auth B]	HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N
CA	C [auth A], F [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.244 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.942	α = 90
b = 88.78	β = 90
c = 93.122	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PROTEUM	data reduction
SAINT	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-03-13 
Deposition Author(s): Carvalho, A.L., Romao, M.J., Pauleta, S., Nobrega, C.

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Funding Organization	Location	Grant Number
Fundacao para a Ciencia e a Tecnologia	Portugal	RECI/BBB-BEP/0124/2012
Fundacao para a Ciencia e a Tecnologia	Portugal	PTDC/BBB-BQB/29442/2017

Revision History  

• Version 1.0: 2019-03-13
  Type: Initial release
  
• Version 2.0: 2022-07-20
  Type: Coordinate replacement
  Reason: Ligand geometry
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Other, Refinement description, Structure summary
• Version 2.1: 2024-01-17
  Changes: Data collection, Refinement description
• Version 2.2: 2024-11-20
  Changes: Structure summary