6QKN | pdb_00006qkn

Structure of the azide-inhibited form of cytochrome c peroxidase from obligate human pathogenic bacterium Neisseria gonorrhoeae

PDB DOI: https://doi.org/10.2210/pdb6QKN/pdb

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

Deposited: 2019-01-29 Released: 2020-02-19
Deposition Author(s): Carvalho, A.L., Romao, M.J., Pauleta, S., Nobrega, C.
Funding Organization(s): Fundacao para a Ciencia e a Tecnologia

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.215 (Depositor), 0.221 (DCC)
R-Value Work:
0.171 (Depositor), 0.180 (DCC)
R-Value Observed:
0.173 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 75.24 kDa
Atom Count: 5,429
Modeled Residue Count: 652
Deposited Residue Count: 658
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome-c peroxidase	A, B	329	Neisseria gonorrhoeae	Mutation(s): 0 Gene Names: ccpA, E8M64_00570, ERS135259_00627, NCTC13484_01765 EC: 1.11.1.5
UniProt
Find proteins for Q5F5Z9 (Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090)) Explore Q5F5Z9 Go to UniProtKB: Q5F5Z9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5F5Z9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEC (Subject of Investigation/LOI) Query on HEC Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B]	C [auth A], D [auth A], G [auth B], H [auth B]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth B] Focus chain H [auth B]
AZI Query on AZI Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B]	F [auth A], J [auth B]	AZIDE ION N₃ IVRMZWNICZWHMI-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Interactions & Density Focus chain F [auth A] Focus chain J [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B]	E [auth A], I [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.215 (Depositor), 0.221 (DCC)
R-Value Work: 0.171 (Depositor), 0.180 (DCC)
R-Value Observed: 0.173 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.12	α = 90
b = 89.14	β = 90
c = 94.83	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-02-19

Deposition Author(s):

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/BIA-BQM/29442/2017

Revision History (Full details and data files)

Version 1.0: 2020-02-19
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: 2024-01-24
Changes: Data collection, Refinement description
Version 2.2: 2024-11-06
Changes: Structure summary