6AI5

Disulfide-free, Zn-directed tetramer of the engineered cyt cb562 variant, C96T/A104AB3

PDB DOI: https://doi.org/10.2210/pdb6AI5/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2018-08-21 Released: 2019-09-11
Deposition Author(s): Song, W.J., Tezcan, F.A.
Funding Organization(s): National Research Foundation (Korea), National Science Foundation (United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.81 Å
R-Value Free:
0.209 (Depositor), 0.220 (DCC)
R-Value Work:
0.175 (Depositor), 0.180 (DCC)
R-Value Observed:
0.177 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Disulfide-free, Zn-directed tetramer of the engineered cyt cb562 variant, C96T/A104AB3

Song, W.J., Tezcan, F.A.

To be published.

Macromolecule Content

Total Structure Weight: 50.36 kDa
Atom Count: 3,994
Modelled Residue Count: 424
Deposited Residue Count: 424
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Soluble cytochrome b562	A, B [auth C], C [auth E], D [auth G]	106	Escherichia coli	Mutation(s): 14
UniProt
Find proteins for P0ABE7 (Escherichia coli) Explore P0ABE7 Go to UniProtKB: P0ABE7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0ABE7
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain M [auth C] SDF format, chain R [auth E] SDF format, chain W [auth G] MOL2 format, chain E [auth A] MOL2 format, chain M [auth C] MOL2 format, chain R [auth E] MOL2 format, chain W [auth G] mmCIF format, chain E [auth A] mmCIF format, chain M [auth C] mmCIF format, chain R [auth E] mmCIF format, chain W [auth G]	E [auth A], M [auth C], R [auth E], W [auth G]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain E [auth A] Focus chain M [auth C] Focus chain R [auth E] Focus chain W [auth G] Interactions & Density Focus chain E [auth A] Focus chain M [auth C] Focus chain R [auth E] Focus chain W [auth G]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain N [auth C] SDF format, chain P [auth C] SDF format, chain Q [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain N [auth C] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain N [auth C] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C]	F [auth A] G [auth A] J [auth A] K [auth A] L [auth A] F [auth A], G [auth A], J [auth A], K [auth A], L [auth A], N [auth C], P [auth C], Q [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain N [auth C] Focus chain P [auth C] Focus chain Q [auth C] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain N [auth C] Focus chain P [auth C] Focus chain Q [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain S [auth E] SDF format, chain T [auth E] SDF format, chain U [auth E] SDF format, chain X [auth G] MOL2 format, chain H [auth A] MOL2 format, chain S [auth E] MOL2 format, chain T [auth E] MOL2 format, chain U [auth E] MOL2 format, chain X [auth G] mmCIF format, chain H [auth A] mmCIF format, chain S [auth E] mmCIF format, chain T [auth E] mmCIF format, chain U [auth E] mmCIF format, chain X [auth G]	H [auth A], S [auth E], T [auth E], U [auth E], X [auth G]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain S [auth E] Focus chain T [auth E] Focus chain U [auth E] Focus chain X [auth G] Interactions & Density Focus chain H [auth A] Focus chain S [auth E] Focus chain T [auth E] Focus chain U [auth E] Focus chain X [auth G]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain O [auth C] SDF format, chain V [auth E] SDF format, chain Y [auth G] MOL2 format, chain I [auth A] MOL2 format, chain O [auth C] MOL2 format, chain V [auth E] MOL2 format, chain Y [auth G] mmCIF format, chain I [auth A] mmCIF format, chain O [auth C] mmCIF format, chain V [auth E] mmCIF format, chain Y [auth G]	I [auth A], O [auth C], V [auth E], Y [auth G]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain O [auth C] Focus chain V [auth E] Focus chain Y [auth G] Interactions & Density Focus chain I [auth A] Focus chain O [auth C] Focus chain V [auth E] Focus chain Y [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.81 Å
R-Value Free: 0.209 (Depositor), 0.220 (DCC)
R-Value Work: 0.175 (Depositor), 0.180 (DCC)
R-Value Observed: 0.177 (Depositor)

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.562	α = 90
b = 76.871	β = 105.84
c = 96.425	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2019-09-11

Deposition Author(s):

Song, W.J.

Tezcan, F.A.

Funding Organization	Location	Grant Number
National Research Foundation (Korea)	Korea, Republic Of	2016R1C1B2007898
National Science Foundation (United States)	United States	CHE1306646

Revision History (Full details and data files)

Version 1.0: 2019-09-11
Type: Initial release
Version 1.1: 2024-03-27
Changes: Data collection, Database references, Derived calculations, Refinement description