5MXZ | pdb_00005mxz

Kustc0563 Y40F mutant

PDB DOI: https://doi.org/10.2210/pdb5MXZ/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Candidatus Kuenenia stuttgartensis
Expression System: Shewanella oneidensis MR-1
Mutation(s): Yes

Deposited: 2017-01-25 Released: 2018-02-14
Deposition Author(s): Mohd, A., Barends, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.225 (Depositor), 0.220 (DCC)
R-Value Work:
0.201 (Depositor), 0.190 (DCC)
R-Value Observed:
0.202 (Depositor)

Starting Model: other
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structure and Function of the c-type cytochrome Kustc0563 from Kuenenia stuttgartiensis

Mohd, A., Barends, T.

To be published.

Macromolecule Content

Total Structure Weight: 11.21 kDa
Atom Count: 785
Modeled Residue Count: 82
Deposited Residue Count: 85
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c-552 Ks_3358	A	85	Candidatus Kuenenia stuttgartensis	Mutation(s): 1 Gene Names: kustc0563
UniProt
Find proteins for Q30JB5 (Kuenenia stuttgartiensis) Explore Q30JB5 Go to UniProtKB: Q30JB5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q30JB5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEC Query on HEC Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain R [auth A] SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain N [auth A] MOL2 format, chain R [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] mmCIF format, chain R [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A]	N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Interactions & Density Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain S [auth A] MOL2 format, chain S [auth A] mmCIF format, chain S [auth A]	S [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain S [auth A] Interactions & Density Focus chain S [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.225 (Depositor), 0.220 (DCC)
R-Value Work: 0.201 (Depositor), 0.190 (DCC)
R-Value Observed: 0.202 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.52	α = 90
b = 47.52	β = 90
c = 99.78	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2018-02-14

Deposition Author(s):

Mohd, A.

Barends, T.

Revision History (Full details and data files)

Version 1.0: 2018-02-14
Type: Initial release
Version 1.1: 2024-05-01
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-10-23
Changes: Structure summary