2Y4D | pdb_00002y4d

X-ray crystallographic structure of E. coli apo-EfeB

PDB DOI: https://doi.org/10.2210/pdb2Y4D/pdb
Entry: 2Y4D supersedes: 2WX6

Classification: OXIDOREDUCTASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-01-05 Released: 2011-01-26
Deposition Author(s): Bamford, V.A., Andrews, S.C., Watson, K.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.265 (Depositor), 0.263 (DCC)
R-Value Work:
0.203 (Depositor), 0.203 (DCC)
R-Value Observed:
0.206 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Efeb, the Peroxidase Component of the Efeuob Bacterial Fe(II) Transport System, Also Shows Novel Removal of Iron from Heme

Bamford, V.A., Andrews, S.C., Watson, K.A.

To be published.

Macromolecule Content

Total Structure Weight: 92.22 kDa
Atom Count: 6,659
Modeled Residue Count: 744
Deposited Residue Count: 806
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PEROXIDASE YCDB	A, B	403	Escherichia coli K-12	Mutation(s): 0 EC: 1.11.1 (PDB Primary Data), 4.98.1.1 (UniProt)
UniProt
Find proteins for P31545 (Escherichia coli (strain K12)) Explore P31545 Go to UniProtKB: P31545
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P31545
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain W [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] MOL2 format, chain W [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] mmCIF format, chain W [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A]	I [auth A], J [auth A], W [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain W [auth B] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain W [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain P [auth B] 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 V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] 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 V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] 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], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		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 P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] 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 P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain Y [auth B] SDF format, chain X [auth B] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A]	L [auth A] M [auth A] N [auth A] O [auth A] X [auth B] L [auth A], M [auth A], N [auth A], O [auth A], X [auth B], Y [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain X [auth B] Focus chain Y [auth B] Interactions & Density Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain X [auth B] Focus chain Y [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.265 (Depositor), 0.263 (DCC)
R-Value Work: 0.203 (Depositor), 0.203 (DCC)
R-Value Observed: 0.206 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.315	α = 90
b = 86.26	β = 90
c = 119.576	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2011-01-26

Deposition Author(s):

Bamford, V.A.

Andrews, S.C.

Watson, K.A.

This entry supersedes: 2WX6

Revision History (Full details and data files)

Version 1.0: 2011-01-26
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2019-05-22
Changes: Data collection, Experimental preparation, Other
Version 1.4: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description