4P0E

YhdE E33A (p212121 space group)

PDB DOI: https://doi.org/10.2210/pdb4P0E/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2014-02-20 Released: 2014-04-30
Deposition Author(s): Jia, Z., Zheng, J., Jin, J., Wang, N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.240
R-Value Work: 0.189
R-Value Observed: 0.191

wwPDB Validation 3D Report Full Report

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

Literature

YhdE E33A

Jia, Z., Zheng, J., Jin, J., Wang, N.

To be published.

Macromolecule Content

Total Structure Weight: 41.88 kDa
Atom Count: 3,035
Modelled Residue Count: 377
Deposited Residue Count: 378
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maf-like protein YhdE	A, B	189	Escherichia coli K-12	Mutation(s): 1 Gene Names: yhdE, b3248, JW3217
UniProt
Find proteins for P25536 (Escherichia coli (strain K12)) Explore P25536 Go to UniProtKB: P25536
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P25536
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions 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] Interactions & Density 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]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain K [auth B] MOL2 format, chain C [auth A] MOL2 format, chain K [auth B]	C [auth A], K [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain K [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.240
R-Value Work: 0.189
R-Value Observed: 0.191
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.883	α = 90
b = 85.897	β = 90
c = 88.44	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-04-30

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-04-30
Type: Initial release
Version 1.1: 2014-05-14
Changes: Structure summary
Version 1.2: 2014-07-09
Changes: Structure summary
Version 1.3: 2017-11-22
Changes: Database references, Derived calculations, Other, Refinement description, Source and taxonomy
Version 1.4: 2023-12-27
Changes: Data collection, Database references, Refinement description

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4P0E

YhdE E33A (p212121 space group)

YhdE E33A

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)