2H72 | pdb_00002h72

Crystal Structure of Thioredoxin mutant E85D in Hexagonal (p61) Space Group

PDB DOI: https://doi.org/10.2210/pdb2H72/pdb

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

Deposited: 2006-06-01 Released: 2007-05-15
Deposition Author(s): Gavira, J.A., Godoy-Ruiz, R., Ibarra-Molero, B., Sanchez-Ruiz, J.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free:
0.268 (Depositor), 0.260 (DCC)
R-Value Work:
0.225 (Depositor), 0.220 (DCC)
R-Value Observed:
0.227 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.7 of the entry. See complete history.

Literature

Crystal Structure of Thioredoxin mutant E85D in Hexagonal (p61) Space Group

Godoy-Ruiz, R., Gavira, J.A., Ibarra-Molero, B., Sanchez-Ruiz, J.M.

To be published.

Macromolecule Content

Total Structure Weight: 23.7 kDa
Atom Count: 1,750
Modeled Residue Count: 214
Deposited Residue Count: 216
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thioredoxin	A, B	108	Escherichia coli	Mutation(s): 1 Gene Names: trxA
UniProt
Find proteins for P0AA25 (Escherichia coli (strain K12)) Explore P0AA25 Go to UniProtKB: P0AA25
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0AA25
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.268 (Depositor), 0.260 (DCC)
R-Value Work: 0.225 (Depositor), 0.220 (DCC)
R-Value Observed: 0.227 (Depositor)

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.507	α = 90
b = 103.507	β = 90
c = 41.396	γ = 120

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
HKL-2000	data scaling
Coot	model building
MolProbity	model building

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2007-05-15

Deposition Author(s):

Ibarra-Molero, B.

Sanchez-Ruiz, J.M.

Revision History (Full details and data files)

Version 1.0: 2007-05-15
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.3: 2012-05-02
Changes: Structure summary
Version 1.4: 2017-10-18
Changes: Refinement description
Version 1.5: 2021-10-20
Changes: Database references, Derived calculations
Version 1.6: 2023-08-30
Changes: Data collection, Refinement description
Version 1.7: 2024-11-13
Changes: Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.