2PKW | pdb_00002pkw

Crystal structure of UPF0341 protein yhiQ from Salmonella typhimurium, Northeast Structural Genomics Consortium Target StR221

PDB DOI: https://doi.org/10.2210/pdb2PKW/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2007-04-18 Released: 2007-05-01
Deposition Author(s): Forouhar, F., Su, M., Seetharaman, J., Fang, Y., Xiao, R., Cunningham, K., Ma, L.-C., Owens, L., Liu, J., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.259 (Depositor), 0.262 (DCC)
R-Value Work:
0.208 (Depositor), 0.212 (DCC)
R-Value Observed:
0.208 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of UPF0341 protein yhiQ from Salmonella typhimurium.

Forouhar, F., Su, M., Seetharaman, J., Fang, Y., Xiao, R., Cunningham, K., Ma, L.-C., Owens, L., Liu, J., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Macromolecule Content

Total Structure Weight: 28.9 kDa
Atom Count: 2,086
Modeled Residue Count: 254
Deposited Residue Count: 260
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UPF0341 protein yhiQ	A	260	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 8 Gene Names: yhiQ, STM3593 EC: 2.1.1.242
UniProt
Find proteins for Q9X6G2 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q9X6G2 Go to UniProtKB: Q9X6G2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9X6G2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRS Query on TRS 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]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.259 (Depositor), 0.262 (DCC)
R-Value Work: 0.208 (Depositor), 0.212 (DCC)
R-Value Observed: 0.208 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.967	α = 90
b = 70.248	β = 90
c = 77.788	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
SnB	phasing
RESOLVE	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2007-05-01

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2007-05-01
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2018-01-24
Changes: Database references, Structure summary
Version 1.5: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary