2OYR | pdb_00002oyr

Crystal Structure of UPF0341 Protein (yhiQ) from Shigella flexneri in complex with S-Adenosyl Homocysteine, Northeast Structural Genomics Target SfR275

PDB DOI: https://doi.org/10.2210/pdb2OYR/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Shigella flexneri 2a
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2007-02-22 Released: 2007-03-06
Deposition Author(s): Forouhar, F., Su, M., Seetharaman, J., Janjua, H., Fang, Y., Xiao, R., Baran, M.C., 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: 2.00 Å
R-Value Free:
0.230 (Depositor), 0.244 (DCC)
R-Value Work:
0.213 (Depositor), 0.229 (DCC)
R-Value Observed:
0.213 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal Structure of UPF0341 Protein (yhiQ) from Shigella flexneri in complex with S-Adenosyl Homocysteine, Northeast Structural Genomics Target SfR275

Forouhar, F., Su, M., Seetharaman, J., Janjua, H., Fang, Y., Xiao, R., Baran, M.C., Liu, J., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Macromolecule Content

Total Structure Weight: 28.69 kDa
Atom Count: 2,150
Modeled Residue Count: 245
Deposited Residue Count: 258
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	258	Shigella flexneri 2a	Mutation(s): 6 Gene Names: yhiQ, SF3528, S_4240 EC: 2.1.1.242
UniProt
Find proteins for Q7UAV7 (Shigella flexneri) Explore Q7UAV7 Go to UniProtKB: Q7UAV7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7UAV7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH Query on SAH 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]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		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: 2.00 Å
R-Value Free: 0.230 (Depositor), 0.244 (DCC)
R-Value Work: 0.213 (Depositor), 0.229 (DCC)
R-Value Observed: 0.213 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.403	α = 90
b = 74.737	β = 90
c = 79.423	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2007-03-06

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2007-03-06
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: 2024-10-16
Changes: Data collection, Database references, Derived calculations, Structure summary