3KKZ | pdb_00003kkz

Crystal structure of the Q5LES9_BACFN protein from Bacteroides fragilis. Northeast Structural Genomics Consortium Target BfR250.

PDB DOI: https://doi.org/10.2210/pdb3KKZ/pdb

Classification: TRANSFERASE
Organism(s): Bacteroides fragilis NCTC 9343
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2009-11-06 Released: 2009-11-24
Deposition Author(s): Vorobiev, S., Neely, H., Seetharaman, J., Wang, D., Ciccosanti, C., Foote, E.L., Sahdev, S., Acton, T.B., Xiao, R., Everett, J.K., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.68 Å
R-Value Free:
0.186 (Depositor), 0.180 (DCC)
R-Value Work:
0.142 (Depositor), 0.134 (DCC)
R-Value Observed:
0.144 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of the Q5LES9_BACFN protein from Bacteroides fragilis.

Vorobiev, S., Neely, H., Seetharaman, J., Wang, D., Ciccosanti, C., Foote, E.L., Sahdev, S., Acton, T.B., Xiao, R., Everett, J.K., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Macromolecule Content

Total Structure Weight: 62.61 kDa
Atom Count: 4,549
Modeled Residue Count: 506
Deposited Residue Count: 534
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uncharacterized protein Q5LES9	A, B	267	Bacteroides fragilis NCTC 9343	Mutation(s): 0 Gene Names: BF1671
UniProt
Find proteins for Q5LES9 (Bacteroides fragilis (strain ATCC 25285 / DSM 2151 / CCUG 4856 / JCM 11019 / LMG 10263 / NCTC 9343 / Onslow / VPI 2553 / EN-2)) Explore Q5LES9 Go to UniProtKB: Q5LES9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5LES9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAM Query on SAM Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	S-ADENOSYLMETHIONINE C₁₅ H₂₂ N₆ O₅ S MEFKEPWMEQBLKI-FCKMPRQPSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.68 Å
R-Value Free: 0.186 (Depositor), 0.180 (DCC)
R-Value Work: 0.142 (Depositor), 0.134 (DCC)
R-Value Observed: 0.144 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.741	α = 90
b = 58.068	β = 98.27
c = 70.158	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SnB	phasing
RESOLVE	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
RESOLVE	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2009-11-24

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2009-11-24
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-25
Changes: Author supporting evidence, Refinement description
Version 1.3: 2024-10-16
Changes: Data collection, Database references, Derived calculations, Structure summary