3EQE | pdb_00003eqe

Crystal structure of the YubC protein from Bacillus subtilis. Northeast Structural Genomics Consortium target SR112.

PDB DOI: https://doi.org/10.2210/pdb3EQE/pdb

Classification: OXIDOREDUCTASE
Organism(s): Bacillus subtilis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-09-30 Released: 2008-10-14
Deposition Author(s): Vorobiev, S.M., Su, M., Seetharaman, J., Benach, J., Forouhar, F., Clayton, G., Cooper, B., Wang, H., Foote, E.L., Ciccosanti, C., Mao, L., Xiao, R., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.82 Å
R-Value Free:
0.296 (Depositor), 0.297 (DCC)
R-Value Work:
0.241 (Depositor), 0.241 (DCC)
R-Value Observed:
0.241 (Depositor)

wwPDB Validation 3D Report Full Report

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

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 4QM8

Literature

Crystal structure of the YubC protein from Bacillus subtilis.

Vorobiev, S.M., Su, M., Seetharaman, J., Benach, J., Forouhar, F., Clayton, G., Cooper, B., Wang, H., Foote, E.L., Ciccosanti, C., Mao, L., Xiao, R., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L.

To be published.

Macromolecule Content

Total Structure Weight: 39.45 kDa
Atom Count: 2,446
Modeled Residue Count: 310
Deposited Residue Count: 342
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative cystein dioxygenase	A, B	171	Bacillus subtilis	Mutation(s): 0 Gene Names: BSU31140, yubC EC: 1.13.11 (PDB Primary Data), 1.13.11.20 (UniProt)
UniProt
Find proteins for O32085 (Bacillus subtilis (strain 168)) Explore O32085 Go to UniProtKB: O32085
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O32085
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FE Query on FE 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]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-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: 2.82 Å
R-Value Free: 0.296 (Depositor), 0.297 (DCC)
R-Value Work: 0.241 (Depositor), 0.241 (DCC)
R-Value Observed: 0.241 (Depositor)

Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.83	α = 90
b = 65.83	β = 90
c = 197.19	γ = 90

Software Package:

Software Name	Purpose
SHELXDE	phasing
CNS	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2008-10-14

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2008-10-14
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-25
Changes: Author supporting evidence
Version 1.3: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary