3MEJ | pdb_00003mej

Crystal structure of putative transcriptional regulator ywtF from Bacillus subtilis, Northeast Structural Genomics Consortium Target SR736

PDB DOI: https://doi.org/10.2210/pdb3MEJ/pdb

Classification: transcriptional regulator
Organism(s): Bacillus subtilis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-03-31 Released: 2010-04-28
Deposition Author(s): Kuzin, A., Su, M., Seetharaman, J., Mao, M., Xiao, R., Ciccosanti, C., Lee, D., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.49 Å
R-Value Free:
0.270 (Depositor), 0.261 (DCC)
R-Value Work:
0.206 (Depositor), 0.199 (DCC)
R-Value Observed:
0.213 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Northeast Structural Genomics Consortium Target SR736

Kuzin, A., Su, M., Seetharaman, J., Mao, M., Xiao, R., Ciccosanti, C., Lee, D., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L.

To be published.

Macromolecule Content

Total Structure Weight: 32.38 kDa
Atom Count: 2,005
Modeled Residue Count: 251
Deposited Residue Count: 286
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
transcriptional regulator ywtF	A	286	Bacillus subtilis	Mutation(s): 0 Gene Names: BSU35840, ywtF EC: 2.7.8
UniProt
Find proteins for Q7WY78 (Bacillus subtilis (strain 168)) Explore Q7WY78 Go to UniProtKB: Q7WY78
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7WY78
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL 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]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		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: 2.49 Å
R-Value Free: 0.270 (Depositor), 0.261 (DCC)
R-Value Work: 0.206 (Depositor), 0.199 (DCC)
R-Value Observed: 0.213 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.21	α = 90
b = 66.21	β = 90
c = 141.82	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
SnB	phasing
REFMAC	refinement

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-04-28

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2010-04-28
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2019-07-17
Changes: Data collection, Derived calculations, Refinement description
Version 1.3: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary
Version 1.4: 2026-02-11
Changes: Data collection