2IEE | pdb_00002iee

Crystal Structure of YCKB_BACSU from Bacillus subtilis. Northeast Structural Genomics Consortium target SR574.

PDB DOI: https://doi.org/10.2210/pdb2IEE/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Bacillus subtilis
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2006-09-18 Released: 2006-10-03
Deposition Author(s): Kuzin, A.P., Su, M., Jayaraman, S., Chen, X.C., Jang, M., Cunningham, K., Ma, C., Xiao, R., Liu, J., Baran, M.C., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.241 (Depositor), 0.254 (DCC)
R-Value Work:
0.202 (Depositor), 0.212 (DCC)
R-Value Observed:
0.202 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of probable ABC transporter extracellular-binding protein yckB from Bacillus subtilis.

Kuzin, A.P., Su, M., Seetharaman, J., Chen, X.C., Jang, M., Cunningham, K., Ma, L.C., Xiao, R., Liu, J., Baran, M.C., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Macromolecule Content

Total Structure Weight: 61.03 kDa
Atom Count: 4,048
Modeled Residue Count: 495
Deposited Residue Count: 542
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable ABC transporter extracellular-binding protein yckB	A, B	271	Bacillus subtilis	Mutation(s): 7 Gene Names: yckB
UniProt
Find proteins for P42400 (Bacillus subtilis (strain 168)) Explore P42400 Go to UniProtKB: P42400
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P42400
Sequence Annotations Expand
Reference Sequence

Small Molecules

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: 2.20 Å
R-Value Free: 0.241 (Depositor), 0.254 (DCC)
R-Value Work: 0.202 (Depositor), 0.212 (DCC)
R-Value Observed: 0.202 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.284	α = 90
b = 49.918	β = 99.73
c = 106.768	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
SnB	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2006-10-03

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2006-10-03
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: 2024-11-13
Changes: Data collection, Database references, Derived calculations, Structure summary