2OBK | pdb_00002obk

X-Ray structure of the putative Se binding protein from Pseudomonas fluorescens. Northeast Structural Genomics Consortium target PlR6.

PDB DOI: https://doi.org/10.2210/pdb2OBK/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Pseudomonas protegens Pf-5
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2006-12-19 Released: 2007-01-02
Deposition Author(s): Kuzin, A.P., Su, M., Seetharaman, J., Chen, C.X., Fang, Y., 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., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.292 (Depositor), 0.307 (DCC)
R-Value Work:
0.215 (Depositor), 0.232 (DCC)
R-Value Observed:
0.215 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

X-Ray structure of the putative Se binding protein from Pseudomonas fluorescens

Kuzin, A.P., Su, M., Seetharaman, J., Chen, C., Fang, Y., 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: 95.61 kDa
Atom Count: 5,443
Modeled Residue Count: 668
Deposited Residue Count: 824
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SelT/selW/selH selenoprotein domain	A, B, C, D, E A, B, C, D, E, F, G, H	103	Pseudomonas protegens Pf-5	Mutation(s): 1 Gene Names: PFL_1582
UniProt
Find proteins for Q4KGC5 (Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23932 / Pf-5)) Explore Q4KGC5 Go to UniProtKB: Q4KGC5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q4KGC5
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.292 (Depositor), 0.307 (DCC)
R-Value Work: 0.215 (Depositor), 0.232 (DCC)
R-Value Observed: 0.215 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.311	α = 90
b = 112.251	β = 90
c = 148.459	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
COMO	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2007-01-02

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2007-01-02
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.3: 2023-08-30
Changes: Data collection, Database references, Refinement description
Version 1.4: 2023-11-15
Changes: Data collection
Version 1.5: 2024-11-13
Changes: Structure summary