3LYW | pdb_00003lyw

Crystal structure of YbbR family protein Dhaf_0833 from Desulfitobacterium hafniense DCB-2. Northeast Structural Genomics Consortium target id DhR29B

PDB DOI: https://doi.org/10.2210/pdb3LYW/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Desulfitobacterium hafniense DCB-2
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-02-28 Released: 2010-04-07
Deposition Author(s): Seetharaman, J., Lew, S., Wang, D., Janjua, H., Cunningham, K., Owens, L., Xiao, R., Liu, J., Baran, M.C., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.258 (Depositor), 0.271 (DCC)
R-Value Work:
0.224 (Depositor), 0.239 (DCC)
R-Value Observed:
0.224 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of YbbR family protein Dhaf_0833 from Desulfitobacterium hafniense DCB-2. Northeast Structural Genomics Consortium target id DhR29B

Seetharaman, J., Lew, S., Wang, D., Janjua, H., Cunningham, K., Owens, L., Xiao, R., Liu, J., Baran, M.C., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L.

To be published.

Macromolecule Content

Total Structure Weight: 10.25 kDa
Atom Count: 752
Modeled Residue Count: 86
Deposited Residue Count: 90
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YbbR family protein	A	90	Desulfitobacterium hafniense DCB-2	Mutation(s): 0 Gene Names: Dhaf_0833
UniProt
Find proteins for B8FX10 (Desulfitobacterium hafniense (strain DSM 10664 / DCB-2)) Explore B8FX10 Go to UniProtKB: B8FX10
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B8FX10
Sequence Annotations Expand
Reference Sequence

Small Molecules

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: 1.90 Å
R-Value Free: 0.258 (Depositor), 0.271 (DCC)
R-Value Work: 0.224 (Depositor), 0.239 (DCC)
R-Value Observed: 0.224 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.827	α = 90
b = 44.827	β = 90
c = 85.997	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
SHELXS	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-04-07

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2010-04-07
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary