3KOJ | pdb_00003koj

Crystal structure of the SSB domain of Q5N255_SYNP6 protein from Synechococcus sp. Northeast Structural Genomics Consortium Target SnR59a.

PDB DOI: https://doi.org/10.2210/pdb3KOJ/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Synechococcus elongatus PCC 6301
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2009-11-13 Released: 2009-11-24
Deposition Author(s): Vorobiev, S., Su, M., Seetharaman, J., Wang, H., Foote, L.E., Ciccosanti, C., Janjua, H., Xiao, R., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.218 (Depositor), 0.220 (DCC)
R-Value Work:
0.201 (Depositor), 0.199 (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 the SSB domain of Q5N255_SYNP6 protein from Synechococcus sp.

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

To be published.

Macromolecule Content

Total Structure Weight: 24.69 kDa
Atom Count: 1,570
Modeled Residue Count: 179
Deposited Residue Count: 216
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uncharacterized protein ycf41	A, B	108	Synechococcus elongatus PCC 6301	Mutation(s): 1 Gene Names: syc1425_d, ycf41
UniProt
Find proteins for A0A0H3K9J4 (Synechococcus sp. (strain ATCC 27144 / PCC 6301 / SAUG 1402/1)) Explore A0A0H3K9J4 Go to UniProtKB: A0A0H3K9J4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H3K9J4
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: 1.90 Å
R-Value Free: 0.218 (Depositor), 0.220 (DCC)
R-Value Work: 0.201 (Depositor), 0.199 (DCC)
R-Value Observed: 0.202 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.843	α = 90
b = 113.028	β = 90
c = 73.382	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SnB	phasing
PHENIX	model building
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-11-24

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2009-11-24
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-25
Changes: Author supporting evidence, Refinement description
Version 1.3: 2021-10-13
Changes: Database references, Derived calculations
Version 1.4: 2024-11-20
Changes: Data collection, Structure summary