3MFX | pdb_00003mfx

Crystal Structure of the sensory box domain of the sensory-box/GGDEF protein SO_1695 from Shewanella oneidensis, Northeast Structural Genomics Consortium Target SoR288B

PDB DOI: https://doi.org/10.2210/pdb3MFX/pdb

Classification: TRANSCRIPTION
Organism(s): Shewanella oneidensis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-04-04 Released: 2010-04-14
Deposition Author(s): Forouhar, F., Abashidze, M., Seetharaman, J., Mao, M., Xiao, R., Ciccosanti, C., Lee, D., Everett, J.K., Nair, R., 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: 2.40 Å
R-Value Free:
0.252 (Depositor), 0.262 (DCC)
R-Value Work:
0.205 (Depositor), 0.212 (DCC)
R-Value Observed:
0.207 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Northeast Structural Genomics Consortium Target SoR288B

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

To be published.

Macromolecule Content

Total Structure Weight: 44.93 kDa
Atom Count: 2,779
Modeled Residue Count: 339
Deposited Residue Count: 387
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sensory box/GGDEF family protein	A, B, C	129	Shewanella oneidensis	Mutation(s): 0 Gene Names: SO_1695 EC: 2.7.7.65
UniProt
Find proteins for Q8EGB0 (Shewanella oneidensis (strain ATCC 700550 / JCM 31522 / CIP 106686 / LMG 19005 / NCIMB 14063 / MR-1)) Explore Q8EGB0 Go to UniProtKB: Q8EGB0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8EGB0
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	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.252 (Depositor), 0.262 (DCC)
R-Value Work: 0.205 (Depositor), 0.212 (DCC)
R-Value Observed: 0.207 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.171	α = 90
b = 70.171	β = 90
c = 341.762	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
SHELX	phasing
REFMAC	refinement

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-04-14

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2010-04-14
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: 2024-11-06
Changes: Data collection, Database references, Structure summary