3IC5 | pdb_00003ic5

N-terminal domain of putative saccharopine dehydrogenase from Ruegeria pomeroyi.

PDB DOI: https://doi.org/10.2210/pdb3IC5/pdb

Classification: structural genomics, unknown function
Organism(s): Ruegeria pomeroyi
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2009-07-17 Released: 2009-07-28
Deposition Author(s): Osipiuk, J., Tesar, C., Freeman, L., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.08 Å
R-Value Free:
0.251 (Depositor), 0.255 (DCC)
R-Value Work:
0.195 (Depositor), 0.204 (DCC)
R-Value Observed:
0.197 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3IC5

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

Literature

X-ray crystal structure of N-terminal domain of putative saccharopine dehydrogenase from Ruegeria pomeroyi.

Osipiuk, J., Tesar, C., Freeman, L., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 24.6 kDa
Atom Count: 1,814
Modeled Residue Count: 230
Deposited Residue Count: 236
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative saccharopine dehydrogenase	A, B	118	Ruegeria pomeroyi	Mutation(s): 1 Gene Names: SPO0234
UniProt
Find proteins for Q5LX24 (Ruegeria pomeroyi (strain ATCC 700808 / DSM 15171 / DSS-3)) Explore Q5LX24 Go to UniProtKB: Q5LX24
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5LX24
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: 2.08 Å
R-Value Free: 0.251 (Depositor), 0.255 (DCC)
R-Value Work: 0.195 (Depositor), 0.204 (DCC)
R-Value Observed: 0.197 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.368	α = 90
b = 57.803	β = 90
c = 73.184	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SHELXD	phasing
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
HKL-3000	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-07-28

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2009-07-28
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2021-10-13
Changes: Database references, Derived calculations
Version 1.4: 2024-10-30
Changes: Data collection, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.