3GJY | pdb_00003gjy

Crystal structure of a probable spermidine synthase from Corynebacterium glutamicum ATCC 13032

PDB DOI: https://doi.org/10.2210/pdb3GJY/pdb

Classification: TRANSFERASE
Organism(s): Corynebacterium glutamicum ATCC 13032
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-03-09 Released: 2009-03-24
Deposition Author(s): Tan, K., Li, H., Freeman, L., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.47 Å
R-Value Free:
0.192 (Depositor), 0.187 (DCC)
R-Value Work:
0.157 (Depositor), 0.154 (DCC)
R-Value Observed:
0.159 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3GJY

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

Literature

The crystal structure of a probable spermidine synthase from Corynebacterium glutamicum ATCC 13032.

Tan, K., Li, H., Freeman, L., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 35.26 kDa
Atom Count: 2,639
Modeled Residue Count: 279
Deposited Residue Count: 317
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spermidine synthase	A	317	Corynebacterium glutamicum ATCC 13032	Mutation(s): 0 Gene Names: Cgl1237, cg1394
UniProt
Find proteins for Q8NR27 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534)) Explore Q8NR27 Go to UniProtKB: Q8NR27
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8NR27
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

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: 1.47 Å
R-Value Free: 0.192 (Depositor), 0.187 (DCC)
R-Value Work: 0.157 (Depositor), 0.154 (DCC)
R-Value Observed: 0.159 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.909	α = 90
b = 65.009	β = 90
c = 87.308	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
DM	model building
ARP/wARP	model building
HKL-3000	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-03-24

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2009-03-24
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.