2ZSU | pdb_00002zsu

Crystal structure of spermidine synthase from Pyrococcus horikoshii OT3, P1 form

PDB DOI: https://doi.org/10.2210/pdb2ZSU/pdb

Classification: TRANSFERASE
Organism(s): Pyrococcus horikoshii
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-09-17 Released: 2008-10-21
Deposition Author(s): Mizutani, H., Kunishima, N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.248 (Depositor), 0.242 (DCC)
R-Value Work:
0.207 (Depositor), 0.198 (DCC)
R-Value Observed:
0.207 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Crystal structure of spermidine synthase from Pyrococcus horikoshii OT3

Mizutani, H., Kunishima, N.

To be published.

Macromolecule Content

Total Structure Weight: 192.63 kDa
Atom Count: 14,310
Modeled Residue Count: 1,654
Deposited Residue Count: 1,680
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
spermidine synthase	A, B, C, D, E A, B, C, D, E, F	280	Pyrococcus horikoshii	Mutation(s): 0 EC: 2.5.1.16
UniProt
Find proteins for O57950 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O57950 Go to UniProtKB: O57950
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O57950
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AG3 Query on AG3 Download:Ideal Coordinates CCD File SDF format, chain I [auth E] SDF format, chain H [auth C] SDF format, chain G [auth A] MOL2 format, chain I [auth E] MOL2 format, chain H [auth C] MOL2 format, chain G [auth A] mmCIF format, chain I [auth E] mmCIF format, chain H [auth C] mmCIF format, chain G [auth A]	G [auth A], H [auth C], I [auth E]	1-{4-[(3-aminopropyl)amino]butyl}guanidine C₈ H₂₁ N₅ XYCUJKFFVBCJEF-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth C] Focus chain I [auth E] Interactions & Density Focus chain G [auth A] Focus chain H [auth C] Focus chain I [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.248 (Depositor), 0.242 (DCC)
R-Value Work: 0.207 (Depositor), 0.198 (DCC)
R-Value Observed: 0.207 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.617	α = 99.81
b = 81.842	β = 103.13
c = 96.653	γ = 107.85

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-10-21

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-10-21
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Refinement description

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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.