6S65 | pdb_00006s65

Crystal Structure of the Homospermidine Synthase (HSS) variant N135F from Blastochloris viridis in Complex with NAD

PDB DOI: https://doi.org/10.2210/pdb6S65/pdb

Classification: TRANSFERASE
Organism(s): Blastochloris viridis
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2019-07-02 Released: 2020-07-15
Deposition Author(s): Helfrich, F., Scheidig, A.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.217 (Depositor), 0.215 (DCC)
R-Value Work:
0.180 (Depositor)
R-Value Observed:
0.182 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of the Homospermidine Synthase (HSS) variant N135F from Blastochloris viridis in Complex with NAD

Scheidig, A.J., Helfrich, F.

To be published.

Macromolecule Content

Total Structure Weight: 107.47 kDa
Atom Count: 8,061
Modeled Residue Count: 932
Deposited Residue Count: 960
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Homospermidine synthase	A, B	480	Blastochloris viridis	Mutation(s): 1 Gene Names: hss EC: 2.5.1.44
UniProt
Find proteins for O32323 (Blastochloris viridis) Explore O32323 Go to UniProtKB: O32323
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O32323
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD (Subject of Investigation/LOI) Query on NAD Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.217 (Depositor), 0.215 (DCC)
R-Value Work: 0.180 (Depositor)
R-Value Observed: 0.182 (Depositor)

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.703	α = 90
b = 110.401	β = 90
c = 159.541	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2020-07-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-07-15
Type: Initial release
Version 1.1: 2024-01-24
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.