6CX8 | pdb_00006cx8

Crystal structure of spermidine/spermine N-acetyltransferase SpeG from Vibrio cholerae in complex with manganese ions.

PDB DOI: https://doi.org/10.2210/pdb6CX8/pdb

Classification: TRANSFERASE
Organism(s): Vibrio cholerae O1 biovar El Tor str. N16961
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-04-02 Released: 2018-04-18
Deposition Author(s): Filippova, E.V., Minasov, G., Kiryukhina, O., Anderson, W.F., Satchell, K.J.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.41 Å
R-Value Free:
0.213 (Depositor), 0.215 (DCC)
R-Value Work:
0.171 (Depositor), 0.177 (DCC)
R-Value Observed:
0.173 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of spermidine/spermine N-acetyltransferase SpeG from Vibrio cholerae in complex with manganese ions.

Filippova, E.V., Minasov, G., Kiryukhina, O., Anderson, W.F., Satchell, K.J.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 126.7 kDa
Atom Count: 8,922
Modeled Residue Count: 1,020
Deposited Residue Count: 1,056
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spermidine N(1)-acetyltransferase	A, B, C, D, E A, B, C, D, E, F	176	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0 Gene Names: speG, VC_A0947 EC: 2.3.1.57
UniProt
Find proteins for Q9KL03 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KL03 Go to UniProtKB: Q9KL03
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9KL03
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain Q [auth F] MOL2 format, chain Q [auth F] mmCIF format, chain Q [auth F]	Q [auth F]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain Q [auth F] Interactions & Density Focus chain Q [auth F]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain M [auth C] SDF format, chain N [auth D] SDF format, chain P [auth E] MOL2 format, chain I [auth A] MOL2 format, chain M [auth C] MOL2 format, chain N [auth D] MOL2 format, chain P [auth E] mmCIF format, chain I [auth A] mmCIF format, chain M [auth C] mmCIF format, chain N [auth D] mmCIF format, chain P [auth E]	I [auth A], M [auth C], N [auth D], P [auth E]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain I [auth A] Focus chain M [auth C] Focus chain N [auth D] Focus chain P [auth E] Interactions & Density Focus chain I [auth A] Focus chain M [auth C] Focus chain N [auth D] Focus chain P [auth E]
IPA Query on IPA Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain J [auth B] SDF format, chain L [auth C] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] mmCIF format, chain H [auth A] mmCIF format, chain J [auth B] mmCIF format, chain L [auth C]	H [auth A], J [auth B], L [auth C]	ISOPROPYL ALCOHOL C₃ H₈ O KFZMGEQAYNKOFK-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Interactions & Density Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth C] SDF format, chain O [auth E] MOL2 format, chain G [auth A] MOL2 format, chain K [auth C] MOL2 format, chain O [auth E] mmCIF format, chain G [auth A] mmCIF format, chain K [auth C] mmCIF format, chain O [auth E]	G [auth A], K [auth C], O [auth E]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain K [auth C] Focus chain O [auth E] Interactions & Density Focus chain G [auth A] Focus chain K [auth C] Focus chain O [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.41 Å
R-Value Free: 0.213 (Depositor), 0.215 (DCC)
R-Value Work: 0.171 (Depositor), 0.177 (DCC)
R-Value Observed: 0.173 (Depositor)

Diffraction Data:

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 157.645	α = 90
b = 135.267	β = 118.58
c = 73.675	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
BLU-MAX	data collection
HKL-3000	data scaling
HKL-3000	data reduction
PHASER	phasing
Coot	model building

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2018-04-18

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History (Full details and data files)

Version 1.0: 2018-04-18
Type: Initial release
Version 1.1: 2019-12-18
Changes: Author supporting evidence
Version 1.2: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description