6DAU | pdb_00006dau

Crystal structure of E33Q and E41Q mutant forms of the spermidine/spermine N-acetyltransferase SpeG from Vibrio cholerae

PDB DOI: https://doi.org/10.2210/pdb6DAU/pdb

Classification: TRANSFERASE
Organism(s): Vibrio cholerae O1 biovar El Tor
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2018-05-02 Released: 2018-07-04
Deposition Author(s): Filippova, E.V., Minasov, G., Beahan, A., Kulyavtsev, P., Tan, L., Tran, D., Kuhn, M.L., 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: 2.26 Å
R-Value Free:
0.216 (Depositor), 0.214 (DCC)
R-Value Work:
0.189 (Depositor), 0.189 (DCC)
R-Value Observed:
0.190 (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 E33Q and E41Q mutant forms of the spermidine/spermine N-acetyltransferase SpeG from Vibrio cholerae.

Filippova, E.V., Minasov, G., Beahan, A., Kulyavtsev, P., Anderson, W.F., Satchell, K.J.F., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 124.48 kDa
Atom Count: 8,878
Modeled Residue Count: 1,014
Deposited Residue Count: 1,038
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spermidine N1-acetyltransferase	A, B, C, D, E A, B, C, D, E, F	173	Vibrio cholerae O1 biovar El Tor	Mutation(s): 2 Gene Names: C4E16_17415 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain I [auth D] SDF format, chain H [auth C] SDF format, chain G [auth A] MOL2 format, chain I [auth D] MOL2 format, chain H [auth C] MOL2 format, chain G [auth A] mmCIF format, chain I [auth D] mmCIF format, chain H [auth C] mmCIF format, chain G [auth A]	G [auth A], H [auth C], I [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth C] Focus chain I [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth C] Focus chain I [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.26 Å
R-Value Free: 0.216 (Depositor), 0.214 (DCC)
R-Value Work: 0.189 (Depositor), 0.189 (DCC)
R-Value Observed: 0.190 (Depositor)

Diffraction Data:

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 160.235	α = 90
b = 133.016	β = 113.39
c = 77.711	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2018-07-04

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: 2018-07-04
Type: Initial release
Version 1.1: 2019-12-18
Changes: Author supporting evidence
Version 1.2: 2023-10-04
Changes: Data collection, Database references, Refinement description