3G8W | pdb_00003g8w

Crystal structure of a probable acetyltransferase from Staphylococcus epidermidis ATCC 12228

PDB DOI: https://doi.org/10.2210/pdb3G8W/pdb

Classification: TRANSFERASE
Organism(s): Staphylococcus epidermidis ATCC 12228
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-02-12 Released: 2009-03-03
Deposition Author(s): Tan, K., Sather, A., Marshall, N., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.256 (Depositor), 0.264 (DCC)
R-Value Work:
0.213 (Depositor), 0.219 (DCC)
R-Value Observed:
0.215 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

The crystal structure of a probable acetyltransferase from Staphylococcus epidermidis ATCC 12228.

Tan, K., Sather, A., Marshall, N., Clancy, S., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 82.58 kDa
Atom Count: 5,447
Modeled Residue Count: 649
Deposited Residue Count: 676
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lactococcal prophage ps3 protein 05	A, B, C, D	169	Staphylococcus epidermidis ATCC 12228	Mutation(s): 0 Gene Names: SE_0588
UniProt
Find proteins for A0A0H2VFJ4 (Staphylococcus epidermidis (strain ATCC 12228 / FDA PCI 1200)) Explore A0A0H2VFJ4 Go to UniProtKB: A0A0H2VFJ4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H2VFJ4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NHE Query on NHE Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth C] SDF format, chain L [auth C] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain Q [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain Q [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth C] mmCIF format, chain L [auth C] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain Q [auth D]	E [auth A] F [auth A] G [auth A] H [auth B] I [auth B] E [auth A], F [auth A], G [auth A], H [auth B], I [auth B], J [auth B], K [auth C], L [auth C], M [auth C], N [auth C], O [auth C], Q [auth D]	2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID C₈ H₁₇ N O₃ S MKWKNSIESPFAQN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain Q [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain Q [auth D]
FLC Query on FLC Download:Ideal Coordinates CCD File SDF format, chain P [auth C] MOL2 format, chain P [auth C] mmCIF format, chain P [auth C]	P [auth C]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain P [auth C] Interactions & Density Focus chain P [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.256 (Depositor), 0.264 (DCC)
R-Value Work: 0.213 (Depositor), 0.219 (DCC)
R-Value Observed: 0.215 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.96	α = 90
b = 110.409	β = 90
c = 220.515	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-03-03

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

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

3G8W | pdb_00003g8w

Crystal structure of a probable acetyltransferase from Staphylococcus epidermidis ATCC 12228

Literature

The crystal structure of a probable acetyltransferase from Staphylococcus epidermidis ATCC 12228.

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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