3DSB

The crystal structure of a possible acetyltransferase from Clostridium difficile 630

PDB DOI: https://doi.org/10.2210/pdb3DSB/pdb

Classification: TRANSFERASE
Organism(s): Clostridioides difficile 630
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-07-11 Released: 2008-09-09
Deposition Author(s): Tan, K., Shackelford, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.48 Å
R-Value Free: 0.205
R-Value Work: 0.168
R-Value Observed: 0.170

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Literature

The crystal structure of a possible acetyltransferase from Clostridium difficile 630

Tan, K., Shackelford, G., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 38.79 kDa
Atom Count: 3,103
Modelled Residue Count: 304
Deposited Residue Count: 314
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative acetyltransferase	A, B	157	Clostridioides difficile 630	Mutation(s): 0 Gene Names: CD2162
UniProt
Find proteins for Q185U9 (Clostridioides difficile (strain 630)) Explore Q185U9 Go to UniProtKB: Q185U9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q185U9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BET Query on BET Download Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A]	D [auth A], F [auth B]	TRIMETHYL GLYCINE C₅ H₁₂ N O₂ KWIUHFFTVRNATP-UHFFFAOYSA-O		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B]	C [auth A], E [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.48 Å
R-Value Free: 0.205
R-Value Work: 0.168
R-Value Observed: 0.170
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.488	α = 90
b = 66.765	β = 90
c = 133.884	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2008-09-09

Deposition Author(s):

Tan, K.

Shackelford, G.

Joachimiak, A.

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2008-09-09
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection, Database references, Derived calculations

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3DSB

The crystal structure of a possible acetyltransferase from Clostridium difficile 630

The crystal structure of a possible acetyltransferase from Clostridium difficile 630

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)