2PDO | pdb_00002pdo

Crystal Structure of the Putative Acetyltransferase of GNAT Family from Shigella flexneri

PDB DOI: https://doi.org/10.2210/pdb2PDO/pdb

Classification: TRANSFERASE
Organism(s): Shigella flexneri 2a str. 2457T
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2007-04-01 Released: 2007-04-24
Deposition Author(s): Kim, Y., Li, H., Holzle, D., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.266 (Depositor), 0.287 (DCC)
R-Value Work:
0.193 (Depositor), 0.221 (DCC)
R-Value Observed:
0.200 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of the Putative Acetyltransferase of GNAT Family from Shigella flexneri

Kim, Y., Li, H., Holzle, D., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 136.08 kDa
Atom Count: 10,253
Modeled Residue Count: 1,122
Deposited Residue Count: 1,152
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetyltransferase ypeA	A, B, C, D, E A, B, C, D, E, F, G, H	144	Shigella flexneri 2a str. 2457T	Mutation(s): 6 Gene Names: ypeA, SF2487, S_2635 EC: 2.3.1
UniProt
Find proteins for P63422 (Shigella flexneri) Explore P63422 Go to UniProtKB: P63422
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P63422
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain S [auth H] SDF format, chain R [auth G] SDF format, chain M [auth E] SDF format, chain J [auth B] SDF format, chain I [auth B] MOL2 format, chain S [auth H] MOL2 format, chain R [auth G] MOL2 format, chain M [auth E] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] mmCIF format, chain S [auth H] mmCIF format, chain R [auth G] mmCIF format, chain M [auth E] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B]	I [auth B], J [auth B], M [auth E], R [auth G], S [auth H]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain J [auth B] Focus chain M [auth E] Focus chain R [auth G] Focus chain S [auth H] Interactions & Density Focus chain I [auth B] Focus chain J [auth B] Focus chain M [auth E] Focus chain R [auth G] Focus chain S [auth H]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain U [auth H] SDF format, chain T [auth H] SDF format, chain Q [auth F] SDF format, chain P [auth F] SDF format, chain O [auth F] SDF format, chain N [auth E] SDF format, chain L [auth D] MOL2 format, chain U [auth H] MOL2 format, chain T [auth H] MOL2 format, chain Q [auth F] MOL2 format, chain P [auth F] MOL2 format, chain O [auth F] MOL2 format, chain N [auth E] MOL2 format, chain L [auth D] mmCIF format, chain U [auth H] mmCIF format, chain T [auth H] mmCIF format, chain Q [auth F] mmCIF format, chain P [auth F] mmCIF format, chain O [auth F] mmCIF format, chain N [auth E] mmCIF format, chain L [auth D]	L [auth D] N [auth E] O [auth F] P [auth F] Q [auth F] L [auth D], N [auth E], O [auth F], P [auth F], Q [auth F], T [auth H], U [auth H]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain L [auth D] Focus chain N [auth E] Focus chain O [auth F] Focus chain P [auth F] Focus chain Q [auth F] Focus chain T [auth H] Focus chain U [auth H] Interactions & Density Focus chain L [auth D] Focus chain N [auth E] Focus chain O [auth F] Focus chain P [auth F] Focus chain Q [auth F] Focus chain T [auth H] Focus chain U [auth H]
ACY Query on ACY Download:Ideal Coordinates CCD File SDF format, chain V [auth H] SDF format, chain K [auth B] MOL2 format, chain V [auth H] MOL2 format, chain K [auth B] mmCIF format, chain V [auth H] mmCIF format, chain K [auth B]	K [auth B], V [auth H]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Focus chain V [auth H] Interactions & Density Focus chain K [auth B] Focus chain V [auth H]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.266 (Depositor), 0.287 (DCC)
R-Value Work: 0.193 (Depositor), 0.221 (DCC)
R-Value Observed: 0.200 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.053	α = 90
b = 134.388	β = 105.93
c = 70.467	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHARP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-04-24

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2007-04-24
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.3: 2024-11-13
Changes: Data collection, Database references, Derived calculations, Structure summary

2PDO | pdb_00002pdo

Crystal Structure of the Putative Acetyltransferase of GNAT Family from Shigella flexneri

Literature

Crystal Structure of the Putative Acetyltransferase of GNAT Family from Shigella flexneri

Biological Assembly 1

Biological Assembly 2

Biological Assembly 3

Biological Assembly 4

Biological Assembly 5

Biological Assembly 6

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Entry History

Deposition Data

Revision History (Full details and data files)