3BLN | pdb_00003bln

Crystal structure of acetyltransferase GNAT family (NP_981174.1) from Bacillus cereus ATCC 10987 at 1.31 A resolution

PDB DOI: https://doi.org/10.2210/pdb3BLN/pdb

Classification: TRANSFERASE
Organism(s): Bacillus cereus ATCC 10987
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-12-11 Released: 2007-12-18
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.31 Å
R-Value Free:
0.173 (Depositor), 0.180 (DCC)
R-Value Work:
0.137 (Depositor), 0.150 (DCC)
R-Value Observed:
0.138 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of acetyltransferase GNAT family (NP_981174.1) from Bacillus cereus ATCC 10987 at 1.31 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 16.92 kDa
Atom Count: 1,487
Modeled Residue Count: 142
Deposited Residue Count: 143
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetyltransferase GNAT family	A	143	Bacillus cereus ATCC 10987	Mutation(s): 0 Gene Names: NP_981174.1, BCE_4881
UniProt
Find proteins for Q72YY9 (Bacillus cereus (strain ATCC 10987 / NRS 248)) Explore Q72YY9 Go to UniProtKB: Q72YY9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q72YY9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MRD Query on MRD Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain G [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain G [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], G [auth A]	(4R)-2-METHYLPENTANE-2,4-DIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-RXMQYKEDSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth A]
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.31 Å
R-Value Free: 0.173 (Depositor), 0.180 (DCC)
R-Value Work: 0.137 (Depositor), 0.150 (DCC)
R-Value Observed: 0.138 (Depositor)

Diffraction Data: https://doi.org/10.18430/M33BLN

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.37	α = 90
b = 89.553	β = 90
c = 37.228	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHARP	phasing
SHELXD	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2007-12-18

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2007-12-18
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2017-10-25
Changes: Author supporting evidence, Refinement description
Version 1.3: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description
Version 1.4: 2023-01-25
Changes: Database references, Derived calculations
Version 1.5: 2024-10-09
Changes: Data collection, Structure summary