2QEC | pdb_00002qec

Crystal structure of histone acetyltransferase HPA2 and related acetyltransferase (NP_600742.1) from Corynebacterium glutamicum ATCC 13032 at 1.90 A resolution

PDB DOI: https://doi.org/10.2210/pdb2QEC/pdb

Classification: TRANSFERASE
Organism(s): Corynebacterium glutamicum ATCC 13032
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2007-06-25 Released: 2007-07-10
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.242 (Depositor), 0.249 (DCC)
R-Value Work:
0.193 (Depositor), 0.203 (DCC)
R-Value Observed:
0.195 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.7 of the entry. See complete history.

Literature

Crystal structure of histone acetyltransferase HPA2 and related acetyltransferase (NP_600742.1) from Corynebacterium glutamicum ATCC 13032 at 1.90 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 22.81 kDa
Atom Count: 1,576
Modeled Residue Count: 181
Deposited Residue Count: 204
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone acetyltransferase HPA2 and related acetyltransferases	A	204	Corynebacterium glutamicum ATCC 13032	Mutation(s): 5 Gene Names: NP_600742.1, Cgl1527, cg1722
UniProt
Find proteins for Q8NQB1 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534)) Explore Q8NQB1 Go to UniProtKB: Q8NQB1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8NQB1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain H [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain H [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain H [auth A]	B [auth A] C [auth A] D [auth A] E [auth A] F [auth A] B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [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: 1.90 Å
R-Value Free: 0.242 (Depositor), 0.249 (DCC)
R-Value Work: 0.193 (Depositor), 0.203 (DCC)
R-Value Observed: 0.195 (Depositor)

Diffraction Data:

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.07	α = 90
b = 79.07	β = 90
c = 181.26	γ = 120

Software Package:

Software Name	Purpose
MolProbity	model building
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
Blu-Ice	data collection
XDS	data reduction
MOSFLM	data reduction
SCALA	data scaling
SHELXD	phasing
autoSHARP	phasing
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2007-07-10

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2007-07-10
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Derived calculations, Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2017-10-25
Changes: Author supporting evidence
Version 1.5: 2021-10-20
Changes: Database references, Derived calculations
Version 1.6: 2023-01-25
Changes: Database references
Version 1.7: 2024-10-30
Changes: Data collection, Structure summary