3JVN | pdb_00003jvn

Crystal Structure of the acetyltransferase VF_1542 from Vibrio fischeri, Northeast Structural Genomics Consortium Target VfR136

PDB DOI: https://doi.org/10.2210/pdb3JVN/pdb

Classification: TRANSFERASE
Organism(s): Aliivibrio fischeri ES114
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2009-09-17 Released: 2009-09-29
Deposition Author(s): Forouhar, F., Neely, H., Seetharaman, J., Mao, M., Xiao, R., Ciccosanti, C., Zhao, L., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.61 Å
R-Value Free:
0.273 (Depositor), 0.283 (DCC)
R-Value Work:
0.233 (Depositor), 0.248 (DCC)
R-Value Observed:
0.334 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Northeast Structural Genomics Consortium Target VfR136

Forouhar, F., Neely, H., Seetharaman, J., Mao, M., Xiao, R., Ciccosanti, C., Zhao, L., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Macromolecule Content

Total Structure Weight: 20.31 kDa
Atom Count: 1,034
Modeled Residue Count: 122
Deposited Residue Count: 166
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetyltransferase	A	166	Aliivibrio fischeri ES114	Mutation(s): 0 Gene Names: VF_1542 EC: 2.3.1
UniProt
Find proteins for Q5E4K9 (Aliivibrio fischeri (strain ATCC 700601 / ES114)) Explore Q5E4K9 Go to UniProtKB: Q5E4K9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5E4K9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 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]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		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: 2.61 Å
R-Value Free: 0.273 (Depositor), 0.283 (DCC)
R-Value Work: 0.233 (Depositor), 0.248 (DCC)
R-Value Observed: 0.334 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.714	α = 90
b = 105.332	β = 90
c = 73.872	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
SnB	phasing
REFMAC	refinement

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-09-29

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2009-09-29
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2019-08-07
Changes: Data collection, Derived calculations, Refinement description
Version 1.4: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary