6WUQ | pdb_00006wuq

Crystal structure of AjiA1 in apo form

PDB DOI: https://doi.org/10.2210/pdb6WUQ/pdb

Classification: LIGASE
Organism(s): Streptomyces sp.
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-05-05 Released: 2020-12-09
Deposition Author(s): Paiva, F.C.R., Chan, K., Leadlay, P., Dias, M.V.B.
Funding Organization(s): Sao Paulo Research Foundation, Brazilian National Council for Scientific and Technological Development

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.224 (Depositor), 0.227 (DCC)
R-Value Work:
0.188 (Depositor), 0.191 (DCC)
R-Value Observed:
0.190 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history.

Literature

The crystal structure of AjiA1 reveals a novel structural motion mechanism in the adenylate-forming enzyme family

Paiva, F.C.R., Chan, K., Samborskyy, M., Silber, A.M., Leadlay, P., Dias, M.V.B.

(2020) Acta Crystallogr D Biol Crystallogr 76: 1201

DOI: https://doi.org/10.1107/S2059798320013431

Macromolecule Content

Total Structure Weight: 96.86 kDa
Atom Count: 6,869
Modeled Residue Count: 859
Deposited Residue Count: 872
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AjiA1	A, B	436	Streptomyces sp.	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain C [auth A]	C [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.224 (Depositor), 0.227 (DCC)
R-Value Work: 0.188 (Depositor), 0.191 (DCC)
R-Value Observed: 0.190 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.777	α = 90
b = 128.777	β = 90
c = 101.449	γ = 120

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-12-09

Deposition Author(s):

Funding Organization	Location	Grant Number
Sao Paulo Research Foundation	Brazil	2018/003511
Brazilian National Council for Scientific and Technological Development	Brazil	141090/2016-2

Revision History (Full details and data files)

Version 1.0: 2020-12-09
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Database references, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.