2X3K

CO-COMPLEX STRUCTURE OF ACHROMOBACTIN SYNTHETASE PROTEIN D (ACSD) WITH AMP AND SULFATE FROM PECTOBACTERIUM CHRYSANTHEMI

PDB DOI: https://doi.org/10.2210/pdb2X3K/pdb

Classification: LIGASE
Organism(s): Dickeya chrysanthemi
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-01-25 Released: 2010-11-10
Deposition Author(s): Schmelz, S., Naismith, J.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.261
R-Value Work: 0.205
R-Value Observed: 0.208

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Adenylate Forming Enzymes Involved in Nrps-Independent Siderophore Biosynthesis

Schmelz, S.

(2010) Ph D Thesis

Macromolecule Content

Total Structure Weight: 142.08 kDa
Atom Count: 9,417
Modelled Residue Count: 1,145
Deposited Residue Count: 1,240
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ACSD	A, B	620	Dickeya chrysanthemi	Mutation(s): 0
UniProt
Find proteins for Q93AT8 (Dickeya chrysanthemi) Explore Q93AT8 Go to UniProtKB: Q93AT8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q93AT8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMP Query on AMP Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B]	C [auth A], E [auth B]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B]	D [auth A], F [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.261
R-Value Work: 0.205
R-Value Observed: 0.208
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.7	α = 95
b = 70	β = 101.9
c = 96	γ = 94.7

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-11-10

Deposition Author(s):

Schmelz, S.

Naismith, J.H.

Revision History (Full details and data files)

Version 1.0: 2010-11-10
Type: Initial release
Version 1.1: 2011-05-07
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description

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2X3K

CO-COMPLEX STRUCTURE OF ACHROMOBACTIN SYNTHETASE PROTEIN D (ACSD) WITH AMP AND SULFATE FROM PECTOBACTERIUM CHRYSANTHEMI

Adenylate Forming Enzymes Involved in Nrps-Independent Siderophore Biosynthesis

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)