3C8W | pdb_00003c8w

Crystal structure of acetoacetate decarboxylase (ADC) (YP_094708.1) from Legionella pneumophila subsp. pneumophila str. Philadelphia 1 at 1.60 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3C8W/pdb

• Classification: LYASE
• Organism(s): Legionella pneumophila subsp. pneumophila str. Philadelphia 1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-02-13 Released: 2008-02-26 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.228 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Literature

Crystal structure of acetoacetate decarboxylase (ADC) (YP_094708.1) from Legionella pneumophila subsp. pneumophila str. Philadelphia 1 at 1.60 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Tetrahedral - T  (Explore in 3D)
Global Stoichiometry: Homo 12-mer - A12 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 115.93 kDa 
• Atom Count: 8,626 
• Modeled Residue Count: 998 
• Deposited Residue Count: 1,020 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetoacetate decarboxylase ADC	A, B, C, D	255	Legionella pneumophila subsp. pneumophila str. Philadelphia 1	Mutation(s): 0  Gene Names: YP_094708.1, lpg0672 EC: 4.1.1.4
UniProt
Find proteins for Q5ZXQ9 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)) Explore Q5ZXQ9  Go to UniProtKB:  Q5ZXQ9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	E [auth A], F [auth B], G [auth C], H [auth D]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LCK	A, B, C, D	L-PEPTIDE LINKING	C10 H18 N2 O4		LYS
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.228 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33C8W

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.1	α = 90
b = 104.1	β = 90
c = 189.64	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-02-26 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2008-02-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.5: 2024-11-06
  Changes: Data collection, Refinement description, Structure summary