1RQX | pdb_00001rqx

Crystal structure of ACC Deaminase complexed with Inhibitor

• PDB DOI: https://doi.org/10.2210/pdb1RQX/pdb

• Classification: HYDROLASE
• Organism(s): Pseudomonas sp. ACP
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-12-07 Released: 2004-08-17 
• Deposition Author(s): Karthikeyan, S., Zhao, Z., Kao, C.L., Zhou, Q., Tao, Z., Zhang, H., Liu, H.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.248 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

Structural analysis of 1-aminocyclopropane-1-carboxylate deaminase: observation of an aminyl intermediate and identification of Tyr 294 as the active-site nucleophile.

Karthikeyan, S., Zhao, Z., Kao, C.L., Zhou, Q., Tao, Z., Zhang, H., Liu, H.W.

(2004) Angew Chem Int Ed Engl 43: 3425-3429

• PubMed: 15221829 
• DOI: https://doi.org/10.1002/anie.200453353
• Primary Citation Related Structures: 
  1RQX

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Organizational Affiliation: 
• Division of Medicinal Chemistry, College of Pharmacy and Department of Chemistry and Biochemistry, University of Texas, Austin, TX 78712, USA.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 148.39 kDa 
• Atom Count: 10,525 
• Modeled Residue Count: 1,326 
• Deposited Residue Count: 1,352 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
1-aminocyclopropane-1-carboxylate deaminase	A, B, C, D	338	Pseudomonas sp. ACP	Mutation(s): 0  EC: 3.5.99.7
UniProt
Find proteins for Q00740 (Pseudomonas sp. (strain ACP)) Explore Q00740  Go to UniProtKB:  Q00740

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	E [auth A], G [auth B], I [auth C], K [auth D]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
MLP	F [auth A], H [auth B], J [auth C], L [auth D]	1-AMINOCYCLOPROPYLPHOSPHONATE C3 H7 N O3 P WKCJTSHOKDLADL-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.248 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.76	α = 90
b = 68.587	β = 90
c = 350.913	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-08-17 
Deposition Author(s): Karthikeyan, S., Zhao, Z., Kao, C.L., Zhou, Q., Tao, Z., Zhang, H., Liu, H.W.

Revision History  

• Version 1.0: 2004-08-17
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description