3RAR | pdb_00003rar

X-ray structure of a bound phosphonate transition state analog and enantioselectivity of Candida rugosa lipase toward chiral carboxylic acids

• PDB DOI: https://doi.org/10.2210/pdb3RAR/pdb

• Classification: HYDROLASE
• Organism(s): Diutina rugosa
• Expression System: Diutina rugosa
• Mutation(s): No 


• Deposited: 2011-03-28 Released: 2011-04-27 
• Deposition Author(s): Grochulski, P., Kazlauskas, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free: 
  0.211 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.177 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Model: experimental

Literature

Insights into the molecular basis of chiral acid recognition by Candida rugosa lipase from an X-ray crystal structure of a bound phosphonate transition state analog

Colton, I.J., Yin, D.T., Grochulski, P., Kazlauskas, R.J.

(2011) Adv Synth Catal 353: 2529-2544

• DOI: https://doi.org/10.1002/adsc.201100459

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 58.08 kDa 
• Atom Count: 4,253 
• Modeled Residue Count: 534 
• Deposited Residue Count: 534 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipase 1	A	534	Diutina rugosa	Mutation(s): 0  Gene Names: LIP1 EC: 3.1.1.3
UniProt
Find proteins for P20261 (Diutina rugosa) Explore P20261  Go to UniProtKB:  P20261
Glycosylation
Glycosylation Sites: 2

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
IAN	F [auth A]	methyl hydrogen (R)-[(R)-methoxy(phenyl)methyl]phosphonate C9 H13 O4 P YPAATCUNRIAADK-SECBINFHSA-N
CA	D [auth A], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free:  0.211 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.177 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65	α = 90
b = 97.5	β = 90
c = 176.1	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-04-27 
Deposition Author(s): Grochulski, P., Kazlauskas, R.

Revision History  

• Version 1.0: 2011-04-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-09-13
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-11-06
  Changes: Structure summary