3RED | pdb_00003red

3.0 A structure of the Prunus mume hydroxynitrile lyase isozyme-1

• PDB DOI: https://doi.org/10.2210/pdb3RED/pdb

• Classification: LYASE
• Organism(s): Prunus mume
• Mutation(s): No 


• Deposited: 2011-04-04 Released: 2012-06-20 
• Deposition Author(s): Cielo, C.B.C., Yamane, T., Asano, Y., Watanabe, N., Suzuki, A., Fukuta, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.03 Å
• R-Value Free: 
  0.253 (Depositor), 0.253 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of a native FAD-dependent Hydroxynitrile Lyase derived from the Japanese apricot, Prunus mume

Cielo, C.B.C., Yamane, T., Asano, Y., Watanabe, N., Suzuki, A., Fukuta, Y.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Biological Assembly 5  

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

Biological assembly 5 assigned by authors and generated by PISA (software)

Biological Assembly 6  

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

Biological assembly 6 assigned by authors and generated by PISA (software)

Biological Assembly 7  

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

Biological assembly 7 assigned by authors and generated by PISA (software)

Biological Assembly 8  

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

Biological assembly 8 assigned by authors and generated by PISA (software)

Biological Assembly 9  

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

Biological assembly 9 assigned by authors and generated by PISA (software)

Biological Assembly 10  

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

Biological assembly 10 assigned by authors and generated by PISA (software)

Biological Assembly 11  

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

Biological assembly 11 assigned by authors and generated by PISA (software)

Biological Assembly 12  

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

Biological assembly 12 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 686.4 kDa 
• Atom Count: 48,604 
• Modeled Residue Count: 6,252 
• Deposited Residue Count: 6,252 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hydroxynitrile lyase	A, B, C, D, E, F, G, H, I, J, K, L	521	Prunus mume	Mutation(s): 0  EC: 4.1.2.10
UniProt
Find proteins for B9X0I1 (Prunus mume) Explore B9X0I1  Go to UniProtKB:  B9X0I1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	M [auth A], N [auth B], O [auth C], P [auth D], Q [auth E], R [auth F], S [auth G], T [auth H], U [auth I], V [auth J], W [auth K], X [auth L]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.03 Å
• R-Value Free:  0.253 (Depositor), 0.253 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.019	α = 89.92
b = 113.302	β = 79.13
c = 169.488	γ = 80.83

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-06-20 
Deposition Author(s): Cielo, C.B.C., Yamane, T., Asano, Y., Watanabe, N., Suzuki, A., Fukuta, Y.

Revision History  

• Version 1.0: 2012-06-20
  Type: Initial release
  
• Version 1.1: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary