7DAO | pdb_00007dao

Crystal structure of native yak lactoperoxidase at 2.28 A resolution

• PDB DOI: https://doi.org/10.2210/pdb7DAO/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Bos mutus
• Mutation(s): No 


• Deposited: 2020-10-16 Released: 2020-10-28 
• Deposition Author(s): Singh, P.K., Ahmad, N., Rani, C., Sharma, P., Sharma, S., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 
  0.243 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.170 (DCC) 

Starting Model: experimental

Literature

Crystal structure of native yak lactoperoxidase at 2.28 A resolution

Singh, P.K., Ahmad, N., Rani, C., Sharma, P., Sharma, S., Singh, T.P.

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)

Macromolecule Content 

• Total Structure Weight: 69.62 kDa 
• Atom Count: 5,228 
• Modeled Residue Count: 595 
• Deposited Residue Count: 595 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lactoperoxidase	A	595	Bos mutus	Mutation(s): 0  EC: 1.11.1.7
UniProt
Find proteins for L8ICE9 (Bos mutus) Explore L8ICE9  Go to UniProtKB:  L8ICE9
Glycosylation
Glycosylation Sites: 4

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM (Subject of Investigation/LOI)	G [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
NAG (Subject of Investigation/LOI)	C [auth A], D [auth A], E [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
ZN	H [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	I [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free:  0.243 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.170 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.162	α = 90
b = 85.242	β = 90
c = 96.443	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-10-28 
Deposition Author(s): Singh, P.K., Ahmad, N., Rani, C., Sharma, P., Sharma, S., Singh, T.P.

Revision History  

• Version 1.0: 2020-10-28
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary