7A0T | pdb_00007a0t

Crystal structure of kievitone hydratase from Nectria haematococca (P21 SG)

• PDB DOI: https://doi.org/10.2210/pdb7A0T/pdb

• Classification: LYASE
• Organism(s): Fusarium vanettenii 77-13-4
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2020-08-10 Released: 2021-08-18 
• Deposition Author(s): Pavkov-Keller, T., Gruber, K.
• Funding Organization(s): Austrian Research Promotion Agency

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.209 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Literature

Structural analysis and reaction mechanism of kievitone hydratase from Nectria haematococca

Pavkov-Keller, T., Steinkellner, G., Engleder, M., Schuermann, M., Blasl, H., Pichler, H., Gruber, K.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 80.98 kDa 
• Atom Count: 5,866 
• Modeled Residue Count: 651 
• Deposited Residue Count: 696 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CrtC domain-containing protein	A, B	348	Fusarium vanettenii 77-13-4	Mutation(s): 0  Gene Names: NECHADRAFT_51190
UniProt
Find proteins for C7ZKN4 (Fusarium vanettenii (strain ATCC MYA-4622 / CBS 123669 / FGSC 9596 / NRRL 45880 / 77-13-4)) Explore C7ZKN4  Go to UniProtKB:  C7ZKN4
Glycosylation
Glycosylation Sites: 2

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D	10		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G40702WU GlyCosmos:  G40702WU GlyGen:  G40702WU

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	F [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
IMD	E [auth A], G [auth B]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.209 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.43	α = 90
b = 79.79	β = 100.679
c = 103.18	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-08-18 
Deposition Author(s): Pavkov-Keller, T., Gruber, K.

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Funding Organization	Location	Grant Number
Austrian Research Promotion Agency	Austria	--

Revision History  

• Version 1.0: 2021-08-18
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Data collection, Structure summary