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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.209 (Depositor), 0.211 (DCC)
R-Value Work:
0.176 (Depositor), 0.178 (DCC)
R-Value Observed:
0.178 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 7A0T

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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.

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C7ZKN4
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A Focus chain B
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	Interactions Focus chain C Focus chain D Interactions & Density Focus chain C Focus chain D
Glycosylation Resources
GlyTouCan: G40702WU GlyCosmos: G40702WU GlyGen: G40702WU

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]
IMD Query on IMD Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain E [auth A] Focus chain G [auth B] Interactions & Density Focus chain E [auth A] Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.209 (Depositor), 0.211 (DCC)
R-Value Work: 0.176 (Depositor), 0.178 (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

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2021-08-18

Deposition Author(s):

Pavkov-Keller, T.

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

Revision History (Full details and data files)

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

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.