6IV7 | pdb_00006iv7

The crystal structure of a SAM-dependent enzyme from aspergillus flavus

PDB DOI: https://doi.org/10.2210/pdb6IV7/pdb

Classification: TRANSFERASE
Organism(s): Aspergillus flavus NRRL3357
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-12-02 Released: 2019-02-06
Deposition Author(s): Zhou, Y.Z., Peng, T., Liao, L.J., Liu, X.K., Zhao, Y.C., Guo, Y., Zeng, Z.X.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free:
0.238 (Depositor), 0.240 (DCC)
R-Value Work:
0.202 (Depositor), 0.200 (DCC)
R-Value Observed:
0.204 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

The crystal structure of A SAM-Dependent enzyme from Aspergillus flavus

Zhou, Y.Z., Peng, T., Liao, L.J., Zhao, Y.C., Liu, X.K., Guo, Y., Zeng, Z.X.

To be published.

Macromolecule Content

Total Structure Weight: 87.24 kDa
Atom Count: 6,316
Modeled Residue Count: 772
Deposited Residue Count: 772
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
methyltransferase lepI	A, B	386	Aspergillus flavus NRRL3357	Mutation(s): 0 Gene Names: lepI, AFLA_066940 EC: 2.1.1
UniProt
Find proteins for B8NJH3 (Aspergillus flavus (strain ATCC 200026 / FGSC A1120 / IAM 13836 / NRRL 3357 / JCM 12722 / SRRC 167)) Explore B8NJH3 Go to UniProtKB: B8NJH3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B8NJH3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH Query on SAH Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free: 0.238 (Depositor), 0.240 (DCC)
R-Value Work: 0.202 (Depositor), 0.200 (DCC)
R-Value Observed: 0.204 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 160.556	α = 90
b = 62.225	β = 113.06
c = 113.354	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2019-02-06

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2019-02-06
Type: Initial release
Version 1.1: 2024-03-27
Changes: Data collection, Database references

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.