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), 0.236 (DCC)
R-Value Work:
0.202 (Depositor), 0.203 (DCC)
R-Value Observed:
0.204 (Depositor)

wwPDB Validation 3D Report Full Report

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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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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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), 0.236 (DCC)
R-Value Work: 0.202 (Depositor), 0.203 (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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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

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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.