7WZF | pdb_00007wzf

Structural and mechanism analysis of YunM

PDB DOI: https://doi.org/10.2210/pdb7WZF/pdb

Classification: TRANSFERASE
Organism(s): Streptomyces yunnanensis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-02-18 Released: 2023-02-22
Deposition Author(s): Duan, S.Y.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.218 (Depositor), 0.217 (DCC)
R-Value Work:
0.206 (Depositor), 0.206 (DCC)
R-Value Observed:
0.206 (Depositor)

Starting Model: experimental
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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

Structural and mechanism analysis of YunM

Duan, S.Y.

To be published.

Macromolecule Content

Total Structure Weight: 30.19 kDa
Atom Count: 2,123
Modeled Residue Count: 243
Deposited Residue Count: 272
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YunM	A	272	Streptomyces yunnanensis	Mutation(s): 0
UniProt
Find proteins for A0A9X8MSQ8 (Streptomyces yunnanensis) Explore A0A9X8MSQ8 Go to UniProtKB: A0A9X8MSQ8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A9X8MSQ8
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.218 (Depositor), 0.217 (DCC)
R-Value Work: 0.206 (Depositor), 0.206 (DCC)
R-Value Observed: 0.206 (Depositor)

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.741	α = 90
b = 107.741	β = 90
c = 109.163	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
BALBES	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-02-22

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2023-02-22
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description

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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.