7ZGT | pdb_00007zgt

C-Methyltransferase PsmD from Streptomyces griseofuscus (apo form)

PDB DOI: https://doi.org/10.2210/pdb7ZGT/pdb

Classification: TRANSFERASE
Organism(s): Streptomyces griseofuscus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-04-04 Released: 2022-12-28
Deposition Author(s): Weiergraeber, O.H., Amariei, D.A., Pozhydaieva, N., Pietruszka, J.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.252 (Depositor), 0.253 (DCC)
R-Value Work:
0.215 (Depositor), 0.216 (DCC)
R-Value Observed:
0.217 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history.

Literature

Enzymatic C3-Methylation of Indoles Using Methyltransferase PsmD-Crystal Structure, Catalytic Mechanism, and Preparative Applications

Amariei, D.A., Pozhydaieva, N., David, B., Schneider, P., Classen, T., Gohlke, H., Weiergraber, O.H., Pietruszka, J.

(2022) ACS Catal

DOI: https://doi.org/10.1021/acscatal.2c04240

Macromolecule Content

Total Structure Weight: 61.93 kDa
Atom Count: 4,207
Modeled Residue Count: 502
Deposited Residue Count: 550
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methyltransferase	A, B	275	Streptomyces griseofuscus	Mutation(s): 0 Gene Names: psmD
UniProt
Find proteins for W8R3D8 (Streptomyces griseofuscus) Explore W8R3D8 Go to UniProtKB: W8R3D8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	W8R3D8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], F [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth B]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.252 (Depositor), 0.253 (DCC)
R-Value Work: 0.215 (Depositor), 0.216 (DCC)
R-Value Observed: 0.217 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.05	α = 90
b = 87.49	β = 90
c = 89	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-12-28

Deposition Author(s):

Weiergraeber, O.H.

Pozhydaieva, N.

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2022-12-28
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Refinement description
Version 1.2: 2024-11-20
Changes: Structure summary

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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.