7CLF | pdb_00007clf

PigF with SAH

PDB DOI: https://doi.org/10.2210/pdb7CLF/pdb

Classification: TRANSFERASE
Organism(s): Serratia marcescens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-07-20 Released: 2021-07-28
Deposition Author(s): Qiu, S., Xu, D., Han, N., Sun, B., Ran, T., Wang, W.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.98 Å
R-Value Free:
0.249 (Depositor), 0.249 (DCC)
R-Value Work:
0.188 (Depositor), 0.188 (DCC)

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

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

Literature

Crystal structures of PigF, an O-methyltransferase involved in the prodigiosin synthetic pathway, reveal an induced-fit substrate-recognition mechanism.

Qiu, S., Xu, D., Xu, M., Zhou, H., Sun, N., Zhang, L., Zhao, M., He, J., Ran, T., Sun, B., Wang, W.

(2022) IUCrJ 9: 316-327

DOI: https://doi.org/10.1107/S2052252521011696

Macromolecule Content

Total Structure Weight: 78.31 kDa
Atom Count: 5,644
Modeled Residue Count: 670
Deposited Residue Count: 692
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methyltransferase domain-containing protein	A, B	346	Serratia marcescens	Mutation(s): 0 Gene Names: pigF, AR325_07835, E4655_02280, FOT62_11605
UniProt
Find proteins for Q5W249 (Serratia marcescens) Explore Q5W249 Go to UniProtKB: Q5W249
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5W249
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 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 D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B]	D [auth A], F [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]
ACT (Subject of Investigation/LOI) Query on ACT Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.98 Å
R-Value Free: 0.249 (Depositor), 0.249 (DCC)
R-Value Work: 0.188 (Depositor), 0.188 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.9	α = 90
b = 109.2	β = 93.1
c = 63.9	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
CRANK2	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-07-28

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31770074
National Natural Science Foundation of China (NSFC)	China	31770050

Revision History (Full details and data files)

Version 1.0: 2021-07-28
Type: Initial release
Version 1.1: 2022-03-16
Changes: Database references
Version 1.2: 2024-05-29
Changes: Data collection, Derived calculations

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