6UVQ

Crystal structure of Apo AtmM

PDB DOI: https://doi.org/10.2210/pdb6UVQ/pdb

Classification: TRANSFERASE
Organism(s): Actinomadura melliaura
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-11-04 Released: 2020-11-25
Deposition Author(s): Alvarado, S.K., Wang, Z., Miller, M.D., Thorson, J.S., Phillips Jr., G.N.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.84 Å
R-Value Free: 0.224
R-Value Work: 0.181
R-Value Observed: 0.183

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

Literature

Structure of Apo AtmM

Alvarado, S.K., Miller, M.D., Thorson, J.S., Phillips Jr., G.N.

To be published.

Macromolecule Content

Total Structure Weight: 57.51 kDa
Atom Count: 4,304
Modelled Residue Count: 514
Deposited Residue Count: 536
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-glucose O-methyltransferase	A, B	268	Actinomadura melliaura	Mutation(s): 0 Gene Names: atM
UniProt
Find proteins for Q0H2W9 (Actinomadura melliaura) Explore Q0H2W9 Go to UniProtKB: Q0H2W9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q0H2W9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B]	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]
MG Query on MG 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]	D [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.84 Å
R-Value Free: 0.224
R-Value Work: 0.181
R-Value Observed: 0.183
Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.463	α = 90
b = 52.997	β = 93.34
c = 70.842	γ = 90

Software Package:

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

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2020-11-25

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01 GM115261
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	U01 GM098248
National Science Foundation (NSF, United States)	United States	STC 1231306

Revision History (Full details and data files)

Version 1.0: 2020-11-25
Type: Initial release
Version 1.1: 2021-09-15
Changes: Database references, Structure summary
Version 1.2: 2023-10-11
Changes: Data collection, Refinement description

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6UVQ

Crystal structure of Apo AtmM

Structure of Apo AtmM

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)