7B0M | pdb_00007b0m

Sugar transaminase from a metagenome collected from troll oil field production water

PDB DOI: https://doi.org/10.2210/pdb7B0M/pdb

Classification: TRANSFERASE
Organism(s): uncultured bacterium
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-11-20 Released: 2021-12-01
Deposition Author(s): Littlechild, J.A., De Rose, S.A., Isupov, M.N., Sayer, C., Karki, S.
Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.43 Å
R-Value Free:
0.197 (Depositor), 0.198 (DCC)
R-Value Work:
0.165 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7B0M

This is version 1.1 of the entry. See complete history.

Literature

Sugar transaminases from hot environments

James, P., Littlechild, J.A., De Rose, S.A., Isupov, M.N., Karki, S., Tabji, A.B., Garcia-Moyano, A., Birkeland, N.K.

To be published.

Macromolecule Content

Total Structure Weight: 43.19 kDa
Atom Count: 3,469
Modeled Residue Count: 369
Deposited Residue Count: 375
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sugar aminotransferase	A [auth AAA]	375	uncultured bacterium	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain F [auth AAA] MOL2 format, chain F [auth AAA] mmCIF format, chain F [auth AAA]	F [auth AAA]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain F [auth AAA] Interactions & Density Focus chain F [auth AAA]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain G [auth AAA] SDF format, chain I [auth AAA] SDF format, chain K [auth AAA] MOL2 format, chain G [auth AAA] MOL2 format, chain I [auth AAA] MOL2 format, chain K [auth AAA] mmCIF format, chain G [auth AAA] mmCIF format, chain I [auth AAA] mmCIF format, chain K [auth AAA]	G [auth AAA], I [auth AAA], K [auth AAA]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain G [auth AAA] Focus chain I [auth AAA] Focus chain K [auth AAA] Interactions & Density Focus chain G [auth AAA] Focus chain I [auth AAA] Focus chain K [auth AAA]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain B [auth AAA] SDF format, chain C [auth AAA] SDF format, chain D [auth AAA] SDF format, chain E [auth AAA] SDF format, chain H [auth AAA] SDF format, chain J [auth AAA] MOL2 format, chain B [auth AAA] MOL2 format, chain C [auth AAA] MOL2 format, chain D [auth AAA] MOL2 format, chain E [auth AAA] MOL2 format, chain H [auth AAA] MOL2 format, chain J [auth AAA] mmCIF format, chain B [auth AAA] mmCIF format, chain C [auth AAA] mmCIF format, chain D [auth AAA] mmCIF format, chain E [auth AAA] mmCIF format, chain H [auth AAA] mmCIF format, chain J [auth AAA]	B [auth AAA] C [auth AAA] D [auth AAA] E [auth AAA] H [auth AAA] B [auth AAA], C [auth AAA], D [auth AAA], E [auth AAA], H [auth AAA], J [auth AAA]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain B [auth AAA] Focus chain C [auth AAA] Focus chain D [auth AAA] Focus chain E [auth AAA] Focus chain H [auth AAA] Focus chain J [auth AAA] Interactions & Density Focus chain B [auth AAA] Focus chain C [auth AAA] Focus chain D [auth AAA] Focus chain E [auth AAA] Focus chain H [auth AAA] Focus chain J [auth AAA]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP Query on LLP	A [auth AAA]	L-PEPTIDE LINKING	C₁₄ H₂₂ N₃ O₇ P		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.43 Å
R-Value Free: 0.197 (Depositor), 0.198 (DCC)
R-Value Work: 0.165 (Depositor)

Diffraction Data:

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.405	α = 90
b = 76.405	β = 90
c = 134.44	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
Coot	model building
MoRDa	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2021-12-01

Deposition Author(s):

Littlechild, J.A.

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/L002035/1

Revision History (Full details and data files)

Version 1.0: 2021-12-01
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Derived calculations, 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.