9AR1 | pdb_00009ar1

Structure of Epimerase Mth373 bound to uridine-5'-diphosphate-xylopyranose

PDB DOI: https://doi.org/10.2210/pdb9AR1/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Methanothermobacter thermautotrophicus str. Delta H
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-02-22 Released: 2025-01-29
Deposition Author(s): Carbone, V., Schofield, L.R., Sutherland-Smith, A.J., Ronimus, R.S.
Funding Organization(s): Marsden Fund

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.97 Å
R-Value Free:
0.204 (Depositor), 0.213 (DCC)
R-Value Work:
0.171 (Depositor), 0.183 (DCC)
R-Value Observed:
0.172 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Literature

Structurally characterizing epimerases from the thermophilic pseudomurein-containing methanogen Methanothermobacter thermautotrophicus delta H

Carbone, V., Schofield, L.R., Sutherland-Smith, A.J., Ronimus, R.S.

To be published.

Macromolecule Content

Total Structure Weight: 85.91 kDa
Atom Count: 5,841
Modeled Residue Count: 618
Deposited Residue Count: 712
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
dTDP-glucose 4,6-dehydratase related protein	A, B	356	Methanothermobacter thermautotrophicus str. Delta H	Mutation(s): 0 Gene Names: MTH_373
UniProt
Find proteins for O26473 (Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)) Explore O26473 Go to UniProtKB: O26473
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O26473
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD (Subject of Investigation/LOI) Query on NAD Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain I [auth B] MOL2 format, chain C [auth A] MOL2 format, chain I [auth B] mmCIF format, chain C [auth A] mmCIF format, chain I [auth B]	C [auth A], I [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain I [auth B]
UDX (Subject of Investigation/LOI) Query on UDX Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	URIDINE-5'-DIPHOSPHATE-XYLOPYRANOSE C₁₄ H₂₂ N₂ O₁₆ P₂ DQQDLYVHOTZLOR-OCIMBMBZSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
UDP (Subject of Investigation/LOI) Query on UDP Download Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	URIDINE-5'-DIPHOSPHATE C₉ H₁₄ N₂ O₁₂ P₂ XCCTYIAWTASOJW-XVFCMESISA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B] mmCIF format, chain K [auth B]	K [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain L [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B]	D [auth A], E [auth A], F [auth A], G [auth A], L [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.97 Å
R-Value Free: 0.204 (Depositor), 0.213 (DCC)
R-Value Work: 0.171 (Depositor), 0.183 (DCC)
R-Value Observed: 0.172 (Depositor)

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.327	α = 90
b = 139.327	β = 90
c = 226.946	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-01-29

Deposition Author(s):

Carbone, V.

Schofield, L.R.

Sutherland-Smith, A.J.

Ronimus, R.S.

Funding Organization	Location	Grant Number
Marsden Fund	New Zealand	--

Revision History (Full details and data files)

Version 1.0: 2025-01-29
Type: Initial release
Version 2.0: 2025-02-19
Changes: Advisory, Atomic model, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary

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Deposit Data

Help and Resources

.id_divider{ color: #ccc; padding: 0 10px 0 10px; } .extended_id_info{ color: #ccc; font-size: 18px; position: relative; top: -10px; left: 4px; } 9AR1 | pdb_00009ar1

Structure of Epimerase Mth373 bound to uridine-5'-diphosphate-xylopyranose

Structurally characterizing epimerases from the thermophilic pseudomurein-containing methanogen Methanothermobacter thermautotrophicus delta H

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations