6T0E

The glucuronoyl esterase OtCE15A S267A variant from Opitutus terrae in complex with benzyl D-glucuronoate and D-glucuronate

PDB DOI: https://doi.org/10.2210/pdb6T0E/pdb

Classification: HYDROLASE
Organism(s): Opitutus terrae PB90-1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2019-10-03 Released: 2019-11-27
Deposition Author(s): Mazurkewich, S., Navarro Poulsen, J.C., Larsbrink, J., Lo Leggio, L.
Funding Organization(s): Knut and Alice Wallenberg Foundation, Novo Nordisk Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free: 0.215
R-Value Work: 0.162
R-Value Observed: 0.164

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 97.61 kDa
Atom Count: 6,933
Modelled Residue Count: 786
Deposited Residue Count: 842
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
glucuronoyl esterase OtCE15A	A, B	421	Opitutus terrae PB90-1	Mutation(s): 1 Gene Names: Oter_0116
UniProt
Find proteins for B1ZMF4 (Opitutus terrae (strain DSM 11246 / JCM 15787 / PB90-1)) Explore B1ZMF4 Go to UniProtKB: B1ZMF4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B1ZMF4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 10 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
M55 (Subject of Investigation/LOI) Query on M55 Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A]	E [auth A]	benzyl alpha-D-glucopyranuronate C₁₃ H₁₆ O₇ MYEUFSLWFIOAGY-SVNGYHJRSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A]	F [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
GCU (Subject of Investigation/LOI) Query on GCU Download Ideal Coordinates CCD File SDF format, chain NA [auth B] SDF format, chain C [auth A] MOL2 format, chain NA [auth B] MOL2 format, chain C [auth A]	C [auth A], NA [auth B]	alpha-D-glucopyranuronic acid C₆ H₁₀ O₇ AEMOLEFTQBMNLQ-WAXACMCWSA-N		Interactions Focus chain C [auth A] Focus chain NA [auth B] Interactions & Density Focus chain C [auth A] Focus chain NA [auth B]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain DA [auth A] SDF format, chain EA [auth A] SDF format, chain FA [auth A] SDF format, chain FB [auth B] SDF format, chain GA [auth A] MOL2 format, chain DA [auth A] MOL2 format, chain EA [auth A] MOL2 format, chain FA [auth A] MOL2 format, chain FB [auth B] MOL2 format, chain GA [auth A]	DA [auth A], EA [auth A], FA [auth A], FB [auth B], GA [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain DA [auth A] Focus chain EA [auth A] Focus chain FA [auth A] Focus chain FB [auth B] Focus chain GA [auth A] Interactions & Density Focus chain DA [auth A] Focus chain EA [auth A] Focus chain FA [auth A] Focus chain FB [auth B] Focus chain GA [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain BA [auth A] SDF format, chain CA [auth A] SDF format, chain DB [auth B] SDF format, chain EB [auth B] SDF format, chain Z [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain DB [auth B] MOL2 format, chain EB [auth B] MOL2 format, chain Z [auth A]	AA [auth A] BA [auth A] CA [auth A] DB [auth B] EB [auth B] AA [auth A], BA [auth A], CA [auth A], DB [auth B], EB [auth B], Z [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CA [auth A] Focus chain DB [auth B] Focus chain EB [auth B] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CA [auth A] Focus chain DB [auth B] Focus chain EB [auth B] Focus chain Z [auth A]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain KB [auth B] SDF format, chain LA [auth A] SDF format, chain LB [auth B] SDF format, chain MB [auth B] SDF format, chain MA [auth A] MOL2 format, chain KB [auth B] MOL2 format, chain LA [auth A] MOL2 format, chain LB [auth B] MOL2 format, chain MB [auth B] MOL2 format, chain MA [auth A]	KB [auth B], LA [auth A], LB [auth B], MA [auth A], MB [auth B]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain KB [auth B] Focus chain LA [auth A] Focus chain LB [auth B] Focus chain MA [auth A] Focus chain MB [auth B] Interactions & Density Focus chain KB [auth B] Focus chain LA [auth A] Focus chain LB [auth B] Focus chain MA [auth A] Focus chain MB [auth B]
TMO Query on TMO Download Ideal Coordinates CCD File SDF format, chain IB [auth B] SDF format, chain JA [auth A] SDF format, chain GB [auth B] SDF format, chain HB [auth B] SDF format, chain IA [auth A] SDF format, chain JB [auth B] SDF format, chain KA [auth A] MOL2 format, chain IB [auth B] MOL2 format, chain JA [auth A] MOL2 format, chain GB [auth B] MOL2 format, chain HB [auth B] MOL2 format, chain IA [auth A] MOL2 format, chain JB [auth B] MOL2 format, chain KA [auth A]	GB [auth B] HB [auth B] IA [auth A] IB [auth B] JA [auth A] GB [auth B], HB [auth B], IA [auth A], IB [auth B], JA [auth A], JB [auth B], KA [auth A]	trimethylamine oxide C₃ H₉ N O UYPYRKYUKCHHIB-UHFFFAOYSA-N		Interactions Focus chain GB [auth B] Focus chain HB [auth B] Focus chain IA [auth A] Focus chain IB [auth B] Focus chain JA [auth A] Focus chain JB [auth B] Focus chain KA [auth A] Interactions & Density Focus chain GB [auth B] Focus chain HB [auth B] Focus chain IA [auth A] Focus chain IB [auth B] Focus chain JA [auth A] Focus chain JB [auth B] Focus chain KA [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AB [auth B] SDF format, chain BB [auth B] SDF format, chain CB [auth B] SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain OA [auth B] SDF format, chain P [auth A] SDF format, chain PA [auth B] SDF format, chain Q [auth A] SDF format, chain QA [auth B] SDF format, chain R [auth A] SDF format, chain SA [auth B] SDF format, chain U [auth A] SDF format, chain UA [auth B] SDF format, chain V [auth A] SDF format, chain WA [auth B] SDF format, chain X [auth A] SDF format, chain XA [auth B] SDF format, chain Y [auth A] SDF format, chain YA [auth B] SDF format, chain H [auth A] SDF format, chain J [auth A] SDF format, chain RA [auth B] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain TA [auth B] SDF format, chain VA [auth B] SDF format, chain W [auth A] SDF format, chain ZA [auth B] MOL2 format, chain AB [auth B] MOL2 format, chain BB [auth B] MOL2 format, chain CB [auth B] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth B] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain SA [auth B] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth B] MOL2 format, chain V [auth A] MOL2 format, chain WA [auth B] MOL2 format, chain X [auth A] MOL2 format, chain XA [auth B] MOL2 format, chain Y [auth A] MOL2 format, chain YA [auth B] MOL2 format, chain H [auth A] MOL2 format, chain J [auth A] MOL2 format, chain RA [auth B] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth B] MOL2 format, chain VA [auth B] MOL2 format, chain W [auth A] MOL2 format, chain ZA [auth B]	AB [auth B] BB [auth B] CB [auth B] G [auth A] H [auth A] AB [auth B], BB [auth B], CB [auth B], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], OA [auth B], P [auth A], PA [auth B], Q [auth A], QA [auth B], R [auth A], RA [auth B], S [auth A], SA [auth B], T [auth A], TA [auth B], U [auth A], UA [auth B], V [auth A], VA [auth B], W [auth A], WA [auth B], X [auth A], XA [auth B], Y [auth A], YA [auth B], ZA [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AB [auth B] Focus chain BB [auth B] Focus chain CB [auth B] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain T [auth A] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain VA [auth B] Focus chain W [auth A] Focus chain WA [auth B] Focus chain X [auth A] Focus chain XA [auth B] Focus chain Y [auth A] Focus chain YA [auth B] Focus chain ZA [auth B] Interactions & Density Focus chain AB [auth B] Focus chain BB [auth B] Focus chain CB [auth B] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain T [auth A] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain VA [auth B] Focus chain W [auth A] Focus chain WA [auth B] Focus chain X [auth A] Focus chain XA [auth B] Focus chain Y [auth A] Focus chain YA [auth B] Focus chain ZA [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain HA [auth A] MOL2 format, chain HA [auth A]	HA [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain HA [auth A] Interactions & Density Focus chain HA [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free: 0.215
R-Value Work: 0.162
R-Value Observed: 0.164
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.719	α = 90
b = 87.611	β = 90
c = 173.91	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2019-11-27

Deposition Author(s):

Mazurkewich, S.

Navarro Poulsen, J.C.

Larsbrink, J.

Lo Leggio, L.

Funding Organization	Location	Grant Number
Knut and Alice Wallenberg Foundation	Sweden	--
Novo Nordisk Foundation	Denmark	NNF17OC0027698

Revision History (Full details and data files)

Version 1.0: 2019-11-27
Type: Initial release
Version 1.1: 2020-01-15
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2024-01-24
Changes: Data collection, Database references, Refinement description, Structure summary