2WBK | pdb_00002wbk

Structure of the Michaelis complex of beta-mannosidase, Man2A, provides insight into the conformational itinerary of mannoside hydrolysis

PDB DOI: https://doi.org/10.2210/pdb2WBK/pdb

Classification: HYDROLASE
Organism(s): Bacteroides thetaiotaomicron VPI-5482
Expression System: Escherichia coli BL21
Mutation(s): Yes

Deposited: 2009-03-02 Released: 2009-03-17
Deposition Author(s): Offen, W.A., Zechel, D.L., Withers, S.G., Gilbert, H.J., Davies, G.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.232 (Depositor), 0.233 (DCC)
R-Value Work:
0.169 (Depositor), 0.170 (DCC)
R-Value Observed:
0.172 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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Literature

Structure of the Michaelis Complex of Beta-Mannosidase, Man2A, Provides Insight Into the Conformational Itinerary of Mannoside Hydrolysis.

Offen, W.A., Zechel, D.L., Withers, S.G., Gilbert, H.J., Davies, G.J.

(2009) Cell 18: 2484

PubMed: 19532864 Search on PubMed
DOI: https://doi.org/10.1039/b902240f
Primary Citation Related Structures:
2WBK

PubMed Abstract:
The Michaelis complex of the beta-mannosidase Man2A shows distortion to a (1)S(5) conformation adding to the growing body of evidence supporting catalysis through a boat conformation.

Organizational Affiliation

Department of Chemistry, The University of York, Heslington, UK.

Macromolecule Content

Total Structure Weight: 200.47 kDa
Atom Count: 14,932
Modeled Residue Count: 1,677
Deposited Residue Count: 1,694
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-MANNOSIDASE	A, B	847	Bacteroides thetaiotaomicron VPI-5482	Mutation(s): 1 EC: 3.2.1.25
UniProt
Find proteins for Q8AAK6 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q8AAK6 Go to UniProtKB: Q8AAK6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8AAK6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
M2F Query on M2F Download:Ideal Coordinates CCD File SDF format, chain HA [auth B] SDF format, chain G [auth A] MOL2 format, chain HA [auth B] MOL2 format, chain G [auth A] mmCIF format, chain HA [auth B] mmCIF format, chain G [auth A]	G [auth A], HA [auth B]	2,4-dinitrophenyl 2-deoxy-2-fluoro-beta-D-mannopyranoside C₁₂ H₁₃ F N₂ O₉ UFSBFVZQJZMIOU-IYKVGLELSA-N		Interactions Focus chain G [auth A] Focus chain HA [auth B] Interactions & Density Focus chain G [auth A] Focus chain HA [auth B]
BR Query on BR Download:Ideal Coordinates CCD File SDF format, chain S [auth A] SDF format, chain UA [auth B] SDF format, chain VA [auth B] SDF format, chain XA [auth B] SDF format, chain WA [auth B] SDF format, chain W [auth A] SDF format, chain V [auth A] SDF format, chain U [auth A] SDF format, chain T [auth A] SDF format, chain DB [auth B] SDF format, chain BB [auth B] SDF format, chain BA [auth A] MOL2 format, chain S [auth A] MOL2 format, chain UA [auth B] MOL2 format, chain VA [auth B] MOL2 format, chain XA [auth B] MOL2 format, chain WA [auth B] MOL2 format, chain W [auth A] MOL2 format, chain V [auth A] MOL2 format, chain U [auth A] MOL2 format, chain T [auth A] MOL2 format, chain DB [auth B] MOL2 format, chain BB [auth B] MOL2 format, chain BA [auth A] mmCIF format, chain S [auth A] mmCIF format, chain UA [auth B] mmCIF format, chain VA [auth B] mmCIF format, chain XA [auth B] mmCIF format, chain WA [auth B] mmCIF format, chain W [auth A] mmCIF format, chain V [auth A] mmCIF format, chain U [auth A] mmCIF format, chain T [auth A] mmCIF format, chain DB [auth B] mmCIF format, chain BB [auth B] mmCIF format, chain BA [auth A]	BA [auth A] BB [auth B] DB [auth B] S [auth A] T [auth A] BA [auth A], BB [auth B], DB [auth B], S [auth A], T [auth A], U [auth A], UA [auth B], V [auth A], VA [auth B], W [auth A], WA [auth B], XA [auth B]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M		Interactions Focus chain BA [auth A] Focus chain BB [auth B] Focus chain DB [auth B] Focus chain S [auth A] Focus chain T [auth A] 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 XA [auth B] Interactions & Density Focus chain BA [auth A] Focus chain BB [auth B] Focus chain DB [auth B] Focus chain S [auth A] Focus chain T [auth A] 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 XA [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain KA [auth B] SDF format, chain P [auth A] SDF format, chain Z [auth A] SDF format, chain Y [auth A] SDF format, chain X [auth A] SDF format, chain TA [auth B] SDF format, chain SA [auth B] SDF format, chain RA [auth B] SDF format, chain QA [auth B] SDF format, chain Q [auth A] SDF format, chain PA [auth B] SDF format, chain OA [auth B] SDF format, chain O [auth A] SDF format, chain NA [auth B] SDF format, chain N [auth A] SDF format, chain MA [auth B] SDF format, chain M [auth A] SDF format, chain LA [auth B] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain JA [auth B] SDF format, chain J [auth A] SDF format, chain IB [auth B] SDF format, chain IA [auth B] SDF format, chain I [auth A] SDF format, chain HB [auth B] SDF format, chain GA [auth B] SDF format, chain FB [auth B] SDF format, chain F [auth A] SDF format, chain EB [auth B] SDF format, chain DA [auth A] SDF format, chain D [auth A] SDF format, chain CB [auth B] SDF format, chain CA [auth A] SDF format, chain C [auth A] SDF format, chain AB [auth B] SDF format, chain AA [auth A] MOL2 format, chain H [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain P [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain X [auth A] MOL2 format, chain TA [auth B] MOL2 format, chain SA [auth B] MOL2 format, chain RA [auth B] MOL2 format, chain QA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain PA [auth B] MOL2 format, chain OA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain NA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain MA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain J [auth A] MOL2 format, chain IB [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain I [auth A] MOL2 format, chain HB [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain FB [auth B] MOL2 format, chain F [auth A] MOL2 format, chain EB [auth B] MOL2 format, chain DA [auth A] MOL2 format, chain D [auth A] MOL2 format, chain CB [auth B] MOL2 format, chain CA [auth A] MOL2 format, chain C [auth A] MOL2 format, chain AB [auth B] MOL2 format, chain AA [auth A] mmCIF format, chain H [auth A] mmCIF format, chain KA [auth B] mmCIF format, chain P [auth A] mmCIF format, chain Z [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain X [auth A] mmCIF format, chain TA [auth B] mmCIF format, chain SA [auth B] mmCIF format, chain RA [auth B] mmCIF format, chain QA [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain PA [auth B] mmCIF format, chain OA [auth B] mmCIF format, chain O [auth A] mmCIF format, chain NA [auth B] mmCIF format, chain N [auth A] mmCIF format, chain MA [auth B] mmCIF format, chain M [auth A] mmCIF format, chain LA [auth B] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain JA [auth B] mmCIF format, chain J [auth A] mmCIF format, chain IB [auth B] mmCIF format, chain IA [auth B] mmCIF format, chain I [auth A] mmCIF format, chain HB [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain FB [auth B] mmCIF format, chain F [auth A] mmCIF format, chain EB [auth B] mmCIF format, chain DA [auth A] mmCIF format, chain D [auth A] mmCIF format, chain CB [auth B] mmCIF format, chain CA [auth A] mmCIF format, chain C [auth A] mmCIF format, chain AB [auth B] mmCIF format, chain AA [auth A]	AA [auth A] AB [auth B] C [auth A] CA [auth A] CB [auth B] AA [auth A], AB [auth B], C [auth A], CA [auth A], CB [auth B], D [auth A], DA [auth A], EB [auth B], F [auth A], FB [auth B], GA [auth B], H [auth A], HB [auth B], I [auth A], IA [auth B], IB [auth B], J [auth A], JA [auth B], K [auth A], KA [auth B], L [auth A], LA [auth B], M [auth A], MA [auth B], N [auth A], NA [auth B], O [auth A], OA [auth B], P [auth A], PA [auth B], Q [auth A], QA [auth B], RA [auth B], SA [auth B], TA [auth B], X [auth A], Y [auth A], Z [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain AB [auth B] Focus chain C [auth A] Focus chain CA [auth A] Focus chain CB [auth B] Focus chain D [auth A] Focus chain DA [auth A] Focus chain EB [auth B] Focus chain F [auth A] Focus chain FB [auth B] Focus chain GA [auth B] Focus chain H [auth A] Focus chain HB [auth B] Focus chain I [auth A] Focus chain IA [auth B] Focus chain IB [auth B] Focus chain J [auth A] Focus chain JA [auth B] Focus chain K [auth A] Focus chain KA [auth B] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain NA [auth B] 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 RA [auth B] Focus chain SA [auth B] Focus chain TA [auth B] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain AB [auth B] Focus chain C [auth A] Focus chain CA [auth A] Focus chain CB [auth B] Focus chain D [auth A] Focus chain DA [auth A] Focus chain EB [auth B] Focus chain F [auth A] Focus chain FB [auth B] Focus chain GA [auth B] Focus chain H [auth A] Focus chain HB [auth B] Focus chain I [auth A] Focus chain IA [auth B] Focus chain IB [auth B] Focus chain J [auth A] Focus chain JA [auth B] Focus chain K [auth A] Focus chain KA [auth B] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain NA [auth B] 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 RA [auth B] Focus chain SA [auth B] Focus chain TA [auth B] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain ZA [auth B] SDF format, chain YA [auth B] SDF format, chain R [auth A] SDF format, chain GB [auth B] SDF format, chain FA [auth A] SDF format, chain EA [auth A] SDF format, chain E [auth A] MOL2 format, chain ZA [auth B] MOL2 format, chain YA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain GB [auth B] MOL2 format, chain FA [auth A] MOL2 format, chain EA [auth A] MOL2 format, chain E [auth A] mmCIF format, chain ZA [auth B] mmCIF format, chain YA [auth B] mmCIF format, chain R [auth A] mmCIF format, chain GB [auth B] mmCIF format, chain FA [auth A] mmCIF format, chain EA [auth A] mmCIF format, chain E [auth A]	E [auth A] EA [auth A] FA [auth A] GB [auth B] R [auth A] E [auth A], EA [auth A], FA [auth A], GB [auth B], R [auth A], YA [auth B], ZA [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain EA [auth A] Focus chain FA [auth A] Focus chain GB [auth B] Focus chain R [auth A] Focus chain YA [auth B] Focus chain ZA [auth B] Interactions & Density Focus chain E [auth A] Focus chain EA [auth A] Focus chain FA [auth A] Focus chain GB [auth B] Focus chain R [auth A] Focus chain YA [auth B] Focus chain ZA [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.232 (Depositor), 0.233 (DCC)
R-Value Work: 0.169 (Depositor), 0.170 (DCC)
R-Value Observed: 0.172 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.447	α = 90
b = 115.504	β = 115.99
c = 97.705	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2009-03-17

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-03-17
Type: Initial release
Version 1.1: 2013-09-25
Changes: Database references, Derived calculations, Non-polymer description, Other, Version format compliance
Version 1.2: 2014-04-02
Changes: Database references
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Derived calculations, Other, Structure summary
Version 1.4: 2023-12-13
Changes: Advisory, Data collection, Database references, Refinement description, Structure summary