1ODZ | pdb_00001odz

Expansion of the glycosynthase repertoire to produce defined manno-oligosaccharides

PDB DOI: https://doi.org/10.2210/pdb1ODZ/pdb

Classification: HYDROLASE
Organism(s): Cellvibrio japonicus
Expression System: Escherichia coli BL21
Mutation(s): Yes

Deposited: 2003-03-17 Released: 2003-07-10
Deposition Author(s): Jahn, M., Stoll, D., Warren, R.A.J., Szabo, L., Singh, P., Gilbert, H.J., Ducros, V.M.A., Davies, G.J., Withers, S.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.177 (Depositor), 0.188 (DCC)
R-Value Work:
0.151 (Depositor), 0.162 (DCC)
R-Value Observed:
0.152 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Expansion of the Glycosynthase Repertoire to Produce Defined Manno-Oligosaccharides

Jahn, M., Stoll, D., Warren, R.A.J., Szabo, L., Singh, P., Gilbert, H.J., Ducros, V.M.A., Davies, G.J., Withers, S.G.

(2003) Chem Commun (Camb) 12: 1327-1329

PubMed: 12841226 Search on PubMed
DOI: https://doi.org/10.1039/b302380j
Primary Citation Related Structures:
1ODZ

PubMed Abstract:
Mutant endo-mannanases, in which the catalytic nucleophile has been replaced, function as glycosynthases in the synthesis of manno-oligosaccharides of defined lengths.

Organizational Affiliation

Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada.

Macromolecule Content

Total Structure Weight: 88.46 kDa
Atom Count: 7,200
Modeled Residue Count: 758
Deposited Residue Count: 772
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mannan endo-1,4-beta-mannosidase	A, B	386	Cellvibrio japonicus	Mutation(s): 1 Gene Names: manA, man26A, CJA_2770 EC: 3.2.1.78
UniProt
Find proteins for P49424 (Cellvibrio japonicus (strain Ueda107)) Explore P49424 Go to UniProtKB: P49424
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P49424
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-alpha-D-mannopyranose	C, D	2		N/A	Interactions Focus chain C Focus chain D Interactions & Density Focus chain C Focus chain D
Glycosylation Resources
GlyTouCan: G78926JO GlyCosmos: G78926JO GlyGen: G78926JO

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A]	F [auth A], I [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain F [auth A] Focus chain I [auth B] Interactions & Density Focus chain F [auth A] Focus chain I [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain G [auth A]	G [auth A], J [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Interactions & Density Focus chain G [auth A] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.177 (Depositor), 0.188 (DCC)
R-Value Work: 0.151 (Depositor), 0.162 (DCC)
R-Value Observed: 0.152 (Depositor)

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.855	α = 90
b = 131.855	β = 90
c = 54.268	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2003-07-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2003-07-10
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2018-06-20
Changes: Data collection, Database references, Source and taxonomy, Structure summary
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
Version 2.1: 2023-12-13
Changes: Data collection, Database references, Refinement description, Structure summary