4XHC | pdb_00004xhc

rhamnosidase from Klebsiella oxytoca with rhamnose bound

PDB DOI: https://doi.org/10.2210/pdb4XHC/pdb

Classification: HYDROLASE
Organism(s): Klebsiella oxytoca
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-01-05 Released: 2015-04-15
Deposition Author(s): O'Neill, E.O., Stevenson, C.E.M., Patterson, M.J., Rejzek, M., Chauvin, A., Lawson, D.M., Field, R.A.
Funding Organization(s): Biotechnology and Biological Sciences Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.202 (Depositor), 0.179 (DCC)
R-Value Work:
0.182 (Depositor)
R-Value Observed:
0.183 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

Crystal structure of a novel two domain GH78 family alpha-rhamnosidase from Klebsiella oxytoca with rhamnose bound.

O'Neill, E.C., Stevenson, C.E., Paterson, M.J., Rejzek, M., Chauvin, A.L., Lawson, D.M., Field, R.A.

(2015) Proteins 83: 1742-1749

PubMed: 25846411 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/prot.24807
Primary Citation Related Structures:
4XHC

PubMed Abstract:
The crystal structure of the GH78 family α-rhamnosidase from Klebsiella oxytoca (KoRha) has been determined at 2.7 Å resolution with rhamnose bound in the active site of the catalytic domain. Curiously, the putative catalytic acid, Asp 222, is preceded by an unusual non-proline cis-peptide bond which helps to project the carboxyl group into the active centre. This KoRha homodimeric structure is significantly smaller than those of the other previously determined GH78 structures. Nevertheless, the enzyme displays α-rhamnosidase activity when assayed in vitro, suggesting that the additional structural domains found in the related enzymes are dispensible for function.

Organizational Affiliation

Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, Nr4 7UH, United Kingdom.

Macromolecule Content

Total Structure Weight: 124.13 kDa
Atom Count: 8,333
Modeled Residue Count: 1,026
Deposited Residue Count: 1,086
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-L-rhamnosidase	A, B	543	Klebsiella oxytoca	Mutation(s): 0 Gene Names: KOX_19945 EC: 3.2.1.40
UniProt
Find proteins for A0A0J9X262 (Klebsiella oxytoca) Explore A0A0J9X262 Go to UniProtKB: A0A0J9X262
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0J9X262
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RAM Query on RAM Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain C [auth A]	C [auth A], F [auth B]	alpha-L-rhamnopyranose C₆ H₁₂ O₅ SHZGCJCMOBCMKK-HGVZOGFYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], G [auth B], H [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.202 (Depositor), 0.179 (DCC)
R-Value Work: 0.182 (Depositor)
R-Value Observed: 0.183 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 148.43	α = 90
b = 148.43	β = 90
c = 202.16	γ = 90

Software Package:

Software Name	Purpose
SHELX	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Aimless	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2015-04-15

Deposition Author(s):

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/J004561/1

Revision History (Full details and data files)

Version 1.0: 2015-04-15
Type: Initial release
Version 1.1: 2015-04-22
Changes: Database references
Version 1.2: 2015-09-02
Changes: Database references
Version 2.0: 2017-08-30
Changes: Atomic model, Author supporting evidence
Version 2.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 2.2: 2024-05-08
Changes: Data collection, Database references, Refinement description, Structure summary