2YHG

Ab initio phasing of a nucleoside hydrolase-related hypothetical protein from Saccharophagus degradans that is associated with carbohydrate metabolism

PDB DOI: https://doi.org/10.2210/pdb2YHG/pdb

Classification: HYDROLASE
Organism(s): Saccharophagus degradans 2-40
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-04-30 Released: 2011-08-03
Deposition Author(s): Hehemann, J.H., Marsters, C., Boraston, A.B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.08 Å
R-Value Free: 0.151
R-Value Work: 0.133
R-Value Observed: 0.134

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Ab initio phasing of a nucleoside hydrolase-related hypothetical protein from Saccharophagus degradans that is associated with carbohydrate metabolism.

Hehemann, J.H., Marsters, C., Boraston, A.B.

(2011) Proteins 79: 2992-2998

PubMed: 21905122 Search on PubMed
DOI: https://doi.org/10.1002/prot.23126
Primary Citation of Related Structures:
2YHG

Organizational Affiliation

Biochemistry & Microbiology, University of Victoria, Victoria, BC, Canada.

Macromolecule Content

Total Structure Weight: 48.26 kDa
Atom Count: 3,729
Modelled Residue Count: 411
Deposited Residue Count: 437
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CELLULOSE-BINDING PROTEIN	A	437	Saccharophagus degradans 2-40	Mutation(s): 0
UniProt
Find proteins for Q21PD3 (Saccharophagus degradans (strain 2-40 / ATCC 43961 / DSM 17024)) Explore Q21PD3 Go to UniProtKB: Q21PD3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q21PD3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BTB Query on BTB Download Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A] mmCIF format, chain M [auth A]	M [auth A]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₈ H₁₉ N O₅ OWMVSZAMULFTJU-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A]	J [auth A], K [auth A], L [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain D [auth A] MOL2 format, chain B [auth A] MOL2 format, chain D [auth A] mmCIF format, chain B [auth A] mmCIF format, chain D [auth A]	B [auth A], D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain D [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain H [auth A] MOL2 format, chain C [auth A] MOL2 format, chain H [auth A] mmCIF format, chain C [auth A] mmCIF format, chain H [auth A]	C [auth A], H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain H [auth A] Interactions & Density Focus chain C [auth A] Focus chain H [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	E [auth A], F [auth A], G [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.08 Å
R-Value Free: 0.151
R-Value Work: 0.133
R-Value Observed: 0.134
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.58	α = 90
b = 61.58	β = 90
c = 125.46	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
ACORN	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-08-03

Deposition Author(s):

Hehemann, J.H.

Marsters, C.

Boraston, A.B.

Revision History (Full details and data files)

Version 1.0: 2011-08-03
Type: Initial release
Version 1.1: 2011-09-21
Changes: Database references
Version 1.2: 2018-06-13
Changes: Advisory, Data collection, Database references