3A47 | pdb_00003a47

Crystal structure of isomaltase from Saccharomyces cerevisiae

PDB DOI: https://doi.org/10.2210/pdb3A47/pdb

Classification: HYDROLASE
Organism(s): Saccharomyces cerevisiae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-07-01 Released: 2010-07-14
Deposition Author(s): Yamamoto, K., Miyake, H., Kusunoki, M., Osaki, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.59 Å
R-Value Free:
0.197 (Depositor), 0.230 (DCC)
R-Value Work:
0.175 (Depositor)
R-Value Observed:
0.176 (Depositor)

Starting Model: experimental
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This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of isomaltase from Saccharomyces cerevisiae

Yamamoto, K., Miyake, H., Kusunoki, M., Osaki, S.

To be published.

Macromolecule Content

Total Structure Weight: 68.72 kDa
Atom Count: 5,330
Modeled Residue Count: 586
Deposited Residue Count: 589
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oligo-1,6-glucosidase	A	589	Saccharomyces cerevisiae	Mutation(s): 0 EC: 3.2.1.10
UniProt
Find proteins for P53051 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53051 Go to UniProtKB: P53051
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P53051
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.59 Å
R-Value Free: 0.197 (Depositor), 0.230 (DCC)
R-Value Work: 0.175 (Depositor)
R-Value Observed: 0.176 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.709	α = 90
b = 115.674	β = 91.33
c = 61.837	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-07-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-07-14
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.