3LDR | pdb_00003ldr

Crystal structure of fructosyltransferase (D191A) from A. japonicus in complex with 1-Kestose

PDB DOI: https://doi.org/10.2210/pdb3LDR/pdb

Classification: HYDROLASE
Organism(s): Aspergillus japonicus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-01-13 Released: 2010-05-12
Deposition Author(s): Chuankhayan, P., Chen, C.J., Chiang, C.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.255 (Depositor)
R-Value Work:
0.215 (Depositor), 0.231 (DCC)
R-Value Observed:
0.220 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3LDR

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

Literature

Crystal structure of Aspergillus japonicus fructosyltransferase complex with donor/acceptor substrates reveal complete sbusites in the active site for catalysis

Chuankhayan, P., Hsieh, C.Y., Huang, Y.C., Hsieh, Y.Y., Guan, H.H., Hsieh, Y.C., Tien, Y.C., Chen, C.D., Chaing, C.M., Chen, C.J.

To be published.

Macromolecule Content

Total Structure Weight: 69.45 kDa
Atom Count: 5,148
Modeled Residue Count: 634
Deposited Residue Count: 634
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fructosyltransferase	A	634	Aspergillus japonicus	Mutation(s): 0
UniProt
Find proteins for Q1W3Z7 (Aspergillus japonicus) Explore Q1W3Z7 Go to UniProtKB: Q1W3Z7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q1W3Z7
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-fructofuranose-(2-1)-beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	B	3		N/A	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G11260CN GlyCosmos: G11260CN

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900029 Query on PRD_900029	B	1-kestose	Oligosaccharide / Nutrient		Interactions Focus chain B Interactions & Density Focus chain B

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.255 (Depositor)
R-Value Work: 0.215 (Depositor), 0.231 (DCC)
R-Value Observed: 0.220 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.076	α = 90
b = 110.431	β = 90
c = 65.881	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-05-12

Deposition Author(s):

Chuankhayan, P.

Revision History (Full details and data files)

Version 1.0: 2010-05-12
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2011-08-24
Changes: Non-polymer description
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2024-03-20
Changes: Data collection, Database references, Structure summary

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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.