6IYG | pdb_00006iyg

The Structure of Maltooligosaccharide-forming Amylase from Pseudomonas saccharophila STB07 with Maltotetraose

PDB DOI: https://doi.org/10.2210/pdb6IYG/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Roseateles saccharophilus
Expression System: Bacillus subtilis
Mutation(s): No

Deposited: 2018-12-15 Released: 2019-12-18
Deposition Author(s): Li, Z.F., Ban, X.F., Zhang, Z.Q., Li, C.M., Gu, Z.B., Jin, T.C., Li, Y.L., Shang, Y.H.
Funding Organization(s): National Natural Science Foundation of China

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.186 (Depositor), 0.170 (DCC)
R-Value Work:
0.167 (Depositor), 0.170 (DCC)
R-Value Observed:
0.168 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Maltotetraose-forming amylase from Pseudomonas saccharophila STB07

Zhang, Z.Q., Ban, X.F., Li, Z.F., Jin, T.C., Li, Y.L., Gu, Z.B., Li, C.M., Shang, Y.H.

To be published.

Macromolecule Content

Total Structure Weight: 59.43 kDa
Atom Count: 3,679
Modeled Residue Count: 415
Deposited Residue Count: 536
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucan 1,4-alpha-maltotetraohydrolase	A	536	Roseateles saccharophilus	Mutation(s): 0 Gene Names: mta EC: 3.2.1.60
UniProt
Find proteins for P22963 (Roseateles saccharophilus) Explore P22963 Go to UniProtKB: P22963
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P22963
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	B	4		N/A	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G87171PZ GlyCosmos: G87171PZ GlyGen: G87171PZ

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	D [auth A], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900010 Query on PRD_900010	B	alpha-maltotetraose	Oligosaccharide / Substrate analog		Interactions Focus chain B Interactions & Density Focus chain B

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.186 (Depositor), 0.170 (DCC)
R-Value Work: 0.167 (Depositor), 0.170 (DCC)
R-Value Observed: 0.168 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.28	α = 90
b = 64.57	β = 90
c = 168.91	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2019-12-18

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31722040
National Natural Science Foundation of China	China	31571882

Revision History (Full details and data files)

Version 1.0: 2019-12-18
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2023-11-22
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.2: 2024-11-13
Changes: Structure summary