3WDJ | pdb_00003wdj

Crystal structure of Pullulanase complexed with maltotetraose from Anoxybacillus sp. LM18-11

PDB DOI: https://doi.org/10.2210/pdb3WDJ/pdb

Classification: HYDROLASE
Organism(s): Anoxybacillus sp. LM18-11
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-06-18 Released: 2014-04-30
Deposition Author(s): Xu, J., Ren, F., Huang, C.H., Zheng, Y., Zhen, J., Ko, T.P., Chen, C.C., Chan, H.C., Guo, R.T., Ma, Y., Song, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.22 Å
R-Value Free:
0.217 (Depositor), 0.227 (DCC)
R-Value Work:
0.181 (Depositor), 0.198 (DCC)
R-Value Observed:
0.181 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Cloning, Expression, Functional and Structural Studies of Pullulanase from Anoxybacillus sp. LM18-11

Xu, J., Ren, F., Huang, C.H., Zheng, Y., Zhen, J., Chen, C.C., Chan, H.C., Guo, R.T., Ma, Y., Song, H.

To be published.

Macromolecule Content

Total Structure Weight: 84.88 kDa
Atom Count: 6,412
Modeled Residue Count: 683
Deposited Residue Count: 710
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Type I pullulanase	A	710	Anoxybacillus sp. LM18-11	Mutation(s): 0 Gene Names: pulA EC: 3.2.1.41
UniProt
Find proteins for K9L0H1 (Anoxybacillus sp. LM18-11) Explore K9L0H1 Go to UniProtKB: K9L0H1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	K9L0H1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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

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 F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [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, C, D, E	alpha-maltotetraose	Oligosaccharide / Substrate analog		Interactions Focus chain B Focus chain C Focus chain D Focus chain E Interactions & Density Focus chain B Focus chain C Focus chain D Focus chain E

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.22 Å
R-Value Free: 0.217 (Depositor), 0.227 (DCC)
R-Value Work: 0.181 (Depositor), 0.198 (DCC)
R-Value Observed: 0.181 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.971	α = 90
b = 65.929	β = 90
c = 90.921	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-04-30

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-04-30
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2023-11-08
Changes: Data collection, Database references, Refinement description, Structure summary