6JHI | pdb_00006jhi

Crystal structure of mutant D470A of Pullulanase from Paenibacillus barengoltzii complexed with maltotetraose

• PDB DOI: https://doi.org/10.2210/pdb6JHI/pdb
• Entry: 6JHI supersedes: 5WWA

• Classification: HYDROLASE
• Organism(s): Paenibacillus barengoltzii
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2019-02-18 Released: 2019-03-06 
• Deposition Author(s): Wu, S.W., Yang, S.Q., Qin, Z., You, X., Huang, P., Jiang, Z.Q.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free: 
  0.210 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.153 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.156 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of mutant D470A of Pullulanase from Paenibacillus barengoltzii complexed with maltotetraose

Wu, S.W., Yang, S.Q., Qin, Z., You, X., Huang, P., Jiang, Z.Q.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 76.32 kDa 
• Atom Count: 5,609 
• Modeled Residue Count: 646 
• Deposited Residue Count: 675 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pulullanase	A	675	Paenibacillus barengoltzii	Mutation(s): 0  EC: 3.2.1.41
UniProt
Find proteins for A0A0C5GWS2 (Paenibacillus barengoltzii) Explore A0A0C5GWS2  Go to UniProtKB:  A0A0C5GWS2

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	B, C, D	2		N/A
Glycosylation Resources
GlyTouCan:  G07411ON GlyCosmos:  G07411ON

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA (Subject of Investigation/LOI)	E [auth A], F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	G [auth A], H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001	B, C, D	alpha-maltose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free:  0.210 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.153 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.156 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.757	α = 90
b = 98.517	β = 90
c = 141.824	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-03-06 
Deposition Author(s): Wu, S.W., Yang, S.Q., Qin, Z., You, X., Huang, P., Jiang, Z.Q.
• This entry supersedes: 5WWA

Revision History  

• Version 1.0: 2019-03-06
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary