5X3K | pdb_00005x3k

Kfla1895 D451A mutant in complex with isomaltose

• PDB DOI: https://doi.org/10.2210/pdb5X3K/pdb

• Classification: HYDROLASE
• Organism(s): Kribbella flavida DSM 17836
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-02-06 Released: 2018-02-07 
• Deposition Author(s): Tanaka, Y., Chen, M., Tagami, T., Yao, M., Kimura, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.216 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Literature

Glycoside hydrolase mutant in complex with product

Tanaka, Y., Chen, M., Tagami, T., Yao, M., Kimura, A.

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 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 166.55 kDa 
• Atom Count: 11,886 
• Modeled Residue Count: 1,417 
• Deposited Residue Count: 1,486 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoside hydrolase family 31	A, B	743	Kribbella flavida DSM 17836	Mutation(s): 1  Gene Names: Kfla_1895 EC: 3.2.1.204
UniProt
Find proteins for D2PPM7 (Kribbella flavida (strain DSM 17836 / JCM 10339 / NBRC 14399)) Explore D2PPM7  Go to UniProtKB:  D2PPM7

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose	C	3		N/A
Glycosylation Resources
GlyTouCan:  G69864PN GlyCosmos:  G69864PN

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose	D	2		N/A
Glycosylation Resources
GlyTouCan:  G69864PN GlyCosmos:  G69864PN

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], Q [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	N [auth A], O [auth A], P [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.216 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 180.584	α = 90
b = 180.584	β = 90
c = 392.291	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-02-07 
Deposition Author(s): Tanaka, Y., Chen, M., Tagami, T., Yao, M., Kimura, A.

Revision History  

• Version 1.0: 2018-02-07
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-03-27
  Changes: Data collection, Database references, Structure summary