3FYT | pdb_00003fyt

Crystal structure of Bacillus pumilus acetyl xylan esterase S181A mutant in complex with beta-D-xylopyranose

• PDB DOI: https://doi.org/10.2210/pdb3FYT/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus pumilus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-01-23 Released: 2010-01-26 
• Deposition Author(s): Krastanova, I., Cassetta, A., Lamba, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.58 Å
• R-Value Free: 
  0.241 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Structural and functional studies of Bacillus pumilus acetyl xylan esterase

Krastanova, I., Cassetta, A., Mastihubova, M., Biely, P., Lamba, D.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Biological Assembly 2  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content 

• Total Structure Weight: 435.29 kDa 
• Atom Count: 30,500 
• Modeled Residue Count: 3,761 
• Deposited Residue Count: 3,840 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetyl xylan esterase	A, B, C, D, E, F, G, H, I, J [auth L], K [auth M], L [auth N]	320	Bacillus pumilus	Mutation(s): 1  Gene Names: axe EC: 3.1.1.6
UniProt
Find proteins for Q9K5F2 (Bacillus pumilus) Explore Q9K5F2  Go to UniProtKB:  Q9K5F2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XYP	AA [auth E], DA [auth F], JA [auth H], QA [auth L], S [auth C], T [auth C]	beta-D-xylopyranose C5 H10 O5 SRBFZHDQGSBBOR-KKQCNMDGSA-N
CL	BA [auth E], CA [auth E], EA [auth F], FA [auth F], GA [auth F], HA [auth G], IA [auth G], KA [auth H], LA [auth H], M [auth A], MA [auth H], N [auth A], NA [auth I], O [auth A], OA [auth I], P [auth B], PA [auth I], Q [auth B], R [auth B], RA [auth L], SA [auth L], TA [auth L], U [auth C], UA [auth M], V [auth C], VA [auth M], W [auth C], WA [auth M], X [auth D], XA [auth N], Y [auth D], YA [auth N], Z [auth D], ZA [auth N]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.58 Å
• R-Value Free:  0.241 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.186	α = 90
b = 167.986	β = 91.17
c = 144.471	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement
PDB_EXTRACT	data extraction
ProDC	data collection
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-01-26 
Deposition Author(s): Krastanova, I., Cassetta, A., Lamba, D.

Revision History  

• Version 1.0: 2010-01-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2021-10-20
  Changes: Database references, Structure summary
• Version 2.2: 2023-09-06
  Changes: Data collection, Refinement description