7CPL | pdb_00007cpl

Xylanase R from Bacillus sp. TAR-1

• PDB DOI: https://doi.org/10.2210/pdb7CPL/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus sp. TAR1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2020-08-07 Released: 2020-09-02 
• Deposition Author(s): Kuwata, K., Suzuki, M., Takita, T., Nakatani, K., Li, T., Katano, Y., Kojima, K., Mizutani, K., Mikami, B., Yatsunami, R., Nakamura, S., Yasukawa, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free: 
  0.172 (Depositor), 0.172 (DCC) 
• R-Value Work: 
  0.134 (Depositor), 0.136 (DCC) 
• R-Value Observed: 
  0.136 (Depositor) 

Starting Model: experimental

Literature

Insight into the mechanism of thermostabilization of GH10 xylanase from Bacillus sp. strain TAR-1 by the mutation of S92 to E.

Suzuki, M., Takita, T., Kuwata, K., Nakatani, K., Li, T., Katano, Y., Kojima, K., Mizutani, K., Mikami, B., Yatsunami, R., Nakamura, S., Yasukawa, K.

(2021) Biosci Biotechnol Biochem 85: 386-390

• PubMed: 33604642 
• DOI: https://doi.org/10.1093/bbb/zbaa003
• Primary Citation Related Structures: 
  7CPK, 7CPL


• PubMed Abstract: 
  

  The mechanism of thermostabilization of GH10 xylanase, XynR, from Bacillus sp. strain TAR-1 by the mutation of S92 to E was investigated. Thermodynamic analysis revealed that thermostabilization was driven by the decrease in entropy change of activation for thermal inactivation. Crystallographic analysis suggested that this mutation suppressed the fluctuation of the amino acid residues at position 92-95.

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Organizational Affiliation: 
• Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.
Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.
Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.
Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.
Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta, Midori-ku, Yokohama 226-8501, Japan.
National Institute of Technology, Numazu College, Ooka, Numazu, Shizuoka 410-8501, Japan.

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: 43.18 kDa 
• Atom Count: 3,474 
• Modeled Residue Count: 358 
• Deposited Residue Count: 360 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endo-1,4-beta-xylanase A	A	360	Bacillus sp. TAR1	Mutation(s): 1  Gene Names: xynA, BH2120 EC: 3.2.1.8
UniProt
Find proteins for P07528 (Halalkalibacterium halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)) Explore P07528  Go to UniProtKB:  P07528

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
NI	M [auth A], N [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
CA	I [auth A], J [auth A], K [auth A], L [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free:  0.172 (Depositor), 0.172 (DCC) 
• R-Value Work:  0.134 (Depositor), 0.136 (DCC) 
• R-Value Observed: 0.136 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.085	α = 90
b = 53.897	β = 90
c = 127.413	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-09-02 
Deposition Author(s): Kuwata, K., Suzuki, M., Takita, T., Nakatani, K., Li, T., Katano, Y., Kojima, K., Mizutani, K., Mikami, B., Yatsunami, R., Nakamura, S., Yasukawa, K.

Revision History  

• Version 1.0: 2020-09-02
  Type: Initial release
  
• Version 1.1: 2021-03-24
  Changes: Database references, Structure summary
• Version 1.2: 2023-11-29
  Changes: Data collection, Database references, Refinement description