3FYT

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.58 Å
R-Value Free: 0.241
R-Value Work: 0.188
R-Value Observed: 0.188

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

Structural and functional studies of Bacillus pumilus acetyl xylan esterase

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

To be published.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetyl xylan esterase	A B C D E 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9K5F2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
XYP Query on XYP Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain DA [auth F] SDF format, chain JA [auth H] SDF format, chain QA [auth L] SDF format, chain S [auth C] SDF format, chain T [auth C] MOL2 format, chain AA [auth E] MOL2 format, chain DA [auth F] MOL2 format, chain JA [auth H] MOL2 format, chain QA [auth L] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C]	AA [auth E] DA [auth F] JA [auth H] QA [auth L] S [auth C] 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		Interactions Focus chain AA [auth E] Focus chain DA [auth F] Focus chain JA [auth H] Focus chain QA [auth L] Focus chain S [auth C] Focus chain T [auth C] Interactions & Density Focus chain AA [auth E] Focus chain DA [auth F] Focus chain JA [auth H] Focus chain QA [auth L] Focus chain S [auth C] Focus chain T [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain CA [auth E] SDF format, chain EA [auth F] SDF format, chain FA [auth F] SDF format, chain GA [auth F] SDF format, chain HA [auth G] SDF format, chain IA [auth G] SDF format, chain KA [auth H] SDF format, chain LA [auth H] SDF format, chain M [auth A] SDF format, chain MA [auth H] SDF format, chain N [auth A] SDF format, chain NA [auth I] SDF format, chain O [auth A] SDF format, chain OA [auth I] SDF format, chain P [auth B] SDF format, chain PA [auth I] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain RA [auth L] SDF format, chain SA [auth L] SDF format, chain TA [auth L] SDF format, chain U [auth C] SDF format, chain UA [auth M] SDF format, chain V [auth C] SDF format, chain VA [auth M] SDF format, chain W [auth C] SDF format, chain WA [auth M] SDF format, chain X [auth D] SDF format, chain XA [auth N] SDF format, chain Y [auth D] SDF format, chain YA [auth N] SDF format, chain Z [auth D] SDF format, chain ZA [auth N] MOL2 format, chain BA [auth E] MOL2 format, chain CA [auth E] MOL2 format, chain EA [auth F] MOL2 format, chain FA [auth F] MOL2 format, chain GA [auth F] MOL2 format, chain HA [auth G] MOL2 format, chain IA [auth G] MOL2 format, chain KA [auth H] MOL2 format, chain LA [auth H] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth H] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth I] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth I] MOL2 format, chain P [auth B] MOL2 format, chain PA [auth I] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain RA [auth L] MOL2 format, chain SA [auth L] MOL2 format, chain TA [auth L] MOL2 format, chain U [auth C] MOL2 format, chain UA [auth M] MOL2 format, chain V [auth C] MOL2 format, chain VA [auth M] MOL2 format, chain W [auth C] MOL2 format, chain WA [auth M] MOL2 format, chain X [auth D] MOL2 format, chain XA [auth N] MOL2 format, chain Y [auth D] MOL2 format, chain YA [auth N] MOL2 format, chain Z [auth D] MOL2 format, chain ZA [auth N]	BA [auth E] CA [auth E] EA [auth F] FA [auth F] GA [auth F] 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		Interactions Focus chain BA [auth E] Focus chain CA [auth E] Focus chain EA [auth F] Focus chain FA [auth F] Focus chain GA [auth F] Focus chain HA [auth G] Focus chain IA [auth G] Focus chain KA [auth H] Focus chain LA [auth H] Focus chain M [auth A] Focus chain MA [auth H] Focus chain N [auth A] Focus chain NA [auth I] Focus chain O [auth A] Focus chain OA [auth I] Focus chain P [auth B] Focus chain PA [auth I] Focus chain Q [auth B] Focus chain R [auth B] Focus chain RA [auth L] Focus chain SA [auth L] Focus chain TA [auth L] Focus chain U [auth C] Focus chain UA [auth M] Focus chain V [auth C] Focus chain VA [auth M] Focus chain W [auth C] Focus chain WA [auth M] Focus chain X [auth D] Focus chain XA [auth N] Focus chain Y [auth D] Focus chain YA [auth N] Focus chain Z [auth D] Focus chain ZA [auth N] Interactions & Density Focus chain BA [auth E] Focus chain CA [auth E] Focus chain EA [auth F] Focus chain FA [auth F] Focus chain GA [auth F] Focus chain HA [auth G] Focus chain IA [auth G] Focus chain KA [auth H] Focus chain LA [auth H] Focus chain M [auth A] Focus chain MA [auth H] Focus chain N [auth A] Focus chain NA [auth I] Focus chain O [auth A] Focus chain OA [auth I] Focus chain P [auth B] Focus chain PA [auth I] Focus chain Q [auth B] Focus chain R [auth B] Focus chain RA [auth L] Focus chain SA [auth L] Focus chain TA [auth L] Focus chain U [auth C] Focus chain UA [auth M] Focus chain V [auth C] Focus chain VA [auth M] Focus chain W [auth C] Focus chain WA [auth M] Focus chain X [auth D] Focus chain XA [auth N] Focus chain Y [auth D] Focus chain YA [auth N] Focus chain Z [auth D] Focus chain ZA [auth N]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.58 Å
R-Value Free: 0.241
R-Value Work: 0.188
R-Value Observed: 0.188
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

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-01-26

Deposition Author(s):

Krastanova, I.

Cassetta, A.

Lamba, D.

Revision History (Full details and data files)

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