3FVT

Crystal Structure of Acetyl Xylan Esterase from Bacillus pumilus, monoclinic crystal form II

PDB DOI: https://doi.org/10.2210/pdb3FVT/pdb

Classification: HYDROLASE
Organism(s): Bacillus pumilus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-01-16 Released: 2010-01-05
Deposition Author(s): Krastanova, I., Cassetta, A., Lamba, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.264
R-Value Work: 0.211
R-Value Observed: 0.211

wwPDB Validation 3D Report Full Report

This is version 1.3 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: 434.41 kDa
Atom Count: 33,650
Modelled Residue Count: 3,808
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): 0 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
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain U [auth E] SDF format, chain Z [auth G] MOL2 format, chain U [auth E] MOL2 format, chain Z [auth G]	U [auth E], Z [auth G]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain U [auth E] Focus chain Z [auth G] Interactions & Density Focus chain U [auth E] Focus chain Z [auth G]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AA [auth G] SDF format, chain BA [auth G] SDF format, chain CA [auth H] SDF format, chain DA [auth H] SDF format, chain EA [auth I] SDF format, chain FA [auth I] SDF format, chain GA [auth L] SDF format, chain HA [auth L] SDF format, chain IA [auth M] SDF format, chain JA [auth M] SDF format, chain KA [auth N] SDF format, chain LA [auth N] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain S [auth D] SDF format, chain T [auth D] SDF format, chain V [auth E] SDF format, chain W [auth E] SDF format, chain X [auth F] SDF format, chain Y [auth F] MOL2 format, chain AA [auth G] MOL2 format, chain BA [auth G] MOL2 format, chain CA [auth H] MOL2 format, chain DA [auth H] MOL2 format, chain EA [auth I] MOL2 format, chain FA [auth I] MOL2 format, chain GA [auth L] MOL2 format, chain HA [auth L] MOL2 format, chain IA [auth M] MOL2 format, chain JA [auth M] MOL2 format, chain KA [auth N] MOL2 format, chain LA [auth N] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D] MOL2 format, chain V [auth E] MOL2 format, chain W [auth E] MOL2 format, chain X [auth F] MOL2 format, chain Y [auth F]	AA [auth G] BA [auth G] CA [auth H] DA [auth H] EA [auth I] AA [auth G], BA [auth G], CA [auth H], DA [auth H], EA [auth I], FA [auth I], GA [auth L], HA [auth L], IA [auth M], JA [auth M], KA [auth N], LA [auth N], M [auth A], N [auth A], O [auth B], P [auth B], Q [auth C], R [auth C], S [auth D], T [auth D], V [auth E], W [auth E], X [auth F], Y [auth F]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth G] Focus chain BA [auth G] Focus chain CA [auth H] Focus chain DA [auth H] Focus chain EA [auth I] Focus chain FA [auth I] Focus chain GA [auth L] Focus chain HA [auth L] Focus chain IA [auth M] Focus chain JA [auth M] Focus chain KA [auth N] Focus chain LA [auth N] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain V [auth E] Focus chain W [auth E] Focus chain X [auth F] Focus chain Y [auth F] Interactions & Density Focus chain AA [auth G] Focus chain BA [auth G] Focus chain CA [auth H] Focus chain DA [auth H] Focus chain EA [auth I] Focus chain FA [auth I] Focus chain GA [auth L] Focus chain HA [auth L] Focus chain IA [auth M] Focus chain JA [auth M] Focus chain KA [auth N] Focus chain LA [auth N] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain V [auth E] Focus chain W [auth E] Focus chain X [auth F] Focus chain Y [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.264
R-Value Work: 0.211
R-Value Observed: 0.211
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.039	α = 90
b = 87.205	β = 112.87
c = 184.825	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement
PDB_EXTRACT	data extraction
MAR345	data collection

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2010-01-05

Deposition Author(s):

Krastanova, I.

Cassetta, A.

Lamba, D.

Revision History (Full details and data files)

Version 1.0: 2010-01-05
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description