3FVR | pdb_00003fvr

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

PDB DOI: https://doi.org/10.2210/pdb3FVR/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: 2.50 Å
R-Value Free:
0.228 (Depositor), 0.228 (DCC)
R-Value Work:
0.184 (Depositor), 0.185 (DCC)
R-Value Observed:
0.184 (Depositor)

Starting Model: experimental
View more details

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: 435.89 kDa
Atom Count: 32,448
Modeled Residue Count: 3,816
Deposited Residue Count: 3,840
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9K5F2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain V [auth D] SDF format, chain IA [auth H] SDF format, chain EA [auth G] MOL2 format, chain V [auth D] MOL2 format, chain IA [auth H] MOL2 format, chain EA [auth G] mmCIF format, chain V [auth D] mmCIF format, chain IA [auth H] mmCIF format, chain EA [auth G]	EA [auth G], IA [auth H], V [auth D]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain EA [auth G] Focus chain IA [auth H] Focus chain V [auth D] Interactions & Density Focus chain EA [auth G] Focus chain IA [auth H] Focus chain V [auth D]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain S [auth C] SDF format, chain BA [auth F] MOL2 format, chain S [auth C] MOL2 format, chain BA [auth F] mmCIF format, chain S [auth C] mmCIF format, chain BA [auth F]	BA [auth F], S [auth C]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain BA [auth F] Focus chain S [auth C] Interactions & Density Focus chain BA [auth F] Focus chain S [auth C]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain SA [auth M] SDF format, chain JA [auth H] SDF format, chain HA [auth H] MOL2 format, chain SA [auth M] MOL2 format, chain JA [auth H] MOL2 format, chain HA [auth H] mmCIF format, chain SA [auth M] mmCIF format, chain JA [auth H] mmCIF format, chain HA [auth H]	HA [auth H], JA [auth H], SA [auth M]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain HA [auth H] Focus chain JA [auth H] Focus chain SA [auth M] Interactions & Density Focus chain HA [auth H] Focus chain JA [auth H] Focus chain SA [auth M]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain R [auth C] SDF format, chain Q [auth C] SDF format, chain PA [auth L] SDF format, chain MA [auth I] SDF format, chain AA [auth F] MOL2 format, chain R [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain PA [auth L] MOL2 format, chain MA [auth I] MOL2 format, chain AA [auth F] mmCIF format, chain R [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain PA [auth L] mmCIF format, chain MA [auth I] mmCIF format, chain AA [auth F]	AA [auth F], MA [auth I], PA [auth L], Q [auth C], R [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain MA [auth I] Focus chain PA [auth L] Focus chain Q [auth C] Focus chain R [auth C] Interactions & Density Focus chain AA [auth F] Focus chain MA [auth I] Focus chain PA [auth L] Focus chain Q [auth C] Focus chain R [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain Z [auth E] SDF format, chain Y [auth E] SDF format, chain X [auth D] SDF format, chain WA [auth N] SDF format, chain W [auth D] SDF format, chain VA [auth N] SDF format, chain UA [auth M] SDF format, chain U [auth C] SDF format, chain TA [auth M] SDF format, chain T [auth C] SDF format, chain RA [auth L] SDF format, chain QA [auth L] SDF format, chain P [auth B] SDF format, chain OA [auth I] SDF format, chain O [auth B] SDF format, chain NA [auth I] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain LA [auth H] SDF format, chain KA [auth H] SDF format, chain GA [auth G] SDF format, chain FA [auth G] SDF format, chain DA [auth F] SDF format, chain CA [auth F] MOL2 format, chain Z [auth E] MOL2 format, chain Y [auth E] MOL2 format, chain X [auth D] MOL2 format, chain WA [auth N] MOL2 format, chain W [auth D] MOL2 format, chain VA [auth N] MOL2 format, chain UA [auth M] MOL2 format, chain U [auth C] MOL2 format, chain TA [auth M] MOL2 format, chain T [auth C] MOL2 format, chain RA [auth L] MOL2 format, chain QA [auth L] MOL2 format, chain P [auth B] MOL2 format, chain OA [auth I] MOL2 format, chain O [auth B] MOL2 format, chain NA [auth I] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain LA [auth H] MOL2 format, chain KA [auth H] MOL2 format, chain GA [auth G] MOL2 format, chain FA [auth G] MOL2 format, chain DA [auth F] MOL2 format, chain CA [auth F] mmCIF format, chain Z [auth E] mmCIF format, chain Y [auth E] mmCIF format, chain X [auth D] mmCIF format, chain WA [auth N] mmCIF format, chain W [auth D] mmCIF format, chain VA [auth N] mmCIF format, chain UA [auth M] mmCIF format, chain U [auth C] mmCIF format, chain TA [auth M] mmCIF format, chain T [auth C] mmCIF format, chain RA [auth L] mmCIF format, chain QA [auth L] mmCIF format, chain P [auth B] mmCIF format, chain OA [auth I] mmCIF format, chain O [auth B] mmCIF format, chain NA [auth I] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain LA [auth H] mmCIF format, chain KA [auth H] mmCIF format, chain GA [auth G] mmCIF format, chain FA [auth G] mmCIF format, chain DA [auth F] mmCIF format, chain CA [auth F]	CA [auth F] DA [auth F] FA [auth G] GA [auth G] KA [auth H] CA [auth F], DA [auth F], FA [auth G], GA [auth G], KA [auth H], LA [auth H], M [auth A], N [auth A], NA [auth I], O [auth B], OA [auth I], P [auth B], QA [auth L], RA [auth L], T [auth C], TA [auth M], U [auth C], UA [auth M], VA [auth N], W [auth D], WA [auth N], X [auth D], Y [auth E], Z [auth E]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain CA [auth F] Focus chain DA [auth F] Focus chain FA [auth G] Focus chain GA [auth G] Focus chain KA [auth H] Focus chain LA [auth H] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth I] Focus chain O [auth B] Focus chain OA [auth I] Focus chain P [auth B] Focus chain QA [auth L] Focus chain RA [auth L] Focus chain T [auth C] Focus chain TA [auth M] Focus chain U [auth C] Focus chain UA [auth M] Focus chain VA [auth N] Focus chain W [auth D] Focus chain WA [auth N] Focus chain X [auth D] Focus chain Y [auth E] Focus chain Z [auth E] Interactions & Density Focus chain CA [auth F] Focus chain DA [auth F] Focus chain FA [auth G] Focus chain GA [auth G] Focus chain KA [auth H] Focus chain LA [auth H] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth I] Focus chain O [auth B] Focus chain OA [auth I] Focus chain P [auth B] Focus chain QA [auth L] Focus chain RA [auth L] Focus chain T [auth C] Focus chain TA [auth M] Focus chain U [auth C] Focus chain UA [auth M] Focus chain VA [auth N] Focus chain W [auth D] Focus chain WA [auth N] Focus chain X [auth D] Focus chain Y [auth E] Focus chain Z [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.228 (Depositor), 0.228 (DCC)
R-Value Work: 0.184 (Depositor), 0.185 (DCC)
R-Value Observed: 0.184 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.485	α = 90
b = 167.686	β = 91.35
c = 144.961	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

View more in-depth experimental data

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