4H41 | pdb_00004h41

Crystal structure of a putative alpha-L-fucosidase (BT_0435) from Bacteroides thetaiotaomicron VPI-5482 at 1.80 A resolution

PDB DOI: https://doi.org/10.2210/pdb4H41/pdb

Classification: HYDROLASE
Organism(s): Bacteroides thetaiotaomicron VPI-5482
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-09-14 Released: 2012-10-10
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.158 (Depositor), 0.170 (DCC)
R-Value Work:
0.133 (Depositor), 0.150 (DCC)
R-Value Observed:
0.134 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of a putative alpha-L-fucosidase (BT_0435) from Bacteroides thetaiotaomicron VPI-5482 at 1.80 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 124.16 kDa
Atom Count: 8,985
Modeled Residue Count: 961
Deposited Residue Count: 1,020
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative alpha-L-fucosidase	A, B, C	340	Bacteroides thetaiotaomicron VPI-5482	Mutation(s): 0 Gene Names: BT_0435, NP_809348.1
UniProt
Find proteins for Q8AAM9 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q8AAM9 Go to UniProtKB: Q8AAM9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8AAM9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PE4 Query on PE4 Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A], H [auth A]	2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL C₁₆ H₃₄ O₈ PJWQOENWHPEPKI-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A]
PG6 Query on PG6 Download Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B]	O [auth B], P [auth B]	1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE C₁₂ H₂₆ O₆ DMDPGPKXQDIQQG-UHFFFAOYSA-N		Interactions Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain O [auth B] Focus chain P [auth B]
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain V [auth C] SDF format, chain U [auth C] SDF format, chain R [auth B] SDF format, chain N [auth B] SDF format, chain I [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain V [auth C] MOL2 format, chain U [auth C] MOL2 format, chain R [auth B] MOL2 format, chain N [auth B] MOL2 format, chain I [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain V [auth C] mmCIF format, chain U [auth C] mmCIF format, chain R [auth B] mmCIF format, chain N [auth B] mmCIF format, chain I [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] I [auth A] N [auth B] R [auth B] E [auth A], F [auth A], I [auth A], N [auth B], R [auth B], U [auth C], V [auth C]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain R [auth B] Focus chain U [auth C] Focus chain V [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain R [auth B] Focus chain U [auth C] Focus chain V [auth C]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain W [auth C] SDF format, chain S [auth B] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] MOL2 format, chain W [auth C] MOL2 format, chain S [auth B] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] mmCIF format, chain W [auth C] mmCIF format, chain S [auth B] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A]	J [auth A], K [auth A], L [auth A], S [auth B], W [auth C]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain S [auth B] Focus chain W [auth C] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain S [auth B] Focus chain W [auth C]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain Q [auth B] MOL2 format, chain Q [auth B] mmCIF format, chain Q [auth B]	Q [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain Q [auth B] Interactions & Density Focus chain Q [auth B]
UNL Query on UNL Download Ideal Coordinates CCD File	D [auth A], M [auth B], T [auth C]	Unknown ligand FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain M [auth B] Focus chain T [auth C] Interactions & Density Focus chain D [auth A] Focus chain M [auth B] Focus chain T [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.158 (Depositor), 0.170 (DCC)
R-Value Work: 0.133 (Depositor), 0.150 (DCC)
R-Value Observed: 0.134 (Depositor)

Diffraction Data: https://doi.org/10.18430/M34H41

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.67	α = 90
b = 125.7	β = 103.72
c = 80.01	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
SCALA	data scaling
BUSTER-TNT	refinement
MOSFLM	data reduction
SHELXD	phasing
BUSTER	refinement

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2012-10-10

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2012-10-10
Type: Initial release
Version 1.1: 2012-10-17
Changes: Refinement description
Version 1.2: 2017-10-25
Changes: Author supporting evidence, Refinement description
Version 1.3: 2018-01-24
Changes: Database references
Version 1.4: 2023-02-01
Changes: Database references, Derived calculations
Version 1.5: 2024-10-16
Changes: Data collection, Structure summary