3EU8

Crystal structure of putative glucoamylase (YP_210071.1) from Bacteroides fragilis NCTC 9343 at 2.12 A resolution

PDB DOI: https://doi.org/10.2210/pdb3EU8/pdb

Classification: HYDROLASE
Organism(s): Bacteroides fragilis NCTC 9343
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-10-09 Released: 2008-10-21
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free: 0.213
R-Value Work: 0.158
R-Value Observed: 0.161

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of putative glucoamylase (YP_210071.1) from Bacteroides fragilis NCTC 9343 at 2.12 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 202.17 kDa
Atom Count: 15,148
Modelled Residue Count: 1,688
Deposited Residue Count: 1,720
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 glucoamylase	A, B, C, D	430	Bacteroides fragilis NCTC 9343	Mutation(s): 0 Gene Names: YP_210071.1, BF0338
UniProt
Find proteins for Q5LIB7 (Bacteroides fragilis (strain ATCC 25285 / DSM 2151 / CCUG 4856 / JCM 11019 / NCTC 9343 / Onslow)) Explore Q5LIB7 Go to UniProtKB: Q5LIB7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5LIB7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain AB [auth B] SDF format, chain AC [auth C] SDF format, chain BA [auth A] SDF format, chain BB [auth B] SDF format, chain CA [auth A] SDF format, chain CB [auth B] SDF format, chain CC [auth D] SDF format, chain DA [auth A] SDF format, chain DB [auth B] SDF format, chain DC [auth D] SDF format, chain EA [auth A] SDF format, chain EB [auth B] SDF format, chain EC [auth D] SDF format, chain F [auth A] SDF format, chain FA [auth A] SDF format, chain FB [auth B] SDF format, chain FC [auth D] SDF format, chain G [auth A] SDF format, chain GA [auth A] SDF format, chain GB [auth B] SDF format, chain GC [auth D] SDF format, chain H [auth A] SDF format, chain HA [auth A] SDF format, chain HC [auth D] SDF format, chain I [auth A] SDF format, chain IA [auth A] SDF format, chain IC [auth D] SDF format, chain J [auth A] SDF format, chain JA [auth A] SDF format, chain JB [auth C] SDF format, chain JC [auth D] SDF format, chain K [auth A] SDF format, chain KB [auth C] SDF format, chain KC [auth D] SDF format, chain L [auth A] SDF format, chain LB [auth C] SDF format, chain LC [auth D] SDF format, chain M [auth A] SDF format, chain MA [auth B] SDF format, chain MB [auth C] SDF format, chain MC [auth D] SDF format, chain N [auth A] SDF format, chain NA [auth B] SDF format, chain NB [auth C] SDF format, chain NC [auth D] SDF format, chain O [auth A] SDF format, chain OA [auth B] SDF format, chain OB [auth C] SDF format, chain OC [auth D] SDF format, chain P [auth A] SDF format, chain PA [auth B] SDF format, chain PB [auth C] SDF format, chain PC [auth D] SDF format, chain Q [auth A] SDF format, chain QA [auth B] SDF format, chain QB [auth C] SDF format, chain R [auth A] SDF format, chain RA [auth B] SDF format, chain RB [auth C] SDF format, chain S [auth A] SDF format, chain SA [auth B] SDF format, chain SB [auth C] SDF format, chain T [auth A] SDF format, chain TA [auth B] SDF format, chain TB [auth C] SDF format, chain U [auth A] SDF format, chain UA [auth B] SDF format, chain UB [auth C] SDF format, chain V [auth A] SDF format, chain VA [auth B] SDF format, chain VB [auth C] SDF format, chain W [auth A] SDF format, chain WA [auth B] SDF format, chain WB [auth C] SDF format, chain X [auth A] SDF format, chain XA [auth B] SDF format, chain XB [auth C] SDF format, chain Y [auth A] SDF format, chain YA [auth B] SDF format, chain YB [auth C] SDF format, chain Z [auth A] SDF format, chain ZA [auth B] SDF format, chain ZB [auth C] MOL2 format, chain AA [auth A] MOL2 format, chain AB [auth B] MOL2 format, chain AC [auth C] MOL2 format, chain BA [auth A] MOL2 format, chain BB [auth B] MOL2 format, chain CA [auth A] MOL2 format, chain CB [auth B] MOL2 format, chain CC [auth D] MOL2 format, chain DA [auth A] MOL2 format, chain DB [auth B] MOL2 format, chain DC [auth D] MOL2 format, chain EA [auth A] MOL2 format, chain EB [auth B] MOL2 format, chain EC [auth D] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth A] MOL2 format, chain FB [auth B] MOL2 format, chain FC [auth D] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain GB [auth B] MOL2 format, chain GC [auth D] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth A] MOL2 format, chain HC [auth D] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth A] MOL2 format, chain IC [auth D] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth A] MOL2 format, chain JB [auth C] MOL2 format, chain JC [auth D] MOL2 format, chain K [auth A] MOL2 format, chain KB [auth C] MOL2 format, chain KC [auth D] MOL2 format, chain L [auth A] MOL2 format, chain LB [auth C] MOL2 format, chain LC [auth D] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth B] MOL2 format, chain MB [auth C] MOL2 format, chain MC [auth D] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth B] MOL2 format, chain NB [auth C] MOL2 format, chain NC [auth D] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth B] MOL2 format, chain OB [auth C] MOL2 format, chain OC [auth D] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth B] MOL2 format, chain PB [auth C] MOL2 format, chain PC [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth B] MOL2 format, chain QB [auth C] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth B] MOL2 format, chain RB [auth C] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth B] MOL2 format, chain SB [auth C] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth B] MOL2 format, chain TB [auth C] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth B] MOL2 format, chain UB [auth C] MOL2 format, chain V [auth A] MOL2 format, chain VA [auth B] MOL2 format, chain VB [auth C] MOL2 format, chain W [auth A] MOL2 format, chain WA [auth B] MOL2 format, chain WB [auth C] MOL2 format, chain X [auth A] MOL2 format, chain XA [auth B] MOL2 format, chain XB [auth C] MOL2 format, chain Y [auth A] MOL2 format, chain YA [auth B] MOL2 format, chain YB [auth C] MOL2 format, chain Z [auth A] MOL2 format, chain ZA [auth B] MOL2 format, chain ZB [auth C]	AA [auth A] AB [auth B] AC [auth C] BA [auth A] BB [auth B] AA [auth A], AB [auth B], AC [auth C], BA [auth A], BB [auth B], CA [auth A], CB [auth B], CC [auth D], DA [auth A], DB [auth B], DC [auth D], EA [auth A], EB [auth B], EC [auth D], F [auth A], FA [auth A], FB [auth B], FC [auth D], G [auth A], GA [auth A], GB [auth B], GC [auth D], H [auth A], HA [auth A], HC [auth D], I [auth A], IA [auth A], IC [auth D], J [auth A], JA [auth A], JB [auth C], JC [auth D], K [auth A], KB [auth C], KC [auth D], L [auth A], LB [auth C], LC [auth D], M [auth A], MA [auth B], MB [auth C], MC [auth D], N [auth A], NA [auth B], NB [auth C], NC [auth D], O [auth A], OA [auth B], OB [auth C], OC [auth D], P [auth A], PA [auth B], PB [auth C], PC [auth D], Q [auth A], QA [auth B], QB [auth C], R [auth A], RA [auth B], RB [auth C], S [auth A], SA [auth B], SB [auth C], T [auth A], TA [auth B], TB [auth C], U [auth A], UA [auth B], UB [auth C], V [auth A], VA [auth B], VB [auth C], W [auth A], WA [auth B], WB [auth C], X [auth A], XA [auth B], XB [auth C], Y [auth A], YA [auth B], YB [auth C], Z [auth A], ZA [auth B], ZB [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain AB [auth B] Focus chain AC [auth C] Focus chain BA [auth A] Focus chain BB [auth B] Focus chain CA [auth A] Focus chain CB [auth B] Focus chain CC [auth D] Focus chain DA [auth A] Focus chain DB [auth B] Focus chain DC [auth D] Focus chain EA [auth A] Focus chain EB [auth B] Focus chain EC [auth D] Focus chain F [auth A] Focus chain FA [auth A] Focus chain FB [auth B] Focus chain FC [auth D] Focus chain G [auth A] Focus chain GA [auth A] Focus chain GB [auth B] Focus chain GC [auth D] Focus chain H [auth A] Focus chain HA [auth A] Focus chain HC [auth D] Focus chain I [auth A] Focus chain IA [auth A] Focus chain IC [auth D] Focus chain J [auth A] Focus chain JA [auth A] Focus chain JB [auth C] Focus chain JC [auth D] Focus chain K [auth A] Focus chain KB [auth C] Focus chain KC [auth D] Focus chain L [auth A] Focus chain LB [auth C] Focus chain LC [auth D] Focus chain M [auth A] Focus chain MA [auth B] Focus chain MB [auth C] Focus chain MC [auth D] Focus chain N [auth A] Focus chain NA [auth B] Focus chain NB [auth C] Focus chain NC [auth D] Focus chain O [auth A] Focus chain OA [auth B] Focus chain OB [auth C] Focus chain OC [auth D] Focus chain P [auth A] Focus chain PA [auth B] Focus chain PB [auth C] Focus chain PC [auth D] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain QB [auth C] Focus chain R [auth A] Focus chain RA [auth B] Focus chain RB [auth C] Focus chain S [auth A] Focus chain SA [auth B] Focus chain SB [auth C] Focus chain T [auth A] Focus chain TA [auth B] Focus chain TB [auth C] Focus chain U [auth A] Focus chain UA [auth B] Focus chain UB [auth C] Focus chain V [auth A] Focus chain VA [auth B] Focus chain VB [auth C] Focus chain W [auth A] Focus chain WA [auth B] Focus chain WB [auth C] Focus chain X [auth A] Focus chain XA [auth B] Focus chain XB [auth C] Focus chain Y [auth A] Focus chain YA [auth B] Focus chain YB [auth C] Focus chain Z [auth A] Focus chain ZA [auth B] Focus chain ZB [auth C] Interactions & Density Focus chain AA [auth A] Focus chain AB [auth B] Focus chain AC [auth C] Focus chain BA [auth A] Focus chain BB [auth B] Focus chain CA [auth A] Focus chain CB [auth B] Focus chain CC [auth D] Focus chain DA [auth A] Focus chain DB [auth B] Focus chain DC [auth D] Focus chain EA [auth A] Focus chain EB [auth B] Focus chain EC [auth D] Focus chain F [auth A] Focus chain FA [auth A] Focus chain FB [auth B] Focus chain FC [auth D] Focus chain G [auth A] Focus chain GA [auth A] Focus chain GB [auth B] Focus chain GC [auth D] Focus chain H [auth A] Focus chain HA [auth A] Focus chain HC [auth D] Focus chain I [auth A] Focus chain IA [auth A] Focus chain IC [auth D] Focus chain J [auth A] Focus chain JA [auth A] Focus chain JB [auth C] Focus chain JC [auth D] Focus chain K [auth A] Focus chain KB [auth C] Focus chain KC [auth D] Focus chain L [auth A] Focus chain LB [auth C] Focus chain LC [auth D] Focus chain M [auth A] Focus chain MA [auth B] Focus chain MB [auth C] Focus chain MC [auth D] Focus chain N [auth A] Focus chain NA [auth B] Focus chain NB [auth C] Focus chain NC [auth D] Focus chain O [auth A] Focus chain OA [auth B] Focus chain OB [auth C] Focus chain OC [auth D] Focus chain P [auth A] Focus chain PA [auth B] Focus chain PB [auth C] Focus chain PC [auth D] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain QB [auth C] Focus chain R [auth A] Focus chain RA [auth B] Focus chain RB [auth C] Focus chain S [auth A] Focus chain SA [auth B] Focus chain SB [auth C] Focus chain T [auth A] Focus chain TA [auth B] Focus chain TB [auth C] Focus chain U [auth A] Focus chain UA [auth B] Focus chain UB [auth C] Focus chain V [auth A] Focus chain VA [auth B] Focus chain VB [auth C] Focus chain W [auth A] Focus chain WA [auth B] Focus chain WB [auth C] Focus chain X [auth A] Focus chain XA [auth B] Focus chain XB [auth C] Focus chain Y [auth A] Focus chain YA [auth B] Focus chain YB [auth C] Focus chain Z [auth A] Focus chain ZA [auth B] Focus chain ZB [auth C]
K Query on K Download Ideal Coordinates CCD File SDF format, chain BC [auth D] SDF format, chain E [auth A] SDF format, chain HB [auth C] SDF format, chain IB [auth C] SDF format, chain KA [auth B] MOL2 format, chain BC [auth D] MOL2 format, chain E [auth A] MOL2 format, chain HB [auth C] MOL2 format, chain IB [auth C] MOL2 format, chain KA [auth B]	BC [auth D], E [auth A], HB [auth C], IB [auth C], KA [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain BC [auth D] Focus chain E [auth A] Focus chain HB [auth C] Focus chain IB [auth C] Focus chain KA [auth B] Interactions & Density Focus chain BC [auth D] Focus chain E [auth A] Focus chain HB [auth C] Focus chain IB [auth C] Focus chain KA [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain LA [auth B] MOL2 format, chain LA [auth B]	LA [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain LA [auth B] Interactions & Density Focus chain LA [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free: 0.213
R-Value Work: 0.158
R-Value Observed: 0.161
Space Group: P 1 2₁ 1
Diffraction Data: https://doi.org/10.18430/M33EU8

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.18	α = 90
b = 71.76	β = 92.3
c = 221.79	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2008-10-21

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2008-10-21
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description
Version 1.4: 2023-02-01
Changes: Database references, Derived calculations