5MQP | pdb_00005mqp

Glycoside hydrolase BT_1002

PDB DOI: https://doi.org/10.2210/pdb5MQP/pdb

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

Deposited: 2016-12-20 Released: 2017-04-05
Deposition Author(s): Basle, A., Ndeh, D., Rogowski, A., Cartmell, A., Luis, A.S., Venditto, I., Labourel, A., Gilbert, H.J.
Funding Organization(s): iotechnology and Biological Research Council, Biotechnology and Biological Sciences Research Council, Wellcome Trust, European Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.224 (Depositor), 0.229 (DCC)
R-Value Work:
0.183 (Depositor), 0.190 (DCC)
R-Value Observed:
0.185 (Depositor)

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

The most complex carbohydrate known is degraded in the human gut by single organisms and not bacterial consortia

Ndeh, D., Rogowski, A., Cartmell, A., Luis, A.S., Basle, A., Gray, J., Venditto, I., Briggs, B., Zhang, X., Labourel, A., Terrapon, N., Buffetto, F., Nepogodiev, S., Xiao, Y., Field, R.A., Zhu, Y., ONeil, M.A., Urbanowicz, B.R., York, W.S., Davies, G.J., Abbott, D.W., Ralet, M.-C., Martens, E.C., Henrissat, B., Gilbert, H.J.

To be published.

Macromolecule Content

Total Structure Weight: 565.92 kDa
Atom Count: 41,129
Modeled Residue Count: 4,801
Deposited Residue Count: 4,992
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoside hydrolase BT_1002	A, B, C, D, E A, B, C, D, E, F, G, H	624	Bacteroides thetaiotaomicron	Mutation(s): 0 Gene Names: Btheta7330_02618
UniProt
Find proteins for Q8A915 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q8A915 Go to UniProtKB: Q8A915
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8A915
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain R [auth H] SDF format, chain Q [auth G] SDF format, chain P [auth F] SDF format, chain O [auth E] SDF format, chain N [auth E] SDF format, chain M [auth D] SDF format, chain L [auth C] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain I [auth A] MOL2 format, chain R [auth H] MOL2 format, chain Q [auth G] MOL2 format, chain P [auth F] MOL2 format, chain O [auth E] MOL2 format, chain N [auth E] MOL2 format, chain M [auth D] MOL2 format, chain L [auth C] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth A] mmCIF format, chain R [auth H] mmCIF format, chain Q [auth G] mmCIF format, chain P [auth F] mmCIF format, chain O [auth E] mmCIF format, chain N [auth E] mmCIF format, chain M [auth D] mmCIF format, chain L [auth C] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth A]	I [auth A] J [auth B] K [auth B] L [auth C] M [auth D] I [auth A], J [auth B], K [auth B], L [auth C], M [auth D], N [auth E], O [auth E], P [auth F], Q [auth G], R [auth H]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth D] Focus chain N [auth E] Focus chain O [auth E] Focus chain P [auth F] Focus chain Q [auth G] Focus chain R [auth H] Interactions & Density Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth D] Focus chain N [auth E] Focus chain O [auth E] Focus chain P [auth F] Focus chain Q [auth G] Focus chain R [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.224 (Depositor), 0.229 (DCC)
R-Value Work: 0.183 (Depositor), 0.190 (DCC)
R-Value Observed: 0.185 (Depositor)

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 208.23	α = 90
b = 133.238	β = 97.67
c = 224.077	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
Coot	model building
REFMAC	refinement
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2017-04-05

Deposition Author(s):

Funding Organization	Location	Grant Number
iotechnology and Biological Research Council	United Kingdom	BB/K020358/1
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/K001949/1
Wellcome Trust	United Kingdom	WT097907MA
European Research Council	United Kingdom	322820

Revision History (Full details and data files)

Version 1.0: 2017-04-05
Type: Initial release
Version 1.1: 2017-08-23
Changes: Author supporting evidence
Version 1.2: 2017-08-30
Changes: Author supporting evidence
Version 1.3: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description

5MQP | pdb_00005mqp

Glycoside hydrolase BT_1002

Literature

The most complex carbohydrate known is degraded in the human gut by single organisms and not bacterial consortia

Biological Assembly 1

Biological Assembly 2

Biological Assembly 3

Biological Assembly 4

Biological Assembly 5

Biological Assembly 6

Biological Assembly 7

Biological Assembly 8

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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