4QFU | pdb_00004qfu

Crystal structure of a glycoside hydrolase family 5 (BVU_2644) from Bacteroides vulgatus ATCC 8482 at 1.90 A resolution

PDB DOI: https://doi.org/10.2210/pdb4QFU/pdb

Classification: HYDROLASE
Organism(s): Phocaeicola vulgatus ATCC 8482
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-05-21 Released: 2014-07-02
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.172 (Depositor), 0.179 (DCC)
R-Value Work:
0.142 (Depositor), 0.148 (DCC)
R-Value Observed:
0.144 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a glycoside hydrolase family 5 (BVU_2644) from Bacteroides vulgatus ATCC 8482 at 1.90 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 685.78 kDa
Atom Count: 51,386
Modeled Residue Count: 5,563
Deposited Residue Count: 5,808
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DUF4038 domain-containing protein	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	484	Phocaeicola vulgatus ATCC 8482	Mutation(s): 0 Gene Names: BVU_2644
UniProt
Find proteins for A6L3N2 (Phocaeicola vulgatus (strain ATCC 8482 / DSM 1447 / JCM 5826 / CCUG 4940 / NBRC 14291 / NCTC 11154)) Explore A6L3N2 Go to UniProtKB: A6L3N2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A6L3N2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MRD Query on MRD Download:Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain AB [auth L] SDF format, chain BA [auth E] SDF format, chain FA [auth F] SDF format, chain IA [auth G] SDF format, chain M [auth A] SDF format, chain MA [auth H] SDF format, chain N [auth A] SDF format, chain NA [auth H] SDF format, chain P [auth B] SDF format, chain PA [auth I] SDF format, chain Q [auth B] SDF format, chain QA [auth I] SDF format, chain SA [auth J] SDF format, chain T [auth C] SDF format, chain TA [auth J] SDF format, chain VA [auth K] SDF format, chain W [auth D] SDF format, chain WA [auth K] SDF format, chain X [auth D] SDF format, chain Z [auth E] SDF format, chain ZA [auth L] SDF format, chain JA [auth G] SDF format, chain EA [auth F] MOL2 format, chain AA [auth E] MOL2 format, chain AB [auth L] MOL2 format, chain BA [auth E] MOL2 format, chain FA [auth F] MOL2 format, chain IA [auth G] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth H] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth H] MOL2 format, chain P [auth B] MOL2 format, chain PA [auth I] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth I] MOL2 format, chain SA [auth J] MOL2 format, chain T [auth C] MOL2 format, chain TA [auth J] MOL2 format, chain VA [auth K] MOL2 format, chain W [auth D] MOL2 format, chain WA [auth K] MOL2 format, chain X [auth D] MOL2 format, chain Z [auth E] MOL2 format, chain ZA [auth L] MOL2 format, chain JA [auth G] MOL2 format, chain EA [auth F] mmCIF format, chain AA [auth E] mmCIF format, chain AB [auth L] mmCIF format, chain BA [auth E] mmCIF format, chain FA [auth F] mmCIF format, chain IA [auth G] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth H] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth H] mmCIF format, chain P [auth B] mmCIF format, chain PA [auth I] mmCIF format, chain Q [auth B] mmCIF format, chain QA [auth I] mmCIF format, chain SA [auth J] mmCIF format, chain T [auth C] mmCIF format, chain TA [auth J] mmCIF format, chain VA [auth K] mmCIF format, chain W [auth D] mmCIF format, chain WA [auth K] mmCIF format, chain X [auth D] mmCIF format, chain Z [auth E] mmCIF format, chain ZA [auth L] mmCIF format, chain JA [auth G] mmCIF format, chain EA [auth F]	AA [auth E] AB [auth L] BA [auth E] EA [auth F] FA [auth F] AA [auth E], AB [auth L], BA [auth E], EA [auth F], FA [auth F], IA [auth G], JA [auth G], M [auth A], MA [auth H], N [auth A], NA [auth H], P [auth B], PA [auth I], Q [auth B], QA [auth I], SA [auth J], T [auth C], TA [auth J], VA [auth K], W [auth D], WA [auth K], X [auth D], Z [auth E], ZA [auth L]	(4R)-2-METHYLPENTANE-2,4-DIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-RXMQYKEDSA-N		Interactions Focus chain AA [auth E] Focus chain AB [auth L] Focus chain BA [auth E] Focus chain EA [auth F] Focus chain FA [auth F] Focus chain IA [auth G] Focus chain JA [auth G] Focus chain M [auth A] Focus chain MA [auth H] Focus chain N [auth A] Focus chain NA [auth H] Focus chain P [auth B] Focus chain PA [auth I] Focus chain Q [auth B] Focus chain QA [auth I] Focus chain SA [auth J] Focus chain T [auth C] Focus chain TA [auth J] Focus chain VA [auth K] Focus chain W [auth D] Focus chain WA [auth K] Focus chain X [auth D] Focus chain Z [auth E] Focus chain ZA [auth L] Interactions & Density Focus chain AA [auth E] Focus chain AB [auth L] Focus chain BA [auth E] Focus chain EA [auth F] Focus chain FA [auth F] Focus chain IA [auth G] Focus chain JA [auth G] Focus chain M [auth A] Focus chain MA [auth H] Focus chain N [auth A] Focus chain NA [auth H] Focus chain P [auth B] Focus chain PA [auth I] Focus chain Q [auth B] Focus chain QA [auth I] Focus chain SA [auth J] Focus chain T [auth C] Focus chain TA [auth J] Focus chain VA [auth K] Focus chain W [auth D] Focus chain WA [auth K] Focus chain X [auth D] Focus chain Z [auth E] Focus chain ZA [auth L]
SAR Query on SAR Download:Ideal Coordinates CCD File SDF format, chain KA [auth G] SDF format, chain U [auth C] SDF format, chain XA [auth K] MOL2 format, chain KA [auth G] MOL2 format, chain U [auth C] MOL2 format, chain XA [auth K] mmCIF format, chain KA [auth G] mmCIF format, chain U [auth C] mmCIF format, chain XA [auth K]	KA [auth G], U [auth C], XA [auth K]	SARCOSINE C₃ H₇ N O₂ FSYKKLYZXJSNPZ-UHFFFAOYSA-N		Interactions Focus chain KA [auth G] Focus chain U [auth C] Focus chain XA [auth K] Interactions & Density Focus chain KA [auth G] Focus chain U [auth C] Focus chain XA [auth K]
NO3 Query on NO3 Download:Ideal Coordinates CCD File SDF format, chain CA [auth E] SDF format, chain GA [auth F] SDF format, chain R [auth B] MOL2 format, chain CA [auth E] MOL2 format, chain GA [auth F] MOL2 format, chain R [auth B] mmCIF format, chain CA [auth E] mmCIF format, chain GA [auth F] mmCIF format, chain R [auth B]	CA [auth E], GA [auth F], R [auth B]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain CA [auth E] Focus chain GA [auth F] Focus chain R [auth B] Interactions & Density Focus chain CA [auth E] Focus chain GA [auth F] Focus chain R [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain BB [auth L] SDF format, chain DA [auth E] SDF format, chain LA [auth G] SDF format, chain O [auth A] SDF format, chain OA [auth H] SDF format, chain RA [auth I] SDF format, chain UA [auth J] SDF format, chain V [auth C] SDF format, chain Y [auth D] SDF format, chain YA [auth K] SDF format, chain S [auth B] SDF format, chain HA [auth F] MOL2 format, chain BB [auth L] MOL2 format, chain DA [auth E] MOL2 format, chain LA [auth G] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth H] MOL2 format, chain RA [auth I] MOL2 format, chain UA [auth J] MOL2 format, chain V [auth C] MOL2 format, chain Y [auth D] MOL2 format, chain YA [auth K] MOL2 format, chain S [auth B] MOL2 format, chain HA [auth F] mmCIF format, chain BB [auth L] mmCIF format, chain DA [auth E] mmCIF format, chain LA [auth G] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth H] mmCIF format, chain RA [auth I] mmCIF format, chain UA [auth J] mmCIF format, chain V [auth C] mmCIF format, chain Y [auth D] mmCIF format, chain YA [auth K] mmCIF format, chain S [auth B] mmCIF format, chain HA [auth F]	BB [auth L] DA [auth E] HA [auth F] LA [auth G] O [auth A] BB [auth L], DA [auth E], HA [auth F], LA [auth G], O [auth A], OA [auth H], RA [auth I], S [auth B], UA [auth J], V [auth C], Y [auth D], YA [auth K]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain BB [auth L] Focus chain DA [auth E] Focus chain HA [auth F] Focus chain LA [auth G] Focus chain O [auth A] Focus chain OA [auth H] Focus chain RA [auth I] Focus chain S [auth B] Focus chain UA [auth J] Focus chain V [auth C] Focus chain Y [auth D] Focus chain YA [auth K] Interactions & Density Focus chain BB [auth L] Focus chain DA [auth E] Focus chain HA [auth F] Focus chain LA [auth G] Focus chain O [auth A] Focus chain OA [auth H] Focus chain RA [auth I] Focus chain S [auth B] Focus chain UA [auth J] Focus chain V [auth C] Focus chain Y [auth D] Focus chain YA [auth K]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.172 (Depositor), 0.179 (DCC)
R-Value Work: 0.142 (Depositor), 0.148 (DCC)
R-Value Observed: 0.144 (Depositor)

Diffraction Data:

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.95	α = 91.6
b = 117.589	β = 92.82
c = 125.249	γ = 98.92

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
XSCALE	data scaling
BUSTER-TNT	refinement
PHASER	phasing
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing
BUSTER	refinement

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-07-02

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2014-07-02
Type: Initial release
Version 1.1: 2017-11-22
Changes: Refinement description
Version 1.2: 2018-01-24
Changes: Database references
Version 1.3: 2024-10-16
Changes: Data collection, Database references, Derived calculations, Structure summary
Version 1.4: 2026-02-18
Changes: Structure summary