6VC6 | pdb_00006vc6

2.1 Angstrom Resolution Crystal Structure of 6-phospho-alpha-glucosidase from Gut Microorganisms in Complex with NAD and Mn2+

PDB DOI: https://doi.org/10.2210/pdb6VC6/pdb

Classification: HYDROLASE
Organism(s): Merdibacter massiliensis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-12-20 Released: 2020-12-23
Deposition Author(s): Wu, R., Kim, Y., Endres, M., Joachimiak, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.13 Å
R-Value Free:
0.229 (Depositor), 0.230 (DCC)
R-Value Work:
0.196 (Depositor), 0.200 (DCC)
R-Value Observed:
0.198 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

2.1 Angstrom Resolution Crystal Structure of 6-phospho-alpha-glucosidase from Gut Microorganisms in Complex with NAD and Mn2+

Wu, R., Kim, Y., Endres, M., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 211.17 kDa
Atom Count: 14,988
Modeled Residue Count: 1,743
Deposited Residue Count: 1,764
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6-phospho-alpha-glucosidase	A, B, C, D	441	Merdibacter massiliensis	Mutation(s): 0 Gene Names: AGLB EC: 3.2.1.122
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD (Subject of Investigation/LOI) Query on NAD Download Ideal Coordinates CCD File SDF format, chain S [auth D] SDF format, chain N [auth C] SDF format, chain J [auth B] SDF format, chain G [auth A] MOL2 format, chain S [auth D] MOL2 format, chain N [auth C] MOL2 format, chain J [auth B] MOL2 format, chain G [auth A] mmCIF format, chain S [auth D] mmCIF format, chain N [auth C] mmCIF format, chain J [auth B] mmCIF format, chain G [auth A]	G [auth A], J [auth B], N [auth C], S [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain S [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain S [auth D]
G6P (Subject of Investigation/LOI) Query on G6P Download Ideal Coordinates CCD File SDF format, chain R [auth D] SDF format, chain M [auth C] SDF format, chain I [auth B] SDF format, chain F [auth A] MOL2 format, chain R [auth D] MOL2 format, chain M [auth C] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] mmCIF format, chain R [auth D] mmCIF format, chain M [auth C] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A]	F [auth A], I [auth B], M [auth C], R [auth D]	6-O-phosphono-alpha-D-glucopyranose C₆ H₁₃ O₉ P NBSCHQHZLSJFNQ-DVKNGEFBSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain R [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain R [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain P [auth C] SDF format, chain O [auth C] SDF format, chain K [auth B] MOL2 format, chain P [auth C] MOL2 format, chain O [auth C] MOL2 format, chain K [auth B] mmCIF format, chain P [auth C] mmCIF format, chain O [auth C] mmCIF format, chain K [auth B]	K [auth B], O [auth C], P [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Focus chain O [auth C] Focus chain P [auth C] Interactions & Density Focus chain K [auth B] Focus chain O [auth C] Focus chain P [auth C]
MN (Subject of Investigation/LOI) Query on MN Download Ideal Coordinates CCD File SDF format, chain Q [auth D] SDF format, chain L [auth C] SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain Q [auth D] MOL2 format, chain L [auth C] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain Q [auth D] mmCIF format, chain L [auth C] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A], H [auth B], L [auth C], Q [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain L [auth C] Focus chain Q [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain L [auth C] Focus chain Q [auth D]

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: 2.13 Å
R-Value Free: 0.229 (Depositor), 0.230 (DCC)
R-Value Work: 0.196 (Depositor), 0.200 (DCC)
R-Value Observed: 0.198 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 194.46	α = 90
b = 62.257	β = 90.35
c = 160.706	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2020-12-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-12-23
Type: Initial release
Version 1.1: 2023-10-11
Changes: Advisory, Data collection, Database references, Refinement description
Version 1.2: 2023-11-15
Changes: Data collection
Version 1.3: 2024-10-09
Changes: Structure summary