6B62 | pdb_00006b62

IMPase (AF2372) with 400 mM Glutamate

PDB DOI: https://doi.org/10.2210/pdb6B62/pdb

Classification: HYDROLASE
Organism(s): Archaeoglobus fulgidus DSM 4304
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-10-01 Released: 2018-10-03
Deposition Author(s): Goldstein, R.I., Roberts, M.
Funding Organization(s): Department of Energy (DOE, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.172 (Depositor), 0.175 (DCC)
R-Value Work:
0.161 (Depositor), 0.164 (DCC)
R-Value Observed:
0.162 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Osmolyte binding capacity of a dual action IMPase/FBPase (AF2372)

Goldstein, R.I., Roberts, M.

To be published.

Macromolecule Content

Total Structure Weight: 57.94 kDa
Atom Count: 4,469
Modeled Residue Count: 504
Deposited Residue Count: 504
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fructose-1,6-bisphosphatase/inositol-1-monophosphatase	A, B	252	Archaeoglobus fulgidus DSM 4304	Mutation(s): 0 Gene Names: suhB, AF_2372 EC: 3.1.3.11 (PDB Primary Data), 3.1.3.25 (PDB Primary Data)
UniProt
Find proteins for O30298 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)) Explore O30298 Go to UniProtKB: O30298
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O30298
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GLU (Subject of Investigation/LOI) Query on GLU Download:Ideal Coordinates CCD File SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] J [auth A] K [auth A] M [auth B] C [auth A], D [auth A], J [auth A], K [auth A], M [auth B], N [auth B], P [auth B], Q [auth B]	GLUTAMIC ACID C₅ H₉ N O₄ WHUUTDBJXJRKMK-VKHMYHEASA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth B] Focus chain Q [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth B] Focus chain Q [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain U [auth B] SDF format, chain L [auth A] SDF format, chain I [auth A] MOL2 format, chain O [auth B] MOL2 format, chain U [auth B] MOL2 format, chain L [auth A] MOL2 format, chain I [auth A] mmCIF format, chain O [auth B] mmCIF format, chain U [auth B] mmCIF format, chain L [auth A] mmCIF format, chain I [auth A]	I [auth A], L [auth A], O [auth B], U [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth A] Focus chain L [auth A] Focus chain O [auth B] Focus chain U [auth B] Interactions & Density Focus chain I [auth A] Focus chain L [auth A] Focus chain O [auth B] Focus chain U [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain R [auth B] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain R [auth B] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain R [auth B] mmCIF format, chain F [auth A]	E [auth A], F [auth A], R [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain R [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain R [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain G [auth A]	G [auth A], H [auth A], S [auth B], T [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain S [auth B] Focus chain T [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain S [auth B] Focus chain T [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.172 (Depositor), 0.175 (DCC)
R-Value Work: 0.161 (Depositor), 0.164 (DCC)
R-Value Observed: 0.162 (Depositor)

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.509	α = 90
b = 89.509	β = 90
c = 103.139	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2018-10-03

Deposition Author(s):

Goldstein, R.I.

Roberts, M.

Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	DE-FG02-91-ER20025

Revision History (Full details and data files)

Version 1.0: 2018-10-03
Type: Initial release
Version 1.1: 2019-12-04
Changes: Author supporting evidence
Version 1.2: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description