3NTL

Crystal Structure of Glucose-1-phosphatase (AgpE) from Enterobacter cloacae

PDB DOI: https://doi.org/10.2210/pdb3NTL/pdb

Classification: HYDROLASE
Organism(s): Enterobacter cloacae
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2010-07-05 Released: 2011-07-27
Deposition Author(s): Grishkovskaya, I., Hoehne, W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free: 0.250
R-Value Work: 0.181
R-Value Observed: 0.185

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

Crystal Structure of Glucose-1-phosphatase (AgpE) from Enterobacter cloacae

Grishkovskaya, I., Herter, T., Wessner, H., Borriss, R., Hoehne, W.

To be published.

Macromolecule Content

Total Structure Weight: 90.65 kDa
Atom Count: 6,947
Modelled Residue Count: 775
Deposited Residue Count: 796
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acid glucose-1-phosphate phosphatase	A, B	398	Enterobacter cloacae	Mutation(s): 1 Gene Names: agp
UniProt
Find proteins for Q6EV19 (Enterobacter cloacae) Explore Q6EV19 Go to UniProtKB: Q6EV19
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6EV19
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IHP Query on IHP Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B]	C [auth A], E [auth B]	INOSITOL HEXAKISPHOSPHATE C₆ H₁₈ O₂₄ P₆ IMQLKJBTEOYOSI-GPIVLXJGSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B]	F [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free: 0.250
R-Value Work: 0.181
R-Value Observed: 0.185
Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 151.079	α = 90
b = 151.079	β = 90
c = 86.644	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-07-27

Deposition Author(s):

Grishkovskaya, I.

Hoehne, W.

Revision History (Full details and data files)

Version 1.0: 2011-07-27
Type: Initial release
Version 1.1: 2020-10-14
Changes: Database references, Derived calculations, Structure summary
Version 1.2: 2023-09-06
Changes: Data collection, Database references, Refinement description

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3NTL

Crystal Structure of Glucose-1-phosphatase (AgpE) from Enterobacter cloacae

Crystal Structure of Glucose-1-phosphatase (AgpE) from Enterobacter cloacae

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)