6RMR | pdb_00006rmr

Crystal structure of Escherichia coli periplasmic glucose-1-phosphatase H18D mutant

PDB DOI: https://doi.org/10.2210/pdb6RMR/pdb

Classification: HYDROLASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli K-12
Mutation(s): Yes

Deposited: 2019-05-07 Released: 2020-05-13
Deposition Author(s): Pfeiffer, P., Oberdorfer, G., Nidetzky, B.
Funding Organization(s): Austrian Science Fund

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.266 (Depositor), 0.269 (DCC)
R-Value Work:
0.225 (Depositor), 0.227 (DCC)
R-Value Observed:
0.229 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of Escherichia coli periplasmic glucose-1-phosphatase H18D mutant

Pfeiffer, P., Oberdorfer, G., Nidetzky, B.

To be published.

Macromolecule Content

Total Structure Weight: 88.53 kDa
Atom Count: 5,912
Modeled Residue Count: 774
Deposited Residue Count: 782
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucose-1-phosphatase	A, B	391	Escherichia coli K-12	Mutation(s): 1 Gene Names: agp, b1002, JW0987 EC: 3.1.3.10
UniProt
Find proteins for P19926 (Escherichia coli (strain K12)) Explore P19926 Go to UniProtKB: P19926
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P19926
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1PE Query on 1PE Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain V [auth B] SDF format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B]	U [auth B], V [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain U [auth B] Focus chain V [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain P [auth B] SDF format, chain L [auth B] SDF format, chain J [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain P [auth B] MOL2 format, chain L [auth B] MOL2 format, chain J [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain P [auth B] mmCIF format, chain L [auth B] mmCIF format, chain J [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.266 (Depositor), 0.269 (DCC)
R-Value Work: 0.225 (Depositor), 0.227 (DCC)
R-Value Observed: 0.229 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.035	α = 90
b = 101.651	β = 90
c = 114.929	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2020-05-13

Deposition Author(s):

Pfeiffer, P.

Oberdorfer, G.

Nidetzky, B.

Funding Organization	Location	Grant Number
Austrian Science Fund	Austria	W985

Revision History (Full details and data files)

Version 1.0: 2020-05-13
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-10-23
Changes: Structure summary