8EK7 | pdb_00008ek7

Crystal structure of Hepes and Mg bound 2,3-diketo-5-methylthiopentyl-1-phosphate enolase-phosphatase from Klebsiella aerogenes

PDB DOI: https://doi.org/10.2210/pdb8EK7/pdb

Classification: ISOMERASE
Organism(s): Klebsiella aerogenes
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-09-20 Released: 2022-09-28
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/Office of the Director

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.230 (Depositor), 0.239 (DCC)
R-Value Work:
0.183 (Depositor), 0.219 (DCC)
R-Value Observed:
0.186 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of Hepes and Mg bound 2,3-diketo-5-methylthiopentyl-1-phosphate enolase-phosphatase from Klebsiella aerogenes

Lovell, S., Liu, L., Seibold, S., Battaile, K.P.

To be published.

Macromolecule Content

Total Structure Weight: 165.64 kDa
Atom Count: 10,637
Modeled Residue Count: 1,311
Deposited Residue Count: 1,518
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Orotidine 5'-phosphate decarboxylase	A, B, C, D, E A, B, C, D, E, F	253	Klebsiella aerogenes	Mutation(s): 0 Gene Names: pyrF, BXQ27_18035, HV316_11080 EC: 4.1.1.23

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain N [auth C] SDF format, chain S [auth E] MOL2 format, chain G [auth A] MOL2 format, chain N [auth C] MOL2 format, chain S [auth E] mmCIF format, chain G [auth A] mmCIF format, chain N [auth C] mmCIF format, chain S [auth E]	G [auth A], N [auth C], S [auth E]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain N [auth C] Focus chain S [auth E] Interactions & Density Focus chain G [auth A] Focus chain N [auth C] Focus chain S [auth E]
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain M [auth B] SDF format, chain R [auth C] SDF format, chain W [auth E] SDF format, chain X [auth F] MOL2 format, chain K [auth A] MOL2 format, chain M [auth B] MOL2 format, chain R [auth C] MOL2 format, chain W [auth E] MOL2 format, chain X [auth F] mmCIF format, chain K [auth A] mmCIF format, chain M [auth B] mmCIF format, chain R [auth C] mmCIF format, chain W [auth E] mmCIF format, chain X [auth F]	K [auth A], M [auth B], R [auth C], W [auth E], X [auth F]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain K [auth A] Focus chain M [auth B] Focus chain R [auth C] Focus chain W [auth E] Focus chain X [auth F] Interactions & Density Focus chain K [auth A] Focus chain M [auth B] Focus chain R [auth C] Focus chain W [auth E] Focus chain X [auth F]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain L [auth B] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain U [auth E] SDF format, chain V [auth E] SDF format, chain T [auth E] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain U [auth E] MOL2 format, chain V [auth E] MOL2 format, chain T [auth E] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain L [auth B] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain U [auth E] mmCIF format, chain V [auth E] mmCIF format, chain T [auth E]	H [auth A] I [auth A] J [auth A] L [auth B] O [auth C] H [auth A], I [auth A], J [auth A], L [auth B], O [auth C], P [auth C], Q [auth C], T [auth E], U [auth E], V [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain T [auth E] Focus chain U [auth E] Focus chain V [auth E] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain T [auth E] Focus chain U [auth E] Focus chain V [auth E]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLZ Query on MLZ	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₇ H₁₆ N₂ O₂		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.230 (Depositor), 0.239 (DCC)
R-Value Work: 0.183 (Depositor), 0.219 (DCC)
R-Value Observed: 0.186 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.517	α = 90
b = 70.141	β = 93.34
c = 115.985	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-09-28

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700059C
National Institutes of Health/Office of the Director	United States	S10OD030394