8DOP | pdb_00008dop

Crystal structure of 2,3-diketo-5-methylthiopentyl-1-phosphate enolase-phosphatase from Klebsiella aerogenes (P1 Form)

PDB DOI: https://doi.org/10.2210/pdb8DOP/pdb

Classification: ISOMERASE
Organism(s): Klebsiella aerogenes
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2022-07-14 Released: 2022-07-27
Deposition Author(s): 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: 2.00 Å
R-Value Free:
0.246 (Depositor), 0.249 (DCC)
R-Value Work:
0.188 (Depositor), 0.195 (DCC)
R-Value Observed:
0.190 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of 2,3-diketo-5-methylthiopentyl-1-phosphate enolase-phosphatase from Klebsiella aerogenes (P1 Form)

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

To be published.

Macromolecule Content

Total Structure Weight: 220.34 kDa
Atom Count: 13,210
Modeled Residue Count: 1,753
Deposited Residue Count: 2,024
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2,3-diketo-5-methylthiopentyl-1-phosphate enolase-phosphatase	A, B, C, D, E A, B, C, D, E, F, G, H	253	Klebsiella aerogenes	Mutation(s): 4 Gene Names: pyrF, BXQ27_18035, HV316_11080, KCTC 2190 EC: 4.1.1.23

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IOD Query on IOD Download:Ideal Coordinates CCD File SDF format, chain Y [auth H] SDF format, chain X [auth H] SDF format, chain W [auth G] SDF format, chain V [auth F] SDF format, chain T [auth E] SDF format, chain S [auth E] SDF format, chain Q [auth D] SDF format, chain O [auth C] SDF format, chain N [auth C] SDF format, chain L [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] MOL2 format, chain Y [auth H] MOL2 format, chain X [auth H] MOL2 format, chain W [auth G] MOL2 format, chain V [auth F] MOL2 format, chain T [auth E] MOL2 format, chain S [auth E] MOL2 format, chain Q [auth D] MOL2 format, chain O [auth C] MOL2 format, chain N [auth C] MOL2 format, chain L [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] mmCIF format, chain Y [auth H] mmCIF format, chain X [auth H] mmCIF format, chain W [auth G] mmCIF format, chain V [auth F] mmCIF format, chain T [auth E] mmCIF format, chain S [auth E] mmCIF format, chain Q [auth D] mmCIF format, chain O [auth C] mmCIF format, chain N [auth C] mmCIF format, chain L [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A]	I [auth A] J [auth A] L [auth B] N [auth C] O [auth C] I [auth A], J [auth A], L [auth B], N [auth C], O [auth C], Q [auth D], S [auth E], T [auth E], V [auth F], W [auth G], X [auth H], Y [auth H]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain Q [auth D] Focus chain S [auth E] Focus chain T [auth E] Focus chain V [auth F] Focus chain W [auth G] Focus chain X [auth H] Focus chain Y [auth H] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain Q [auth D] Focus chain S [auth E] Focus chain T [auth E] Focus chain V [auth F] Focus chain W [auth G] Focus chain X [auth H] Focus chain Y [auth H]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain Z [auth H] SDF format, chain U [auth E] SDF format, chain R [auth D] SDF format, chain P [auth C] SDF format, chain M [auth B] SDF format, chain K [auth A] MOL2 format, chain Z [auth H] MOL2 format, chain U [auth E] MOL2 format, chain R [auth D] MOL2 format, chain P [auth C] MOL2 format, chain M [auth B] MOL2 format, chain K [auth A] mmCIF format, chain Z [auth H] mmCIF format, chain U [auth E] mmCIF format, chain R [auth D] mmCIF format, chain P [auth C] mmCIF format, chain M [auth B] mmCIF format, chain K [auth A]	K [auth A] M [auth B] P [auth C] R [auth D] U [auth E] K [auth A], M [auth B], P [auth C], R [auth D], U [auth E], Z [auth H]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain R [auth D] Focus chain U [auth E] Focus chain Z [auth H] Interactions & Density Focus chain K [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain R [auth D] Focus chain U [auth E] Focus chain Z [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.246 (Depositor), 0.249 (DCC)
R-Value Work: 0.188 (Depositor), 0.195 (DCC)
R-Value Observed: 0.190 (Depositor)

Diffraction Data:

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.021	α = 108.39
b = 71.159	β = 102.23
c = 93.183	γ = 89.99

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
CRANK2	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-07-27

Deposition Author(s):

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