3EC7 | pdb_00003ec7

Crystal Structure of Putative Dehydrogenase from Salmonella typhimurium LT2

PDB DOI: https://doi.org/10.2210/pdb3EC7/pdb

Classification: OXIDOREDUCTASE
Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-08-29 Released: 2008-09-23
Deposition Author(s): Kim, Y., Evdokimova, E., Kudritska, M., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.231 (Depositor), 0.233 (DCC)
R-Value Work:
0.176 (Depositor), 0.182 (DCC)
R-Value Observed:
0.179 (Depositor)

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 Putative Dehydrogenase from Salmonella typhimurium LT2

Kim, Y., Evdokimova, E., Kudritska, M., Savchenko, A., Edwards, A., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 329.02 kDa
Atom Count: 23,658
Modeled Residue Count: 2,684
Deposited Residue Count: 2,856
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative Dehydrogenase	A, B, C, D, E A, B, C, D, E, F, G, H	357	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 0 EC: 1.1.1.18
UniProt
Find proteins for Q8ZK57 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q8ZK57 Go to UniProtKB: Q8ZK57
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8ZK57
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain O [auth C] SDF format, chain Y [auth F] SDF format, chain U [auth E] SDF format, chain Q [auth D] SDF format, chain M [auth B] SDF format, chain DA [auth H] SDF format, chain AA [auth G] MOL2 format, chain I [auth A] MOL2 format, chain O [auth C] MOL2 format, chain Y [auth F] MOL2 format, chain U [auth E] MOL2 format, chain Q [auth D] MOL2 format, chain M [auth B] MOL2 format, chain DA [auth H] MOL2 format, chain AA [auth G] mmCIF format, chain I [auth A] mmCIF format, chain O [auth C] mmCIF format, chain Y [auth F] mmCIF format, chain U [auth E] mmCIF format, chain Q [auth D] mmCIF format, chain M [auth B] mmCIF format, chain DA [auth H] mmCIF format, chain AA [auth G]	AA [auth G] DA [auth H] I [auth A] M [auth B] O [auth C] AA [auth G], DA [auth H], I [auth A], M [auth B], O [auth C], Q [auth D], U [auth E], Y [auth F]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain AA [auth G] Focus chain DA [auth H] Focus chain I [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain Q [auth D] Focus chain U [auth E] Focus chain Y [auth F] Interactions & Density Focus chain AA [auth G] Focus chain DA [auth H] Focus chain I [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain Q [auth D] Focus chain U [auth E] Focus chain Y [auth F]
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain BA [auth G] SDF format, chain EA [auth H] SDF format, chain J [auth A] SDF format, chain N [auth B] SDF format, chain P [auth C] SDF format, chain R [auth D] SDF format, chain V [auth E] SDF format, chain Z [auth F] MOL2 format, chain BA [auth G] MOL2 format, chain EA [auth H] MOL2 format, chain J [auth A] MOL2 format, chain N [auth B] MOL2 format, chain P [auth C] MOL2 format, chain R [auth D] MOL2 format, chain V [auth E] MOL2 format, chain Z [auth F] mmCIF format, chain BA [auth G] mmCIF format, chain EA [auth H] mmCIF format, chain J [auth A] mmCIF format, chain N [auth B] mmCIF format, chain P [auth C] mmCIF format, chain R [auth D] mmCIF format, chain V [auth E] mmCIF format, chain Z [auth F]	BA [auth G] EA [auth H] J [auth A] N [auth B] P [auth C] BA [auth G], EA [auth H], J [auth A], N [auth B], P [auth C], R [auth D], V [auth E], Z [auth F]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain BA [auth G] Focus chain EA [auth H] Focus chain J [auth A] Focus chain N [auth B] Focus chain P [auth C] Focus chain R [auth D] Focus chain V [auth E] Focus chain Z [auth F] Interactions & Density Focus chain BA [auth G] Focus chain EA [auth H] Focus chain J [auth A] Focus chain N [auth B] Focus chain P [auth C] Focus chain R [auth D] Focus chain V [auth E] Focus chain Z [auth F]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain CA [auth G] SDF format, chain X [auth E] SDF format, chain W [auth E] SDF format, chain S [auth D] SDF format, chain FA [auth H] MOL2 format, chain CA [auth G] MOL2 format, chain X [auth E] MOL2 format, chain W [auth E] MOL2 format, chain S [auth D] MOL2 format, chain FA [auth H] mmCIF format, chain CA [auth G] mmCIF format, chain X [auth E] mmCIF format, chain W [auth E] mmCIF format, chain S [auth D] mmCIF format, chain FA [auth H]	CA [auth G], FA [auth H], S [auth D], W [auth E], X [auth E]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain CA [auth G] Focus chain FA [auth H] Focus chain S [auth D] Focus chain W [auth E] Focus chain X [auth E] Interactions & Density Focus chain CA [auth G] Focus chain FA [auth H] Focus chain S [auth D] Focus chain W [auth E] Focus chain X [auth E]
ACY Query on ACY Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A]	K [auth A], L [auth A]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain K [auth A] Focus chain L [auth A]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain GA [auth H] SDF format, chain T [auth D] MOL2 format, chain GA [auth H] MOL2 format, chain T [auth D] mmCIF format, chain GA [auth H] mmCIF format, chain T [auth D]	GA [auth H], T [auth D]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain GA [auth H] Focus chain T [auth D] Interactions & Density Focus chain GA [auth H] Focus chain T [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F, G, H	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.231 (Depositor), 0.233 (DCC)
R-Value Work: 0.176 (Depositor), 0.182 (DCC)
R-Value Observed: 0.179 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.001	α = 88.05
b = 98.981	β = 81.78
c = 105.79	γ = 89.92

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
MLPHARE	phasing
DM	model building
SHELXD	phasing
RESOLVE	model building
Coot	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
RESOLVE	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2008-09-23

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2008-09-23
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Source and taxonomy, Version format compliance
Version 1.2: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary