3S42 | pdb_00003s42

Crystal Structure of the 3-Dehydroquinate Dehydratase (aroD) from Salmonella enterica Typhimurium LT2 with Malonate and Boric Acid at the Active Site

PDB DOI: https://doi.org/10.2210/pdb3S42/pdb

Classification: LYASE
Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2011-05-18 Released: 2011-06-01
Deposition Author(s): Light, S.H., Minasov, G., Duban, M.-E., Halavaty, A.S., Krishna, S.N., Shuvalova, L., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free:
0.175 (Depositor), 0.182 (DCC)
R-Value Work:
0.144 (Depositor), 0.154 (DCC)
R-Value Observed:
0.145 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Crystal Structure of the 3-Dehydroquinate Dehydratase (aroD) from Salmonella enterica Typhimurium LT2 with Malonate and Boric Acid at the Active Site

Light, S.H., Minasov, G., Duban, M.-E., Halavaty, A.S., Krishna, S.N., Shuvalova, L., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 61.07 kDa
Atom Count: 5,261
Modeled Residue Count: 526
Deposited Residue Count: 552
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-dehydroquinate dehydratase	A [auth B], B [auth A]	276	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0 Gene Names: aroD, STM1358 EC: 4.2.1.10
UniProt
Find proteins for P58687 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P58687 Go to UniProtKB: P58687
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P58687
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MLA Query on MLA Download:Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain J [auth A] MOL2 format, chain C [auth B] MOL2 format, chain J [auth A] mmCIF format, chain C [auth B] mmCIF format, chain J [auth A]	C [auth B], J [auth A]	MALONIC ACID C₃ H₄ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Focus chain J [auth A] Interactions & Density Focus chain C [auth B] Focus chain J [auth A]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain F [auth B] SDF format, chain I [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain E [auth B] MOL2 format, chain D [auth B] MOL2 format, chain F [auth B] MOL2 format, chain I [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain E [auth B] mmCIF format, chain D [auth B] mmCIF format, chain F [auth B] mmCIF format, chain I [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain E [auth B]	D [auth B] E [auth B] F [auth B] I [auth A] K [auth A] D [auth B], E [auth B], F [auth B], I [auth A], K [auth A], L [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Focus chain E [auth B] Focus chain F [auth B] Focus chain I [auth A] Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain D [auth B] Focus chain E [auth B] Focus chain F [auth B] Focus chain I [auth A] Focus chain K [auth A] Focus chain L [auth A]
IMD Query on IMD Download:Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
BO3 Query on BO3 Download:Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A] mmCIF format, chain M [auth A]	M [auth A]	BORIC ACID B H₃ O₃ KGBXLFKZBHKPEV-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]
NI Query on NI Download:Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.175 (Depositor), 0.182 (DCC)
R-Value Work: 0.144 (Depositor), 0.154 (DCC)
R-Value Observed: 0.145 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.562	α = 90
b = 72.569	β = 90
c = 171.353	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2011-06-01

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2011-06-01
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2014-10-29
Changes: Structure summary
Version 1.3: 2015-04-29
Changes: Non-polymer description
Version 1.4: 2017-11-08
Changes: Refinement description
Version 1.5: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description