1V1J

Crystal structure of type II Dehydroquintae Dehydratase from Streptomyces coelicolor in complex with 3-fluoro

PDB DOI: https://doi.org/10.2210/pdb1V1J/pdb

Classification: LYASE
Organism(s): Streptomyces coelicolor
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2004-04-16 Released: 2005-01-26
Deposition Author(s): Roszak, A.W., Coggins, J.R., Lapthorn, A.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.238 (Depositor), 0.240 (DCC)
R-Value Work:
0.215 (Depositor), 0.220 (DCC)
R-Value Observed:
0.217 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

(1R,4S,5R)-3-Fluoro-1,4,5-Trihydroxy-2-Cyclohexene-1-Carboxylic Acid: The Fluoro Analogue of the Enolate Intermediate in the Reaction Catalyzed by Type II Dehydroquinases

Frederickson, M., Roszak, A.W., Coggins, J.R., Lapthorn, A.J., Abell, C.

(2004) Org Biomol Chem 2: 1592

PubMed: 15162210 Search on PubMed
DOI: https://doi.org/10.1039/b404535a
Primary Citation of Related Structures:
1V1J

PubMed Abstract:
The fluoro analogue of the enolate intermediate in the reaction catalyzed by type II dehydroquinases has been prepared from naturally occurring (-)-quinic acid over seven steps and has been shown to be the most potent inhibitor reported to date of the type II enzyme from Mycobacterium tuberculosis.

Organizational Affiliation

University Chemical Laboratory, Lensfield Road, Cambridge, UK CB2 1EW.

Macromolecule Content

Total Structure Weight: 203.2 kDa
Atom Count: 14,496
Modelled Residue Count: 1,800
Deposited Residue Count: 1,884
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-DEHYDROQUINATE DEHYDRATASE	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	157	Streptomyces coelicolor	Mutation(s): 0 EC: 4.2.1.10
UniProt
Find proteins for P15474 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)) Explore P15474 Go to UniProtKB: P15474
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P15474
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FA3 Query on FA3 Download Ideal Coordinates CCD File SDF format, chain BA [auth L] SDF format, chain M [auth A] SDF format, chain O [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth D] SDF format, chain R [auth E] SDF format, chain T [auth F] SDF format, chain U [auth G] SDF format, chain V [auth H] SDF format, chain W [auth I] SDF format, chain Y [auth J] SDF format, chain Z [auth K] MOL2 format, chain BA [auth L] MOL2 format, chain M [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth E] MOL2 format, chain T [auth F] MOL2 format, chain U [auth G] MOL2 format, chain V [auth H] MOL2 format, chain W [auth I] MOL2 format, chain Y [auth J] MOL2 format, chain Z [auth K] mmCIF format, chain BA [auth L] mmCIF format, chain M [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain R [auth E] mmCIF format, chain T [auth F] mmCIF format, chain U [auth G] mmCIF format, chain V [auth H] mmCIF format, chain W [auth I] mmCIF format, chain Y [auth J] mmCIF format, chain Z [auth K]	BA [auth L] M [auth A] O [auth B] P [auth C] Q [auth D] BA [auth L], M [auth A], O [auth B], P [auth C], Q [auth D], R [auth E], T [auth F], U [auth G], V [auth H], W [auth I], Y [auth J], Z [auth K]	2-ANHYDRO-3-FLUORO-QUINIC ACID C₇ H₉ F O₅ DGZQZSSRYAJDAX-XAHCXIQSSA-N		Interactions Focus chain BA [auth L] Focus chain M [auth A] Focus chain O [auth B] Focus chain P [auth C] Focus chain Q [auth D] Focus chain R [auth E] Focus chain T [auth F] Focus chain U [auth G] Focus chain V [auth H] Focus chain W [auth I] Focus chain Y [auth J] Focus chain Z [auth K] Interactions & Density Focus chain BA [auth L] Focus chain M [auth A] Focus chain O [auth B] Focus chain P [auth C] Focus chain Q [auth D] Focus chain R [auth E] Focus chain T [auth F] Focus chain U [auth G] Focus chain V [auth H] Focus chain W [auth I] Focus chain Y [auth J] Focus chain Z [auth K]
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain AA [auth K] SDF format, chain N [auth A] SDF format, chain S [auth E] SDF format, chain X [auth I] MOL2 format, chain AA [auth K] MOL2 format, chain N [auth A] MOL2 format, chain S [auth E] MOL2 format, chain X [auth I] mmCIF format, chain AA [auth K] mmCIF format, chain N [auth A] mmCIF format, chain S [auth E] mmCIF format, chain X [auth I]	AA [auth K], N [auth A], S [auth E], X [auth I]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain AA [auth K] Focus chain N [auth A] Focus chain S [auth E] Focus chain X [auth I] Interactions & Density Focus chain AA [auth K] Focus chain N [auth A] Focus chain S [auth E] Focus chain X [auth I]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.238 (Depositor), 0.240 (DCC)
R-Value Work: 0.215 (Depositor), 0.220 (DCC)
R-Value Observed: 0.217 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.475	α = 90
b = 138.941	β = 90
c = 141.925	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2005-01-26

Deposition Author(s):

Roszak, A.W.

Coggins, J.R.

Lapthorn, A.J.

Revision History (Full details and data files)

Version 1.0: 2005-01-26
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-06-28
Changes: Data collection
Version 1.4: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Other, Refinement description