6CV6 | pdb_00006cv6

Crystal structure of 3-dehydroquinate dehydratase, type II, from Burkholderia phymatum STM815

PDB DOI: https://doi.org/10.2210/pdb6CV6/pdb

Classification: LYASE
Organism(s): Paraburkholderia phymatum STM815
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2018-03-27 Released: 2018-04-11
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.201 (Depositor), 0.166 (DCC)
R-Value Work:
0.156 (Depositor)
R-Value Observed:
0.157 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of 3-dehydroquinate dehydratase, type II, from Burkholderia phymatum STM815

Abendroth, J., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 225.87 kDa
Atom Count: 14,369
Modeled Residue Count: 1,737
Deposited Residue Count: 1,992
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, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	166	Paraburkholderia phymatum STM815	Mutation(s): 0 Gene Names: aroQ, Bphy_6025 EC: 4.2.1.10
UniProt
Find proteins for B2JVW0 (Paraburkholderia phymatum (strain DSM 17167 / CIP 108236 / LMG 21445 / STM815)) Explore B2JVW0 Go to UniProtKB: B2JVW0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B2JVW0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TAR Query on TAR Download:Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain EA [auth F] SDF format, chain HA [auth G] SDF format, chain KA [auth H] SDF format, chain NA [auth I] SDF format, chain O [auth A] SDF format, chain QA [auth J] SDF format, chain R [auth B] SDF format, chain TA [auth K] SDF format, chain V [auth C] SDF format, chain WA [auth L] SDF format, chain Y [auth D] MOL2 format, chain BA [auth E] MOL2 format, chain EA [auth F] MOL2 format, chain HA [auth G] MOL2 format, chain KA [auth H] MOL2 format, chain NA [auth I] MOL2 format, chain O [auth A] MOL2 format, chain QA [auth J] MOL2 format, chain R [auth B] MOL2 format, chain TA [auth K] MOL2 format, chain V [auth C] MOL2 format, chain WA [auth L] MOL2 format, chain Y [auth D] mmCIF format, chain BA [auth E] mmCIF format, chain EA [auth F] mmCIF format, chain HA [auth G] mmCIF format, chain KA [auth H] mmCIF format, chain NA [auth I] mmCIF format, chain O [auth A] mmCIF format, chain QA [auth J] mmCIF format, chain R [auth B] mmCIF format, chain TA [auth K] mmCIF format, chain V [auth C] mmCIF format, chain WA [auth L] mmCIF format, chain Y [auth D]	BA [auth E] EA [auth F] HA [auth G] KA [auth H] NA [auth I] BA [auth E], EA [auth F], HA [auth G], KA [auth H], NA [auth I], O [auth A], QA [auth J], R [auth B], TA [auth K], V [auth C], WA [auth L], Y [auth D]	D(-)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-LWMBPPNESA-N		Interactions Focus chain BA [auth E] Focus chain EA [auth F] Focus chain HA [auth G] Focus chain KA [auth H] Focus chain NA [auth I] Focus chain O [auth A] Focus chain QA [auth J] Focus chain R [auth B] Focus chain TA [auth K] Focus chain V [auth C] Focus chain WA [auth L] Focus chain Y [auth D] Interactions & Density Focus chain BA [auth E] Focus chain EA [auth F] Focus chain HA [auth G] Focus chain KA [auth H] Focus chain NA [auth I] Focus chain O [auth A] Focus chain QA [auth J] Focus chain R [auth B] Focus chain TA [auth K] Focus chain V [auth C] Focus chain WA [auth L] Focus chain Y [auth D]
TLA Query on TLA Download:Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain CA [auth F] SDF format, chain DA [auth F] SDF format, chain FA [auth G] SDF format, chain GA [auth G] SDF format, chain IA [auth H] SDF format, chain JA [auth H] SDF format, chain LA [auth I] SDF format, chain M [auth A] SDF format, chain MA [auth I] SDF format, chain N [auth A] SDF format, chain OA [auth J] SDF format, chain P [auth B] SDF format, chain PA [auth J] SDF format, chain Q [auth B] SDF format, chain RA [auth K] SDF format, chain SA [auth K] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain UA [auth L] SDF format, chain VA [auth L] SDF format, chain W [auth D] SDF format, chain X [auth D] SDF format, chain Z [auth E] MOL2 format, chain AA [auth E] MOL2 format, chain CA [auth F] MOL2 format, chain DA [auth F] MOL2 format, chain FA [auth G] MOL2 format, chain GA [auth G] MOL2 format, chain IA [auth H] MOL2 format, chain JA [auth H] MOL2 format, chain LA [auth I] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth I] MOL2 format, chain N [auth A] MOL2 format, chain OA [auth J] MOL2 format, chain P [auth B] MOL2 format, chain PA [auth J] MOL2 format, chain Q [auth B] MOL2 format, chain RA [auth K] MOL2 format, chain SA [auth K] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain UA [auth L] MOL2 format, chain VA [auth L] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] MOL2 format, chain Z [auth E] mmCIF format, chain AA [auth E] mmCIF format, chain CA [auth F] mmCIF format, chain DA [auth F] mmCIF format, chain FA [auth G] mmCIF format, chain GA [auth G] mmCIF format, chain IA [auth H] mmCIF format, chain JA [auth H] mmCIF format, chain LA [auth I] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth I] mmCIF format, chain N [auth A] mmCIF format, chain OA [auth J] mmCIF format, chain P [auth B] mmCIF format, chain PA [auth J] mmCIF format, chain Q [auth B] mmCIF format, chain RA [auth K] mmCIF format, chain SA [auth K] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain UA [auth L] mmCIF format, chain VA [auth L] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D] mmCIF format, chain Z [auth E]	AA [auth E] CA [auth F] DA [auth F] FA [auth G] GA [auth G] AA [auth E], CA [auth F], DA [auth F], FA [auth G], GA [auth G], IA [auth H], JA [auth H], LA [auth I], M [auth A], MA [auth I], N [auth A], OA [auth J], P [auth B], PA [auth J], Q [auth B], RA [auth K], SA [auth K], T [auth C], U [auth C], UA [auth L], VA [auth L], W [auth D], X [auth D], Z [auth E]	L(+)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-JCYAYHJZSA-N		Interactions Focus chain AA [auth E] Focus chain CA [auth F] Focus chain DA [auth F] Focus chain FA [auth G] Focus chain GA [auth G] Focus chain IA [auth H] Focus chain JA [auth H] Focus chain LA [auth I] Focus chain M [auth A] Focus chain MA [auth I] Focus chain N [auth A] Focus chain OA [auth J] Focus chain P [auth B] Focus chain PA [auth J] Focus chain Q [auth B] Focus chain RA [auth K] Focus chain SA [auth K] Focus chain T [auth C] Focus chain U [auth C] Focus chain UA [auth L] Focus chain VA [auth L] Focus chain W [auth D] Focus chain X [auth D] Focus chain Z [auth E] Interactions & Density Focus chain AA [auth E] Focus chain CA [auth F] Focus chain DA [auth F] Focus chain FA [auth G] Focus chain GA [auth G] Focus chain IA [auth H] Focus chain JA [auth H] Focus chain LA [auth I] Focus chain M [auth A] Focus chain MA [auth I] Focus chain N [auth A] Focus chain OA [auth J] Focus chain P [auth B] Focus chain PA [auth J] Focus chain Q [auth B] Focus chain RA [auth K] Focus chain SA [auth K] Focus chain T [auth C] Focus chain U [auth C] Focus chain UA [auth L] Focus chain VA [auth L] Focus chain W [auth D] Focus chain X [auth D] Focus chain Z [auth E]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain S [auth B] MOL2 format, chain S [auth B] mmCIF format, chain S [auth B]	S [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain S [auth B] Interactions & Density Focus chain S [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.201 (Depositor), 0.166 (DCC)
R-Value Work: 0.156 (Depositor)
R-Value Observed: 0.157 (Depositor)

Diffraction Data:

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 152.39	α = 90
b = 152.39	β = 90
c = 177.95	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MoRDa	phasing
Coot	model building

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2018-04-11

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2018-04-11
Type: Initial release
Version 1.1: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description