5YL5 | pdb_00005yl5

Crystal structure of dodecameric Dehydroquinate dehydratase from Acinetobacter baumannii at 1.9A resolution

PDB DOI: https://doi.org/10.2210/pdb5YL5/pdb

Classification: LYASE
Organism(s): Acinetobacter baumannii ATCC 17978
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-10-17 Released: 2017-11-01
Deposition Author(s): Iqbal, N., Kaur, P., Sharma, S., Singh, T.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.218 (Depositor), 0.221 (DCC)
R-Value Work:
0.181 (Depositor), 0.191 (DCC)
R-Value Observed:
0.182 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5YL5

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

Literature

Crystal structure of dodecameric Dehydroquinate dehydratase from Acinetobacter baumannii at 1.9A resolution

Iqbal, N., Kaur, P., Sharma, S., Singh, T.P.

To be published.

Macromolecule Content

Total Structure Weight: 200.23 kDa
Atom Count: 14,153
Modeled Residue Count: 1,742
Deposited Residue Count: 1,812
Unique protein chains: 1

Macromolecules

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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	151	Acinetobacter baumannii ATCC 17978	Mutation(s): 0 Gene Names: aroQ, A1S_2009 EC: 4.2.1.10
UniProt
Find proteins for A3M692 (Acinetobacter baumannii (strain ATCC 17978 / DSM 105126 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377)) Explore A3M692 Go to UniProtKB: A3M692
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A3M692
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain S [auth D] MOL2 format, chain S [auth D] mmCIF format, chain S [auth D]	S [auth D]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain S [auth D] Interactions & Density Focus chain S [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain AA [auth H] SDF format, chain DA [auth I] SDF format, chain FA [auth K] SDF format, chain P [auth B] SDF format, chain Y [auth F] SDF format, chain Z [auth G] SDF format, chain U [auth E] SDF format, chain T [auth E] SDF format, chain R [auth D] SDF format, chain Q [auth C] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain GA [auth L] SDF format, chain EA [auth J] SDF format, chain CA [auth I] SDF format, chain BA [auth H] MOL2 format, chain AA [auth H] MOL2 format, chain DA [auth I] MOL2 format, chain FA [auth K] MOL2 format, chain P [auth B] MOL2 format, chain Y [auth F] MOL2 format, chain Z [auth G] MOL2 format, chain U [auth E] MOL2 format, chain T [auth E] MOL2 format, chain R [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain GA [auth L] MOL2 format, chain EA [auth J] MOL2 format, chain CA [auth I] MOL2 format, chain BA [auth H] mmCIF format, chain AA [auth H] mmCIF format, chain DA [auth I] mmCIF format, chain FA [auth K] mmCIF format, chain P [auth B] mmCIF format, chain Y [auth F] mmCIF format, chain Z [auth G] mmCIF format, chain U [auth E] mmCIF format, chain T [auth E] mmCIF format, chain R [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain GA [auth L] mmCIF format, chain EA [auth J] mmCIF format, chain CA [auth I] mmCIF format, chain BA [auth H]	AA [auth H] BA [auth H] CA [auth I] DA [auth I] EA [auth J] AA [auth H], BA [auth H], CA [auth I], DA [auth I], EA [auth J], FA [auth K], GA [auth L], M [auth A], N [auth A], P [auth B], Q [auth C], R [auth D], T [auth E], U [auth E], Y [auth F], Z [auth G]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth H] Focus chain BA [auth H] Focus chain CA [auth I] Focus chain DA [auth I] Focus chain EA [auth J] Focus chain FA [auth K] Focus chain GA [auth L] Focus chain M [auth A] Focus chain N [auth A] Focus chain P [auth B] Focus chain Q [auth C] Focus chain R [auth D] Focus chain T [auth E] Focus chain U [auth E] Focus chain Y [auth F] Focus chain Z [auth G] Interactions & Density Focus chain AA [auth H] Focus chain BA [auth H] Focus chain CA [auth I] Focus chain DA [auth I] Focus chain EA [auth J] Focus chain FA [auth K] Focus chain GA [auth L] Focus chain M [auth A] Focus chain N [auth A] Focus chain P [auth B] Focus chain Q [auth C] Focus chain R [auth D] Focus chain T [auth E] Focus chain U [auth E] Focus chain Y [auth F] Focus chain Z [auth G]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain V [auth E] SDF format, chain W [auth E] SDF format, chain X [auth E] SDF format, chain O [auth A] MOL2 format, chain V [auth E] MOL2 format, chain W [auth E] MOL2 format, chain X [auth E] MOL2 format, chain O [auth A] mmCIF format, chain V [auth E] mmCIF format, chain W [auth E] mmCIF format, chain X [auth E] mmCIF format, chain O [auth A]	O [auth A], V [auth E], W [auth E], X [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain O [auth A] Focus chain V [auth E] Focus chain W [auth E] Focus chain X [auth E] Interactions & Density Focus chain O [auth A] Focus chain V [auth E] Focus chain W [auth E] Focus chain X [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.218 (Depositor), 0.221 (DCC)
R-Value Work: 0.181 (Depositor), 0.191 (DCC)
R-Value Observed: 0.182 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.796	α = 90
b = 155.129	β = 90
c = 155.465	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2017-11-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-11-01
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.