5KKW | pdb_00005kkw

Crystal structure of SAR11_1068 bound to a sulfobetaine (3-(1-methylpiperidinium-1-yl)propane-1-sulfonate)

PDB DOI: https://doi.org/10.2210/pdb5KKW/pdb
Entry: 5KKW supersedes: 5HMT

Classification: LYASE
Organism(s): Candidatus Pelagibacter ubique HTCC1062
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-06-22 Released: 2017-07-05
Deposition Author(s): Clifton, B.E., Carr, P.D., Jackson, C.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free:
0.238 (Depositor), 0.239 (DCC)
R-Value Work:
0.205 (Depositor)
R-Value Observed:
0.207 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 5KKW

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of SAR11_1068 bound to a sulfobetaine (3-(1-methylpiperidinium-1-yl)propane-1-sulfonate)

Clifton, B.E., Kaczmarski, J.A., Carr, P.D., Jackson, C.J.

To be published.

Macromolecule Content

Total Structure Weight: 28.22 kDa
Atom Count: 1,972
Modeled Residue Count: 237
Deposited Residue Count: 249
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclohexadienyl dehydratase	A	249	Candidatus Pelagibacter ubique HTCC1062	Mutation(s): 0 Gene Names: pheC, SAR11_1068
UniProt
Find proteins for Q4FLR5 (Pelagibacter ubique (strain HTCC1062)) Explore Q4FLR5 Go to UniProtKB: Q4FLR5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q4FLR5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
KH2 Query on KH2 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	3-(1-methylpiperidinium-1-yl)propane-1-sulfonate C₉ H₁₉ N O₃ S DQNQWAVIDNVATL-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free: 0.238 (Depositor), 0.239 (DCC)
R-Value Work: 0.205 (Depositor)
R-Value Observed: 0.207 (Depositor)

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.665	α = 90
b = 77.665	β = 90
c = 44.851	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2017-07-05

Deposition Author(s):

This entry supersedes: 5HMT

Revision History (Full details and data files)

Version 1.0: 2017-07-05
Type: Initial release
Version 1.1: 2017-11-01
Changes: Author supporting evidence
Version 1.2: 2023-09-27
Changes: Data collection, Database references, Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.