5IZZ | pdb_00005izz

Crystal structure of a marine metagenome TRAP solute binding protein specific for aromatic acid ligands (Sorcerer II Global Ocean Sampling Expedition, unidentified microbe, locus tag GOS_1523157, Triple Surface Mutant K158A_K223A_K313A) in complex with metahydroxyphenylacetate, thermal exchange of ligand

PDB DOI: https://doi.org/10.2210/pdb5IZZ/pdb

Classification: TRANSPORT PROTEIN
Organism(s): uncultured bacterium
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-03-26 Released: 2017-01-18
Deposition Author(s): Vetting, M.W., Al Obaidi, N.F., Hogle, S.L., Dupont, C.L., Almo, S.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.153 (Depositor), 0.154 (DCC)
R-Value Work:
0.115 (Depositor), 0.116 (DCC)
R-Value Observed:
0.117 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

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

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 6WGM

Literature

Crystal structure of a marine metagenome TRAP solute binding protein specific for aromatic acid ligands (Sorcerer II Global Ocean Sampling Expedition, unidentified microbe, locus tag GOS_1523157, Triple Surface Mutant K158A_K223A_K313A) in complex with metahydroxyphenylacetate, thermal exchange of ligand

Vetting, M.W., Al Obaidi, N.F., Hogle, S.L., Dupont, C.L., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 37.51 kDa
Atom Count: 2,935
Modeled Residue Count: 318
Deposited Residue Count: 341
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TRAP TRANSPORTER SOLUTE BINDING PROTEIN	A	341	uncultured bacterium	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3HP Query on 3HP 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-HYDROXYPHENYLACETATE C₈ H₈ O₃ FVMDYYGIDFPZAX-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.153 (Depositor), 0.154 (DCC)
R-Value Work: 0.115 (Depositor), 0.116 (DCC)
R-Value Observed: 0.117 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.784	α = 90
b = 84.275	β = 113.48
c = 45.91	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MOLREP	phasing
HKL-3000	data reduction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2017-01-18

Deposition Author(s):

Al Obaidi, N.F.

Revision History (Full details and data files)

Version 1.0: 2017-01-18
Type: Initial release
Version 1.1: 2023-09-27
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.