5I7I

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) in complex with co-crystallized 3-hydroxybenzoate

PDB DOI: https://doi.org/10.2210/pdb5I7I/pdb

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

Deposited: 2016-02-17 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: 1.30 Å
R-Value Free: 0.173
R-Value Work: 0.148
R-Value Observed: 0.149

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 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) in complex with co-purified 4-hydroxybenzoate

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

To be published.

Macromolecule Content

Total Structure Weight: 74.49 kDa
Atom Count: 6,122
Modelled Residue Count: 638
Deposited Residue Count: 682
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TRAP solute Binding Protein	A, B	341	uncultured marine bacterium	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3HB Query on 3HB Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	3-HYDROXYBENZOIC ACID C₇ H₆ O₃ IJFXRHURBJZNAO-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B]	D [auth A], F [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free: 0.173
R-Value Work: 0.148
R-Value Observed: 0.149
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.091	α = 90
b = 82.588	β = 98.39
c = 75.961	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MOLREP	phasing
MOSFLM	data reduction

Structure Validation

View Full Validation Report

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: 2024-03-06
Changes: Data collection, Database references
Version 1.2: 2024-04-03
Changes: Refinement description

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.