5I5P | pdb_00005i5p

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

PDB DOI: https://doi.org/10.2210/pdb5I5P/pdb

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

Deposited: 2016-02-15 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:
0.181 (Depositor), 0.184 (DCC)
R-Value Work:
0.144 (Depositor), 0.148 (DCC)
R-Value Observed:
0.146 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.4 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: 76.49 kDa
Atom Count: 5,696
Modeled Residue Count: 639
Deposited Residue Count: 682
Unique protein chains: 1

Macromolecules

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| 3D Structure

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PHB Query on PHB Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain H [auth B] mmCIF format, chain C [auth A] mmCIF format, chain H [auth B]	C [auth A], H [auth B]	P-HYDROXYBENZOIC ACID C₇ H₆ O₃ FJKROLUGYXJWQN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain D [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain D [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain D [auth A]	D [auth A], I [auth B], J [auth B], K [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]
BR Query on BR Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B]	E [auth A] F [auth A] G [auth A] L [auth B] M [auth B] E [auth A], F [auth A], G [auth A], L [auth B], M [auth B], N [auth B]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.181 (Depositor), 0.184 (DCC)
R-Value Work: 0.144 (Depositor), 0.148 (DCC)
R-Value Observed: 0.146 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.305	α = 90
b = 82.492	β = 98.59
c = 76.577	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2017-01-18

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-01-18
Type: Initial release
Version 1.1: 2018-01-31
Changes: Experimental preparation
Version 1.2: 2023-09-27
Changes: Data collection, Database references, Refinement description
Version 1.3: 2023-11-15
Changes: Data collection
Version 1.4: 2024-11-13
Changes: Structure summary