6WGM

Crystal structure of a marine metagenome TRAP solute binding protein specific for pyroglutamate (Sorcerer II Global Ocean Sampling Expedition, unidentified microbe, scf7180008839099) in complex with co-purified pyroglutamate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.152 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 5IGA 5IZZ 5I5P 5I7I


Literature

Crystal structure of a marine metagenome TRAP solute binding protein specific for aromatic acid ligands (Sorcerer II Global Ocean Sampling Expedition, unidentified microbe, GOS_140), in complex with co-purified pyroglutamate

Vetting, M.W.Fedorov, E.Hogle, S.L.Dupont, C.L.Almo, S.C.Ghosh, A.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TRAP-type C4-dicarboxylate transport system, periplasmic component323uncultured bacteriumMutation(s): 0 
Gene Names: HIMB100_00003270
UniProt
Find proteins for G5ZWD6 (SAR116 cluster alpha proteobacterium HIMB100)
Explore G5ZWD6 
Go to UniProtKB:  G5ZWD6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG5ZWD6
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PCA (Subject of Investigation/LOI)
Query on PCA

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B [auth A]PYROGLUTAMIC ACID
C5 H7 N O3
ODHCTXKNWHHXJC-VKHMYHEASA-N
EDO
Query on EDO

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C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
FMT
Query on FMT

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J [auth A]
K [auth A]
L [auth A]
M [auth A]
N [auth A]
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
CL
Query on CL

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I [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.152 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.251α = 90
b = 56.251β = 90
c = 193.919γ = 120
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-29
    Type: Initial release
  • Version 1.1: 2020-05-13
    Changes: Structure summary
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description