5CM6 | pdb_00005cm6

CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM PSEUDOALTEROMONAS ATLANTICA T6c(Patl_2292, TARGET EFI-510180) WITH BOUND SODIUM AND PYRUVATE

PDB DOI: https://doi.org/10.2210/pdb5CM6/pdb
Entry: 5CM6 supersedes: 4X26

Classification: TRANSPORT PROTEIN
Organism(s): Paraglaciecola sp. T6c
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-07-16 Released: 2015-07-29
Deposition Author(s): Yadava, U., Vetting, M.W., Al Obaidi, N.F., Toro, R., Morisco, L.L., Benach, J., Wasserman, S.R., Attonito, J.D., Scott Glenn, A., Chamala, S., Chowdhury, S., Lafleur, J., Love, J., Seidel, R.D., Whalen, K.L., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.83 Å
R-Value Free:
0.243 (Depositor), 0.243 (DCC)
R-Value Work:
0.184 (Depositor), 0.185 (DCC)
R-Value Observed:
0.187 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Literature

CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM PSEUDOALTEROMONAS ATLANTICA T6c(Patl_2292, TARGET EFI-510180) WITH BOUND SODIUM AND PYRUVATE

Yadava, U., Vetting, M.W., Al Obaidi, N.F., Toro, R., Morisco, L.L., Benach, J., Wasserman, S.R., Attonito, J.D., Scott Glenn, A., Chamala, S., Chowdhury, S., Lafleur, J., Love, J., Seidel, R.D., Whalen, K.L., Gerlt, J.A., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 83.26 kDa
Atom Count: 5,850
Modeled Residue Count: 660
Deposited Residue Count: 716
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TRAP dicarboxylate transporter-DctP subunit	A, B	358	Paraglaciecola sp. T6c	Mutation(s): 0 Gene Names: Patl_2292
UniProt
Find proteins for A0ABU9T055 (Paraglaciecola mesophila) Explore A0ABU9T055 Go to UniProtKB: A0ABU9T055
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ABU9T055
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PYR Query on PYR Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth B]	PYRUVIC ACID C₃ H₄ O₃ LCTONWCANYUPML-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
NA Query on NA 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]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Modified Residues 1 Unique
ID	Chains	Modified Residue	Modification Type	Formula	2D Diagram
MSE Query on MSE	A, B	MET	Selenomethionine	C₅ H₁₁ N O₂ Se

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.83 Å
R-Value Free: 0.243 (Depositor), 0.243 (DCC)
R-Value Work: 0.184 (Depositor), 0.185 (DCC)
R-Value Observed: 0.187 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.345	α = 90
b = 83.345	β = 90
c = 198.082	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2015-07-29

Deposition Author(s):

Enzyme Function Initiative (EFI)

This entry supersedes: 4X26

Revision History (Full details and data files)

Version 1.0: 2015-07-29
Type: Initial release
Version 2.0: 2023-11-15
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Source and taxonomy
Version 2.1: 2024-10-16
Changes: Structure summary