4YIC

CRYSTAL STRUCTURE OF A TRAP TRANSPORTER SOLUTE BINDING PROTEIN (IPR025997) FROM BORDETELLA BRONCHISEPTICA RB50 (BB0280, TARGET EFI-500035) WITH BOUND PICOLINIC ACID

PDB DOI: https://doi.org/10.2210/pdb4YIC/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Bordetella bronchiseptica RB50
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-03-01 Released: 2015-04-01
Deposition Author(s): Vetting, M.W., Al Obaidi, N.F., Toro, R., Morisco, L.L., Benach, J., Koss, 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)
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.173
R-Value Work: 0.143
R-Value Observed: 0.144

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

CRYSTAL STRUCTURE OF A TRAP TRANSPORTER SOLUTE BINDING PROTEIN (IPR025997) FROM BORDETELLA BRONCHISEPTICA RB50 (BB0280, TARGET EFI-500035) WITH BOUND PICOLINIC ACID

Vetting, M.W., Al Obaidi, N.F., Toro, R., Morisco, L.L., Benach, J., Koss, 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)

To be published.

Macromolecule Content

Total Structure Weight: 85.65 kDa
Atom Count: 6,147
Modelled Residue Count: 687
Deposited Residue Count: 770
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 TRANSPORTER SOLUTE BINDING PROTEIN	A, B	385	Bordetella bronchiseptica RB50	Mutation(s): 0
UniProt
Find proteins for A0A0J9X284 (Bordetella bronchiseptica (strain ATCC BAA-588 / NCTC 13252 / RB50)) Explore A0A0J9X284 Go to UniProtKB: A0A0J9X284
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0J9X284
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
6PC Query on 6PC Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B]	F [auth A], J [auth B]	PYRIDINE-2-CARBOXYLIC ACID C₆ H₅ N O₂ SIOXPEMLGUPBBT-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Interactions & Density Focus chain F [auth A] Focus chain J [auth B]
IMD Query on IMD Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A]	G [auth A]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain I [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B]	D [auth A], E [auth A], I [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth B]
CA Query on CA 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]	C [auth A], H [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.173
R-Value Work: 0.143
R-Value Observed: 0.144
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.681	α = 90
b = 86.141	β = 100.86
c = 72.339	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2015-04-01

Deposition Author(s):

Enzyme Function Initiative (EFI)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM093342

Revision History (Full details and data files)

Version 1.0: 2015-04-01
Type: Initial release
Version 1.1: 2017-09-20
Changes: Author supporting evidence, Derived calculations, Source and taxonomy
Version 1.2: 2019-12-25
Changes: Author supporting evidence
Version 1.3: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description

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Deposit Data

Help and Resources

4YIC

CRYSTAL STRUCTURE OF A TRAP TRANSPORTER SOLUTE BINDING PROTEIN (IPR025997) FROM BORDETELLA BRONCHISEPTICA RB50 (BB0280, TARGET EFI-500035) WITH BOUND PICOLINIC ACID

CRYSTAL STRUCTURE OF A TRAP TRANSPORTER SOLUTE BINDING PROTEIN (IPR025997) FROM BORDETELLA BRONCHISEPTICA RB50 (BB0280, TARGET EFI-500035) WITH BOUND PICOLINIC ACID

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)