4X9T | pdb_00004x9t

Crystal structure of a TctC solute binding protein from Polaromonas (Bpro_3516, Target EFI-510338), no ligand

PDB DOI: https://doi.org/10.2210/pdb4X9T/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Polaromonas sp. JS666
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-12-11 Released: 2014-12-24
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: 1.24 Å
R-Value Free:
0.190 (Depositor), 0.191 (DCC)
R-Value Work:
0.163 (Depositor), 0.166 (DCC)
R-Value Observed:
0.165 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a TctC solute binding protein from Polaromonas (Bpro_3516, Target EFI-510338), no ligand

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)

To be published.

Macromolecule Content

Total Structure Weight: 34.42 kDa
Atom Count: 2,556
Modeled Residue Count: 288
Deposited Residue Count: 317
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein UPF0065	A	317	Polaromonas sp. JS666	Mutation(s): 0 Gene Names: Bpro_3516
UniProt
Find proteins for A0ABW0QCC3 (Polaromonas jejuensis) Explore A0ABW0QCC3 Go to UniProtKB: A0ABW0QCC3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ABW0QCC3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.24 Å
R-Value Free: 0.190 (Depositor), 0.191 (DCC)
R-Value Work: 0.163 (Depositor), 0.166 (DCC)
R-Value Observed: 0.165 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.976	α = 90
b = 79.244	β = 90
c = 111.583	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-12-24

Deposition Author(s):

Enzyme Function Initiative (EFI)

Revision History (Full details and data files)

Version 1.0: 2014-12-24
Type: Initial release
Version 1.1: 2015-02-04
Changes: Derived calculations
Version 1.2: 2015-02-11
Changes: Other
Version 1.3: 2024-10-16
Changes: Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary