4OVP

CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM SULFITOBACTER sp. NAS-14.1, TARGET EFI-510292, WITH BOUND ALPHA-D-MANURONATE

PDB DOI: https://doi.org/10.2210/pdb4OVP/pdb

Classification: SOLUTE-BINDING PROTEIN
Organism(s): Sulfitobacter sp. NAS-14.1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-12-11 Released: 2014-01-08
Deposition Author(s): Vetting, M.W., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Stead, M., Attonito, J.D., Scott Glenn, A., Chowdhury, S., Evans, B., Hillerich, B., Love, J., Seidel, R.D., Imker, H.J., 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: 1.70 Å
R-Value Free: 0.180
R-Value Work: 0.149
R-Value Observed: 0.151

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.7 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 73.62 kDa
Atom Count: 5,365
Modelled Residue Count: 610
Deposited Residue Count: 652
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C4-dicarboxylate transport system substrate-binding protein	A, B	326	Sulfitobacter sp. NAS-14.1	Mutation(s): 0 Gene Names: NAS141_03721
UniProt
Find proteins for A3T0D1 (Sulfitobacter sp. (strain NAS-14.1)) Explore A3T0D1 Go to UniProtKB: A3T0D1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A3T0D1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MAV Query on MAV Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B]	C [auth A], D [auth B]	alpha-D-mannopyranuronic acid C₆ H₁₀ O₇ AEMOLEFTQBMNLQ-BYHBOUFCSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [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: 1.70 Å
R-Value Free: 0.180
R-Value Work: 0.149
R-Value Observed: 0.151
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.481	α = 90
b = 82.345	β = 140.07
c = 106.829	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHENIX	refinement

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2014-01-08

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: 2014-01-08
Type: Initial release
Version 1.1: 2014-01-22
Changes: Structure summary
Version 1.2: 2015-02-04
Changes: Derived calculations
Version 1.3: 2015-02-25
Changes: Database references
Version 1.4: 2017-09-27
Changes: Author supporting evidence, Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary
Version 1.5: 2019-12-25
Changes: Author supporting evidence, Data collection
Version 1.6: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Refinement description
Version 1.7: 2023-12-27
Changes: Data collection, Database references, Structure summary