4NQR

The crystal structure of a solute-binding protein (N280D mutant) from Anabaena variabilis ATCC 29413 in complex with alanine

PDB DOI: https://doi.org/10.2210/pdb4NQR/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Trichormus variabilis ATCC 29413
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2013-11-25 Released: 2013-12-18
Deposition Author(s): Tan, K., Li, H., Jedrzejczak, R., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.09 Å
R-Value Free: 0.137
R-Value Work: 0.120
R-Value Observed: 0.121

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

The crystal structure of a solute-binding protein (N280D mutant) from Anabaena variabilis ATCC 29413 in complex with alanine.

Tan, K., Li, H., Jedrzejczak, R., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 85.25 kDa
Atom Count: 6,823
Modelled Residue Count: 728
Deposited Residue Count: 790
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amino acid/amide ABC transporter substrate-binding protein, HAAT family	A, B	395	Trichormus variabilis ATCC 29413	Mutation(s): 1 Gene Names: Anabaena variabilis, Ava_0465
UniProt
Find proteins for Q3MFZ5 (Trichormus variabilis (strain ATCC 29413 / PCC 7937)) Explore Q3MFZ5 Go to UniProtKB: Q3MFZ5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q3MFZ5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A]	I [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
ALA Query on ALA Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain J [auth B] MOL2 format, chain C [auth A] MOL2 format, chain J [auth B]	C [auth A], J [auth B]	ALANINE C₃ H₇ N O₂ QNAYBMKLOCPYGJ-REOHCLBHSA-N		Interactions Focus chain C [auth A] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain J [auth B]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A]	E [auth A], F [auth A], G [auth A], H [auth A]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain K [auth B] MOL2 format, chain D [auth A] MOL2 format, chain K [auth B]	D [auth A], K [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain K [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: 1.09 Å
R-Value Free: 0.137
R-Value Work: 0.120
R-Value Observed: 0.121
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.673	α = 90
b = 100.742	β = 90
c = 150.305	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
DM	model building
ARP	model building
WARP	model building
HKL-3000	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing