4MX8

Crystal Structure of TroA-like Periplasmic Binding Protein Peripla_BP_2 from Xylanimonas cellulosilytica

PDB DOI: https://doi.org/10.2210/pdb4MX8/pdb

Classification: SOLUTE-BINDING PROTEIN
Organism(s): Xylanimonas cellulosilytica DSM 15894
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2013-09-26 Released: 2013-12-11
Deposition Author(s): Kim, Y., Wu, R., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.91 Å
R-Value Free: 0.196
R-Value Work: 0.159
R-Value Observed: 0.161

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of TroA-like Periplasmic Binding Protein Peripla_BP_2 from Xylanimonas cellulosilytica

Kim, Y., Wu, R., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

To be published.

Macromolecule Content

Total Structure Weight: 199.96 kDa
Atom Count: 13,799
Modelled Residue Count: 1,809
Deposited Residue Count: 1,890
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Periplasmic binding protein	A, B, C, D, E A, B, C, D, E, F	315	Xylanimonas cellulosilytica DSM 15894	Mutation(s): 0 Gene Names: Xcel_1393
UniProt
Find proteins for D1BRG9 (Xylanimonas cellulosilytica (strain DSM 15894 / JCM 12276 / CECT 5975 / KCTC 9989 / LMG 20990 / NBRC 107835 / XIL07)) Explore D1BRG9 Go to UniProtKB: D1BRG9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D1BRG9
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.91 Å
R-Value Free: 0.196
R-Value Work: 0.159
R-Value Observed: 0.161
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 201.663	α = 90
b = 116.547	β = 112.19
c = 177.158	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
SHELXS	phasing
MLPHARE	phasing
RESOLVE	model building
SOLVE	phasing
BUCCANEER	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
RESOLVE	phasing
BUCCANEER	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2013-12-11

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2013-12-11
Type: Initial release
Version 1.1: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.