4MX8 | pdb_00004mx8

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 (Depositor), 0.197 (DCC)
R-Value Work:
0.159 (Depositor), 0.161 (DCC)
R-Value Observed:
0.161 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4MX8

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
Modeled Residue Count: 1,809
Deposited Residue Count: 1,890
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 (Depositor), 0.197 (DCC)
R-Value Work: 0.159 (Depositor), 0.161 (DCC)
R-Value Observed: 0.161 (Depositor)

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

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View more in-depth experimental data

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

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.