4MDY | pdb_00004mdy

Crystal structure of periplasmic solute binding protein from Mycobacterium smegmatis str. MC2 155

PDB DOI: https://doi.org/10.2210/pdb4MDY/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Mycolicibacterium smegmatis MC2 155
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-08-23 Released: 2013-09-04
Deposition Author(s): Chang, C., Wu, R., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free:
0.201 (Depositor), 0.206 (DCC)
R-Value Work:
0.146 (Depositor), 0.160 (DCC)
R-Value Observed:
0.149 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4MDY

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of periplasmic solute binding protein from Mycobacterium smegmatis str. MC2 155

Chang, C., Wu, R., Endres, M., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 31.6 kDa
Atom Count: 2,398
Modeled Residue Count: 285
Deposited Residue Count: 295
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Periplasmic binding protein	A	295	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0 Gene Names: MSMEG_0438, MSMEI_0427
UniProt
Find proteins for A0QPL3 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QPL3 Go to UniProtKB: A0QPL3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0QPL3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [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: 1.78 Å
R-Value Free: 0.201 (Depositor), 0.206 (DCC)
R-Value Work: 0.146 (Depositor), 0.160 (DCC)
R-Value Observed: 0.149 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.606	α = 90
b = 90.449	β = 90
c = 33.974	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MLPHARE	phasing
DM	phasing
SHELXDE	phasing
ARP/wARP	model building
RESOLVE	phasing
Coot	model building

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-09-04

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2013-09-04
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2024-10-16
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.