4TOZ | pdb_00004toz

MppA Periplasmic Murein Tripeptide Binding Protein, Unliganded Open Form

PDB DOI: https://doi.org/10.2210/pdb4TOZ/pdb

Classification: PEPTIDE BINDING PROTEIN
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-06-06 Released: 2015-06-10
Deposition Author(s): Jeffery, C.J., Bhatt, F.
Funding Organization(s): American Heart Association

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.205 (Depositor), 0.205 (DCC)
R-Value Work:
0.180 (Depositor), 0.180 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Open Conformation of the E. coli Periplasmic Murein Tripeptide Binding Protein, MppA, at High Resolution

Bhatt, F., Patel, V., Jeffery, C.J.

To be published.

Macromolecule Content

Total Structure Weight: 117.6 kDa
Atom Count: 9,803
Modeled Residue Count: 1,030
Deposited Residue Count: 1,046
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Periplasmic murein peptide-binding protein	A, B	523	Escherichia coli K-12	Mutation(s): 0 Gene Names: mppA, ynaH, b1329, JW1322
UniProt
Find proteins for P77348 (Escherichia coli (strain K12)) Explore P77348 Go to UniProtKB: P77348
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P77348
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.205 (Depositor), 0.205 (DCC)
R-Value Work: 0.180 (Depositor), 0.180 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.97	α = 90
b = 76.81	β = 91.58
c = 89.57	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
AMoRE	phasing
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2015-06-10

Deposition Author(s):

Funding Organization	Location	Grant Number
American Heart Association	United States	--

Revision History (Full details and data files)

Version 1.0: 2015-06-10
Type: Initial release
Version 1.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy

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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.