4PWU | pdb_00004pwu

Crystal structure of a modulator protein MzrA (KPN_03524) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 2.45 A resolution

PDB DOI: https://doi.org/10.2210/pdb4PWU/pdb

Classification: SIGNALING PROTEIN
Organism(s): Klebsiella pneumoniae subsp. pneumoniae MGH 78578
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-03-21 Released: 2014-06-18
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free:
0.250 (Depositor), 0.260 (DCC)
R-Value Work:
0.199 (Depositor), 0.210 (DCC)
R-Value Observed:
0.201 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of a modulator protein MzrA (KPN_03524) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 2.45 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 42.84 kDa
Atom Count: 2,360
Modeled Residue Count: 307
Deposited Residue Count: 392
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Modulator protein MzrA	A, B, C, D	98	Klebsiella pneumoniae subsp. pneumoniae MGH 78578	Mutation(s): 0 Gene Names: mzrA, KPN78578_34950, KPN_03524
UniProt
Find proteins for A6TED5 (Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)) Explore A6TED5 Go to UniProtKB: A6TED5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A6TED5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth D] SDF format, chain G [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth D] MOL2 format, chain G [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth D] mmCIF format, chain G [auth D]	E [auth A], F [auth D], G [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth D] Focus chain G [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth D] Focus chain G [auth D]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.250 (Depositor), 0.260 (DCC)
R-Value Work: 0.199 (Depositor), 0.210 (DCC)
R-Value Observed: 0.201 (Depositor)

Diffraction Data: https://doi.org/10.18430/M34PWU

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.77	α = 90
b = 74.38	β = 99.26
c = 74.2	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
XSCALE	data scaling
BUSTER-TNT	refinement
XDS	data reduction
SHELXD	phasing
BUSTER	refinement

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2014-06-18

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2014-06-18
Type: Initial release
Version 1.1: 2017-10-11
Changes: Data collection, Refinement description
Version 1.2: 2018-01-24
Changes: Database references
Version 1.3: 2023-02-01
Changes: Database references, Derived calculations
Version 1.4: 2024-11-20
Changes: Data collection, 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.