6PZL | pdb_00006pzl

P. mirabilis hemolysin A mutant - Q125A

PDB DOI: https://doi.org/10.2210/pdb6PZL/pdb

Classification: TOXIN
Organism(s): Proteus mirabilis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2019-08-01 Released: 2020-08-05
Deposition Author(s): Weaver, T.M., Novak, W.R.P., Bhattacharyya, B.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.17 Å
R-Value Free:
0.184 (Depositor), 0.197 (DCC)
R-Value Work:
0.161 (Depositor)
R-Value Observed:
0.161 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6PZL

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

Literature

Structure of the HpmA265 Q125A variant

Weaver, T.M., Novak, W.R.P., Grilley, D.P., Wimmer, M.R., Woods, C.N., Bhattacharyya, B.

To be published.

Macromolecule Content

Total Structure Weight: 25.51 kDa
Atom Count: 1,962
Modeled Residue Count: 230
Deposited Residue Count: 242
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemolysin	A	242	Proteus mirabilis	Mutation(s): 1 Gene Names: hpmA
UniProt
Find proteins for P16466 (Proteus mirabilis) Explore P16466 Go to UniProtKB: P16466
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P16466
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 B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.17 Å
R-Value Free: 0.184 (Depositor), 0.197 (DCC)
R-Value Work: 0.161 (Depositor)
R-Value Observed: 0.161 (Depositor)

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.047	α = 90
b = 60.224	β = 90
c = 116.35	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
Coot	model building

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-08-05

Deposition Author(s):

Bhattacharyya, B.

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	MCB1050435
National Science Foundation (NSF, United States)	United States	MCB1434473

Revision History (Full details and data files)

Version 1.0: 2020-08-05
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-10-23
Changes: 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.