6NQC | pdb_00006nqc

Crystal structure of a peptidase from an acI-B1 Actinobacterium

PDB DOI: https://doi.org/10.2210/pdb6NQC/pdb

Classification: HYDROLASE
Organism(s): actinobacterium SCGC AAA027-L06
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-01-20 Released: 2020-01-22
Deposition Author(s): Forest, K.T., Dwulit-Smith, J.R., Satyshur, K.A.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free:
0.227 (Depositor), 0.228 (DCC)
R-Value Work:
0.164 (Depositor), 0.164 (DCC)
R-Value Observed:
0.167 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Structure of a peptidase from an acI-B1 Actinobacterium

Dwulit-Smith, J., Satyshur, K.A., McMahon, K.D., Forest, K.T.

To be published.

Macromolecule Content

Total Structure Weight: 28.74 kDa
Atom Count: 2,066
Modeled Residue Count: 244
Deposited Residue Count: 259
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyanophycinase-like exopeptidase	A	259	actinobacterium SCGC AAA027-L06	Mutation(s): 0 Gene Names: A27L6_002500000020

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 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]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free: 0.227 (Depositor), 0.228 (DCC)
R-Value Work: 0.164 (Depositor), 0.164 (DCC)
R-Value Observed: 0.167 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.693	α = 90
b = 88.916	β = 90
c = 131.311	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
SCALEPACK	data scaling
PHENIX	phasing
PHENIX	refinement

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-01-22

Deposition Author(s):

Dwulit-Smith, J.R.

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	MCB 1518160

Revision History (Full details and data files)

Version 1.0: 2020-01-22
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, Refinement description

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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.