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), 0.230 (DCC)
R-Value Work:
0.164 (Depositor), 0.160 (DCC)
R-Value Observed:
0.167 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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), 0.230 (DCC)
R-Value Work: 0.164 (Depositor), 0.160 (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

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.