7NUY | pdb_00007nuy

New polymorhp of proteinase K obtained by free interface diffusion technique

PDB DOI: https://doi.org/10.2210/pdb7NUY/pdb

Classification: HYDROLASE
Organism(s): Parengyodontium album
Mutation(s): No

Deposited: 2021-03-15 Released: 2022-01-19
Deposition Author(s): Gavira, J.A., Artusio, F., Castellvi, A., Pisano, R.
Funding Organization(s): Ministry of Economy and Competitiveness (MINECO)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.221 (Depositor), 0.221 (DCC)
R-Value Work:
0.172 (Depositor), 0.172 (DCC)
R-Value Observed:
0.175 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7NUY

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

Literature

Tuning Transport Phenomena in Agarose Gels for the Control of Protein Nucleation Density and Crystal Form

Artusio, F., Castellvi, A., Pisano, R., Gavira, J.A.

(2021) Crystals (Basel)

DOI: https://doi.org/10.3390/cryst11050466

Macromolecule Content

Total Structure Weight: 29.34 kDa
Atom Count: 2,587
Modeled Residue Count: 279
Deposited Residue Count: 279
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteinase K	A	279	Parengyodontium album	Mutation(s): 0 EC: 3.4.21.64
UniProt
Find proteins for P06873 (Parengyodontium album) Explore P06873 Go to UniProtKB: P06873
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P06873
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 E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A], D [auth A], E [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.221 (Depositor), 0.221 (DCC)
R-Value Work: 0.172 (Depositor), 0.172 (DCC)
R-Value Observed: 0.175 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.5	α = 90
b = 70.96	β = 90
c = 78.75	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
MOLREP	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-01-19

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Economy and Competitiveness (MINECO)	Spain	BIO2016-74875-P

Revision History (Full details and data files)

Version 1.0: 2022-01-19
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Refinement description
Version 1.2: 2024-11-13
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.