4B5L | pdb_00004b5l

The 1.6 A High Energy Room Temperature Structure of Proteinase K at 38.4 keV and 0.04 MGy

PDB DOI: https://doi.org/10.2210/pdb4B5L/pdb

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

Deposited: 2012-08-05 Released: 2012-08-15
Deposition Author(s): Jakoncic, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.184 (Depositor), 0.185 (DCC)
R-Value Work:
0.158 (Depositor), 0.159 (DCC)
R-Value Observed:
0.160 (Depositor)

Starting Model: experimental
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This is version 1.4 of the entry. See complete history.

Literature

High Energy Macromolecular Crystallography Enables Data Collection at Room Temperature

Jakoncic, J., Stojanoff, V., Honkimaki, V.

To be published.

Macromolecule Content

Total Structure Weight: 29 kDa
Atom Count: 2,207
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
CA Query on CA 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]	CALCIUM ION Ca BHPQYMZQTOCNFJ-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: 1.60 Å
R-Value Free: 0.184 (Depositor), 0.185 (DCC)
R-Value Work: 0.158 (Depositor), 0.159 (DCC)
R-Value Observed: 0.160 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.538	α = 90
b = 68.538	β = 90
c = 108.375	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-08-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-08-15
Type: Initial release
Version 1.1: 2019-01-30
Changes: Data collection, Experimental preparation, Other
Version 1.2: 2019-02-06
Changes: Data collection, Experimental preparation
Version 1.3: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description
Version 1.4: 2024-10-16
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.