4FON | pdb_00004fon

High Energy Remote SAD structure solution of Proteinase K from the 37.8 keV Tellurium K edge

PDB DOI: https://doi.org/10.2210/pdb4FON/pdb

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

Deposited: 2012-06-20 Released: 2012-08-22
Deposition Author(s): Jakoncic, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.05 Å
R-Value Free:
0.131 (Depositor), 0.128 (DCC)
R-Value Work:
0.112 (Depositor), 0.110 (DCC)
R-Value Observed:
0.113 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Macromolecular Crystallography at High(er) Energy

Honkimaki, V., Stojanoff, V., DiMichiel, M., Jakoncic, J.

To be published.

Macromolecule Content

Total Structure Weight: 29.52 kDa
Atom Count: 2,596
Modeled Residue Count: 279
Deposited Residue Count: 279
Unique protein chains: 1

Macromolecules

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| 3D Structure

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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TE Query on TE Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	TELLURIUM Te VTLHPSMQDDEFRU-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A]	K [auth A], L [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain K [auth A] Focus chain L [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A]	I [auth A], J [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain I [auth A] Focus chain J [auth A]
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]
O Query on O Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	OXYGEN ATOM O XLYOFNOQVPJJNP-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.05 Å
R-Value Free: 0.131 (Depositor), 0.128 (DCC)
R-Value Work: 0.112 (Depositor), 0.110 (DCC)
R-Value Observed: 0.113 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.18	α = 90
b = 68.18	β = 90
c = 102.688	γ = 90

Software Package:

Software Name	Purpose
SPEC	data collection
SHELXS	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-08-22

Deposition Author(s):

Jakoncic, J.

Revision History (Full details and data files)

Version 1.0: 2012-08-22
Type: Initial release
Version 1.1: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary