6RZP | pdb_00006rzp

Multicrystal structure of Proteinase K at room temperature using a multilayer monochromator.

PDB DOI: https://doi.org/10.2210/pdb6RZP/pdb

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

Deposited: 2019-06-13 Released: 2019-07-17
Deposition Author(s): Sandy, J., Sandy, E., Sanchez-Weatherby, J., Mikolajek, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.161 (Depositor), 0.161 (DCC)
R-Value Work:
0.105 (Depositor), 0.111 (DCC)
R-Value Observed:
0.111 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6RZP

This is version 1.3 of the entry. See complete history.

Literature

Protein-to-structure pipeline for ambient-temperature crystallography at VMXi

Mikolajek, H., Sanchez-Weatherby, J., Sandy, J., Gildea, R.G., Campeotto, I., Cheruvara, H., Clarke, J.D., Foster, T., Fujii, S., Paulsen, I.T., Shah, B.S., Hough, M.A.

(2023) IUCrJ

DOI: https://doi.org/10.1107/S2052252523003810

Macromolecule Content

Total Structure Weight: 29.34 kDa
Atom Count: 2,251
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 Gene Names: PROK 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
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
GOL Query on GOL 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]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.161 (Depositor), 0.161 (DCC)
R-Value Work: 0.105 (Depositor), 0.111 (DCC)
R-Value Observed: 0.111 (Depositor)

Diffraction Data:

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.368	α = 90
b = 68.368	β = 90
c = 103.978	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
DIALS	data scaling
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2019-07-17

Deposition Author(s):

Sanchez-Weatherby, J.

Revision History (Full details and data files)

Version 1.0: 2019-07-17
Type: Initial release
Version 1.1: 2023-05-17
Changes: Database references
Version 1.2: 2024-02-07
Changes: Data collection, Refinement description
Version 1.3: 2024-10-09
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.