4R5Q | pdb_00004r5q

Crystal structure and nuclease activity of the CRISPR-associated Cas4 protein Pcal_0546 from Pyrobaculum calidifontis containing a [2Fe-2S] cluster

PDB DOI: https://doi.org/10.2210/pdb4R5Q/pdb
Entry: 4R5Q supersedes: 4ONB

Classification: HYDROLASE
Organism(s): Pyrobaculum calidifontis JCM 11548
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-08-21 Released: 2014-09-17
Deposition Author(s): Nocek, B., Skarina, T., Lemak, S., Brown, G., Savchenko, A., Joachimiak, A., Yakunin, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free:
0.253 (Depositor), 0.257 (DCC)
R-Value Work:
0.228 (Depositor), 0.232 (DCC)
R-Value Observed:
0.229 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4R5Q

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

Literature

Crystal structure and nuclease activity of the CRISPR-associated Cas4 protein Pcal_0546 from Pyrobaculum calidifontis containing a [2Fe-2S] cluster

Nocek, B., Skarina, T., Lemak, S., Brown, G., Savchenko, A., Joachimiak, A., Yakunin, A.

To be published.

Macromolecule Content

Total Structure Weight: 25.23 kDa
Atom Count: 1,737
Modeled Residue Count: 215
Deposited Residue Count: 216
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR-associated exonuclease, Cas4 family	A	216	Pyrobaculum calidifontis JCM 11548	Mutation(s): 0 Gene Names: Pcal_0546 EC: 3.1.12.1
UniProt
Find proteins for A3MTK6 (Pyrobaculum calidifontis (strain DSM 21063 / JCM 11548 / VA1)) Explore A3MTK6 Go to UniProtKB: A3MTK6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A3MTK6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FES Query on FES 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]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
MG Query on MG 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]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-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: 2.65 Å
R-Value Free: 0.253 (Depositor), 0.257 (DCC)
R-Value Work: 0.228 (Depositor), 0.232 (DCC)
R-Value Observed: 0.229 (Depositor)

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.836	α = 90
b = 117.836	β = 90
c = 89.412	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
DM	model building
SHELX	model building
Coot	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
SHELX	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-09-17

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

This entry supersedes: 4ONB

Revision History (Full details and data files)

Version 1.0: 2014-09-17
Type: Initial release
Version 1.1: 2017-10-25
Changes: Author supporting evidence, Refinement description
Version 1.2: 2024-11-20
Changes: Data collection, Database references, Derived calculations, 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.