4MAK | pdb_00004mak

Crystal structure of a putative ssRNA endonuclease Cas2, CRISPR adaptation protein from E.coli

PDB DOI: https://doi.org/10.2210/pdb4MAK/pdb

Classification: HYDROLASE
Organism(s): Escherichia coli str. K-12 substr. MG1655
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-08-16 Released: 2013-09-04
Deposition Author(s): Nocek, B., Skarina, T., Brown, G., Yakunin, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free:
0.173 (Depositor), 0.172 (DCC)
R-Value Work:
0.132 (Depositor), 0.134 (DCC)
R-Value Observed:
0.136 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a putative ssRNA endonuclease Cas2, CRISPR adaptation protein from E.coli

Nocek, B., Skarina, T., Brown, G., Yakunin, A., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 21.16 kDa
Atom Count: 1,413
Modeled Residue Count: 149
Deposited Residue Count: 188
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR-associated endoribonuclease Cas2	A, B	94	Escherichia coli str. K-12 substr. MG1655	Mutation(s): 0 Gene Names: ygbF, cas2, b2754, JW5438 EC: 3.1
UniProt
Find proteins for P45956 (Escherichia coli (strain K12)) Explore P45956 Go to UniProtKB: P45956
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P45956
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free: 0.173 (Depositor), 0.172 (DCC)
R-Value Work: 0.132 (Depositor), 0.134 (DCC)
R-Value Observed: 0.136 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.048	α = 90
b = 66.009	β = 90
c = 69.972	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
CCP4	model building
MOLREP	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
CCP4	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-09-04

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2013-09-04
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection, Database references, Derived calculations

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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.