5YI6 | pdb_00005yi6

CRISPR associated protein Cas6

PDB DOI: https://doi.org/10.2210/pdb5YI6/pdb

Classification: HYDROLASE
Organism(s): Methanocaldococcus jannaschii DSM 2661
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-10-03 Released: 2018-09-12
Deposition Author(s): Ko, T.P., Hsieh, T.J., Chen, Y.
Funding Organization(s): Ministry of Science and Technology, R.O.C., Ministry of Science and Technology, ROC, National Science Council (Taiwan)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.195 (Depositor), 0.194 (DCC)
R-Value Work:
0.167 (Depositor), 0.167 (DCC)
R-Value Observed:
0.167 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Expression, Purification, Crystallization, and X-ray Structural Analysis of CRISPR-Associated Protein Cas6 from Methanocaldococcus jannaschii

Lee, M.C., Tseng, S.T., Yang, J.C., Hsieh, T.J., Wu, S.C., Kuan, S.M., Chen, M.J., Chang, M.C., Wang, C.C., Chen, H.L., Fang, G.C., Huang, W.J., Ko, T.P., Chen, Y.

(2018) Crystals (Basel) 7

DOI: https://doi.org/10.3390/cryst7110344

Macromolecule Content

Total Structure Weight: 128.05 kDa
Atom Count: 9,290
Modeled Residue Count: 961
Deposited Residue Count: 1,048
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR-associated endoribonuclease Cas6 1	A, B, C, D	262	Methanocaldococcus jannaschii DSM 2661	Mutation(s): 0 Gene Names: cas6a EC: 3.1
UniProt
Find proteins for Q57820 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q57820 Go to UniProtKB: Q57820
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q57820
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain Y [auth C] SDF format, chain X [auth C] SDF format, chain W [auth C] SDF format, chain V [auth C] SDF format, chain U [auth C] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain HA [auth D] SDF format, chain H [auth A] SDF format, chain GA [auth D] SDF format, chain G [auth A] SDF format, chain FA [auth D] SDF format, chain F [auth A] SDF format, chain EA [auth D] SDF format, chain DA [auth D] SDF format, chain CA [auth D] SDF format, chain AA [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain X [auth C] MOL2 format, chain W [auth C] MOL2 format, chain V [auth C] MOL2 format, chain U [auth C] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain HA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain FA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain EA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain AA [auth C] mmCIF format, chain Z [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain X [auth C] mmCIF format, chain W [auth C] mmCIF format, chain V [auth C] mmCIF format, chain U [auth C] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain HA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain GA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain FA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain EA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain AA [auth C]	AA [auth C] CA [auth D] DA [auth D] EA [auth D] F [auth A] AA [auth C], CA [auth D], DA [auth D], EA [auth D], F [auth A], FA [auth D], G [auth A], GA [auth D], H [auth A], HA [auth D], I [auth A], J [auth A], K [auth A], L [auth A], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], U [auth C], V [auth C], W [auth C], X [auth C], Y [auth C], Z [auth C]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain AA [auth C] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain F [auth A] Focus chain FA [auth D] Focus chain G [auth A] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain F [auth A] Focus chain FA [auth D] Focus chain G [auth A] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain T [auth C] SDF format, chain M [auth B] SDF format, chain E [auth A] SDF format, chain BA [auth D] MOL2 format, chain T [auth C] MOL2 format, chain M [auth B] MOL2 format, chain E [auth A] MOL2 format, chain BA [auth D] mmCIF format, chain T [auth C] mmCIF format, chain M [auth B] mmCIF format, chain E [auth A] mmCIF format, chain BA [auth D]	BA [auth D], E [auth A], M [auth B], T [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain E [auth A] Focus chain M [auth B] Focus chain T [auth C] Interactions & Density Focus chain BA [auth D] Focus chain E [auth A] Focus chain M [auth B] Focus chain T [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.195 (Depositor), 0.194 (DCC)
R-Value Work: 0.167 (Depositor), 0.167 (DCC)
R-Value Observed: 0.167 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 200.835	α = 90
b = 85.255	β = 118.47
c = 100.065	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2018-09-12

Deposition Author(s):

Ko, T.P.

Hsieh, T.J.

Chen, Y.

Funding Organization	Location	Grant Number
Ministry of Science and Technology, R.O.C.	Taiwan	MOST105-0210-01-12-01
Ministry of Science and Technology, ROC	Taiwan	MOST106-0210-01-15-04
National Science Council (Taiwan)	Taiwan	NSC99-2313-B-241-001
National Science Council (Taiwan)	Taiwan	NSC100-2313-B-241-006