5A0W | pdb_00005a0w

THE CRYSTAL STRUCTURE OF I-DMOI E117A IN COMPLEX WITH ITS TARGET DNA AND IN THE PRESENCE OF 2MM MN

PDB DOI: https://doi.org/10.2210/pdb5A0W/pdb
NAKB: 5A0W

Classification: HYDROLASE/DNA
Organism(s): Desulfurococcus mucosus, synthetic construct
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-04-23 Released: 2016-05-11
Deposition Author(s): Molina, R., Besker, N., Prieto, J., Montoya, G., D'Abramo, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.208 (Depositor), 0.165 (DCC)
R-Value Work:
0.171 (Depositor), 0.160 (DCC)
R-Value Observed:
0.172 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Structural and Dynamical Characterization of the I- Dmo Catalytic Activity

Molina, R., Besker, N., Prieto, J., Montoya, G., D'Abramo, M.

To be published.

Macromolecule Content

Total Structure Weight: 116.58 kDa
Atom Count: 8,087
Modeled Residue Count: 701
Deposited Residue Count: 747
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HOMING ENDONUCLEASE I-DMOI	A, D, G	199	Desulfurococcus mucosus	Mutation(s): 0 EC: 3.1
UniProt
Find proteins for P21505 (Desulfurococcus mucosus) Explore P21505 Go to UniProtKB: P21505
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P21505
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Length	Organism	Image
25MER	B, E, H	25	synthetic construct
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Length	Organism	Image
25MER	C, F, I	25	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain T [auth F] SDF format, chain P [auth C] SDF format, chain O [auth C] SDF format, chain K [auth A] SDF format, chain AA [auth I] MOL2 format, chain T [auth F] MOL2 format, chain P [auth C] MOL2 format, chain O [auth C] MOL2 format, chain K [auth A] MOL2 format, chain AA [auth I] mmCIF format, chain T [auth F] mmCIF format, chain P [auth C] mmCIF format, chain O [auth C] mmCIF format, chain K [auth A] mmCIF format, chain AA [auth I]	AA [auth I], K [auth A], O [auth C], P [auth C], T [auth F]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain AA [auth I] Focus chain K [auth A] Focus chain O [auth C] Focus chain P [auth C] Focus chain T [auth F] Interactions & Density Focus chain AA [auth I] Focus chain K [auth A] Focus chain O [auth C] Focus chain P [auth C] Focus chain T [auth F]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain Z [auth H] SDF format, chain V [auth G] SDF format, chain U [auth F] SDF format, chain R [auth D] SDF format, chain N [auth B] SDF format, chain L [auth A] MOL2 format, chain Z [auth H] MOL2 format, chain V [auth G] MOL2 format, chain U [auth F] MOL2 format, chain R [auth D] MOL2 format, chain N [auth B] MOL2 format, chain L [auth A] mmCIF format, chain Z [auth H] mmCIF format, chain V [auth G] mmCIF format, chain U [auth F] mmCIF format, chain R [auth D] mmCIF format, chain N [auth B] mmCIF format, chain L [auth A]	L [auth A] N [auth B] R [auth D] U [auth F] V [auth G] L [auth A], N [auth B], R [auth D], U [auth F], V [auth G], Z [auth H]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain N [auth B] Focus chain R [auth D] Focus chain U [auth F] Focus chain V [auth G] Focus chain Z [auth H] Interactions & Density Focus chain L [auth A] Focus chain N [auth B] Focus chain R [auth D] Focus chain U [auth F] Focus chain V [auth G] Focus chain Z [auth H]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain Y [auth H] SDF format, chain X [auth G] SDF format, chain W [auth G] SDF format, chain S [auth F] SDF format, chain Q [auth D] SDF format, chain M [auth A] SDF format, chain J [auth A] MOL2 format, chain Y [auth H] MOL2 format, chain X [auth G] MOL2 format, chain W [auth G] MOL2 format, chain S [auth F] MOL2 format, chain Q [auth D] MOL2 format, chain M [auth A] MOL2 format, chain J [auth A] mmCIF format, chain Y [auth H] mmCIF format, chain X [auth G] mmCIF format, chain W [auth G] mmCIF format, chain S [auth F] mmCIF format, chain Q [auth D] mmCIF format, chain M [auth A] mmCIF format, chain J [auth A]	J [auth A] M [auth A] Q [auth D] S [auth F] W [auth G] J [auth A], M [auth A], Q [auth D], S [auth F], W [auth G], X [auth G], Y [auth H]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain J [auth A] Focus chain M [auth A] Focus chain Q [auth D] Focus chain S [auth F] Focus chain W [auth G] Focus chain X [auth G] Focus chain Y [auth H] Interactions & Density Focus chain J [auth A] Focus chain M [auth A] Focus chain Q [auth D] Focus chain S [auth F] Focus chain W [auth G] Focus chain X [auth G] Focus chain Y [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.208 (Depositor), 0.165 (DCC)
R-Value Work: 0.171 (Depositor), 0.160 (DCC)
R-Value Observed: 0.172 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.928	α = 90
b = 69.77	β = 120.06
c = 106.985	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2016-05-11

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-05-11
Type: Initial release
Version 1.1: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Other, Refinement description