5K78 | pdb_00005k78

Dbr1 in complex with 16-mer branched RNA

PDB DOI: https://doi.org/10.2210/pdb5K78/pdb
NAKB: 5K78

Classification: HYDROLASE/RNA
Organism(s): Entamoeba histolytica, Saccharomyces cerevisiae
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2016-05-25 Released: 2016-12-07
Deposition Author(s): Clark, N.E., Taylor, A.B., Hart, P.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.64 Å
R-Value Free:
0.246 (Depositor), 0.257 (DCC)
R-Value Work:
0.195 (Depositor)
R-Value Observed:
0.197 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

The RNA lariat debranching enzyme Dbr1: metal dependence and branched RNA co-crystal structures

Clark, N.E., Katolik, A., Roberts, K., Taylor, A.B., Holloway, S.P., Schuermann, J.P., Montemayor, E.J., Stevens, S.W., Fitzpatrick, P.F., Damha, M.J., Hart, P.J.

(2016) Proc Natl Acad Sci U S A

DOI: https://doi.org/10.1073/pnas.1612729114

Macromolecule Content

Total Structure Weight: 221.83 kDa
Atom Count: 14,682
Modeled Residue Count: 1,765
Deposited Residue Count: 1,834
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA lariat debranching enzyme, putative	A, B, C, D, E	360	Entamoeba histolytica	Mutation(s): 1 Gene Names: EHI_062730 EC: 3.1.4
UniProt
Find proteins for C4M1P9 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM)) Explore C4M1P9 Go to UniProtKB: C4M1P9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C4M1P9
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 2
branch 1 of branched RNA 5'-UACUAA(2'-GUAUGU)CAAGU-3'	F [auth X], H [auth Y]	11	Saccharomyces cerevisiae
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 3
branch 2 of branched RNA 5'-UACUAA(2'-GUAUGU)CAAGU-3'	G [auth x], I [auth y]	6	Saccharomyces cerevisiae
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain L [auth A] SDF format, chain P [auth B] SDF format, chain R [auth B] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain Q [auth B] SDF format, chain M [auth A] SDF format, chain FA [auth E] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain P [auth B] MOL2 format, chain R [auth B] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain M [auth A] MOL2 format, chain FA [auth E] mmCIF format, chain AA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain L [auth A] mmCIF format, chain P [auth B] mmCIF format, chain R [auth B] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain M [auth A] mmCIF format, chain FA [auth E]	AA [auth D] BA [auth D] CA [auth D] FA [auth E] L [auth A] AA [auth D], BA [auth D], CA [auth D], FA [auth E], L [auth A], M [auth A], P [auth B], Q [auth B], R [auth B], U [auth C], V [auth C], W [auth C], X [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain FA [auth E] Focus chain L [auth A] Focus chain M [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain FA [auth E] Focus chain L [auth A] Focus chain M [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain EA [auth E] SDF format, chain K [auth A] SDF format, chain T [auth C] SDF format, chain Z [auth D] SDF format, chain O [auth B] MOL2 format, chain EA [auth E] MOL2 format, chain K [auth A] MOL2 format, chain T [auth C] MOL2 format, chain Z [auth D] MOL2 format, chain O [auth B] mmCIF format, chain EA [auth E] mmCIF format, chain K [auth A] mmCIF format, chain T [auth C] mmCIF format, chain Z [auth D] mmCIF format, chain O [auth B]	EA [auth E], K [auth A], O [auth B], T [auth C], Z [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain EA [auth E] Focus chain K [auth A] Focus chain O [auth B] Focus chain T [auth C] Focus chain Z [auth D] Interactions & Density Focus chain EA [auth E] Focus chain K [auth A] Focus chain O [auth B] Focus chain T [auth C] Focus chain Z [auth D]
FE2 Query on FE2 Download:Ideal Coordinates CCD File SDF format, chain DA [auth E] SDF format, chain J [auth A] SDF format, chain N [auth B] SDF format, chain S [auth C] SDF format, chain Y [auth D] MOL2 format, chain DA [auth E] MOL2 format, chain J [auth A] MOL2 format, chain N [auth B] MOL2 format, chain S [auth C] MOL2 format, chain Y [auth D] mmCIF format, chain DA [auth E] mmCIF format, chain J [auth A] mmCIF format, chain N [auth B] mmCIF format, chain S [auth C] mmCIF format, chain Y [auth D]	DA [auth E], J [auth A], N [auth B], S [auth C], Y [auth D]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Interactions Focus chain DA [auth E] Focus chain J [auth A] Focus chain N [auth B] Focus chain S [auth C] Focus chain Y [auth D] Interactions & Density Focus chain DA [auth E] Focus chain J [auth A] Focus chain N [auth B] Focus chain S [auth C] Focus chain Y [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.64 Å
R-Value Free: 0.246 (Depositor), 0.257 (DCC)
R-Value Work: 0.195 (Depositor)
R-Value Observed: 0.197 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.893	α = 90
b = 142.673	β = 90
c = 215.131	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2016-12-07

Deposition Author(s):

Clark, N.E.

Taylor, A.B.

Hart, P.J.

Revision History (Full details and data files)

Version 1.0: 2016-12-07
Type: Initial release
Version 1.1: 2016-12-14
Changes: Derived calculations
Version 1.2: 2017-09-27
Changes: Author supporting evidence
Version 1.3: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description