3MQW | pdb_00003mqw

Crystal structure of a putative endoribonuclease L-PSP from Entamoeba histolytica with higher solvent content and an ordered N-terminal tag

PDB DOI: https://doi.org/10.2210/pdb3MQW/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Entamoeba histolytica
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-04-28 Released: 2010-05-12
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.183 (Depositor), 0.190 (DCC)
R-Value Work:
0.147 (Depositor), 0.150 (DCC)
R-Value Observed:
0.148 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a putative endoribonuclease L-PSP from Entamoeba histolytica

Gardberg, A., Abendroth, J., Staker, B.

To be published.

Macromolecule Content

Total Structure Weight: 96.28 kDa
Atom Count: 6,943
Modeled Residue Count: 817
Deposited Residue Count: 888
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative Endoribonuclease L-PSP	A, B, C, D, E A, B, C, D, E, F	148	Entamoeba histolytica	Mutation(s): 0 Gene Names: EHI_087570, HM-1:IMSS
UniProt
Find proteins for C4LXT9 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM)) Explore C4LXT9 Go to UniProtKB: C4LXT9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C4LXT9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FLC Query on FLC Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain M [auth C] SDF format, chain U [auth E] SDF format, chain Q [auth D] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain M [auth C] MOL2 format, chain U [auth E] MOL2 format, chain Q [auth D] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain M [auth C] mmCIF format, chain U [auth E] mmCIF format, chain Q [auth D]	G [auth A], I [auth B], M [auth C], Q [auth D], U [auth E]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain Q [auth D] Focus chain U [auth E] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain Q [auth D] Focus chain U [auth E]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain R [auth D] SDF format, chain T [auth E] SDF format, chain W [auth F] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain R [auth D] MOL2 format, chain T [auth E] MOL2 format, chain W [auth F] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain R [auth D] mmCIF format, chain T [auth E] mmCIF format, chain W [auth F]	J [auth B] K [auth B] N [auth C] O [auth C] R [auth D] J [auth B], K [auth B], N [auth C], O [auth C], R [auth D], T [auth E], W [auth F]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain R [auth D] Focus chain T [auth E] Focus chain W [auth F] Interactions & Density Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain R [auth D] Focus chain T [auth E] Focus chain W [auth F]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain P [auth C] SDF format, chain S [auth D] SDF format, chain V [auth E] SDF format, chain X [auth F] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain P [auth C] MOL2 format, chain S [auth D] MOL2 format, chain V [auth E] MOL2 format, chain X [auth F] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain P [auth C] mmCIF format, chain S [auth D] mmCIF format, chain V [auth E] mmCIF format, chain X [auth F]	H [auth A] L [auth B] P [auth C] S [auth D] V [auth E] H [auth A], L [auth B], P [auth C], S [auth D], V [auth E], X [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain S [auth D] Focus chain V [auth E] Focus chain X [auth F] Interactions & Density Focus chain H [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain S [auth D] Focus chain V [auth E] Focus chain X [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.183 (Depositor), 0.190 (DCC)
R-Value Work: 0.147 (Depositor), 0.150 (DCC)
R-Value Observed: 0.148 (Depositor)

Diffraction Data: https://doi.org/10.18430/M33MQW

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84	α = 90
b = 99.72	β = 90
c = 106.1	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2010-05-12

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2010-05-12
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description