3ZWF | pdb_00003zwf

Crystal structure of Human tRNase Z, short form (ELAC1).

PDB DOI: https://doi.org/10.2210/pdb3ZWF/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-07-29 Released: 2011-08-10
Deposition Author(s): Allerston, C.K., Krojer, T., Berridge, G., Burgess-Brown, N., Chaikuad, A., Chalk, R., Elkins, J.M., Gileadi, C., Latwiel, S.V.A., Savitsky, P., Vollmar, M., Arrowsmith, C.H., Weigelt, J., Edwards, A., Bountra, C., von Delft, F., Gileadi, O.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.210 (Depositor), 0.212 (DCC)
R-Value Work:
0.187 (Depositor), 0.189 (DCC)
R-Value Observed:
0.188 (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

Crystal Structure of Human Trnase Z, Short Form (Elac1).

Allerston, C.K., Krojer, T., Berridge, G., Burgess-Brown, N., Chaikuad, A., Chalk, R., Elkins, J.M., Gileadi, C., Latwiel, S.V.A., Savitsky, P., Vollmar, M., Arrowsmith, C.H., Weigelt, J., Edwards, A., Bountra, C., von Delft, F., Gileadi, O.

To be published.

Macromolecule Content

Total Structure Weight: 82.54 kDa
Atom Count: 4,292
Modeled Residue Count: 518
Deposited Residue Count: 736
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ZINC PHOSPHODIESTERASE ELAC PROTEIN 1	A, B	368	Homo sapiens	Mutation(s): 0 EC: 3.1.26.11
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H777 (Homo sapiens) Explore Q9H777 Go to UniProtKB: Q9H777
PHAROS: Q9H777 GTEx: ENSG00000141642
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9H777
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain N [auth B] MOL2 format, chain F [auth A] MOL2 format, chain N [auth B] mmCIF format, chain F [auth A] mmCIF format, chain N [auth B]	F [auth A], N [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain F [auth A] Focus chain N [auth B] Interactions & Density Focus chain F [auth A] Focus chain N [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B]	D [auth A], E [auth A], L [auth B], M [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain L [auth B] Focus chain M [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] mmCIF format, chain C [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B]	C [auth A] G [auth A] H [auth A] I [auth A] J [auth A] C [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], P [auth B], Q [auth B], R [auth B], S [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain O [auth B] MOL2 format, chain O [auth B] mmCIF format, chain O [auth B]	O [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain O [auth B] Interactions & Density Focus chain O [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.210 (Depositor), 0.212 (DCC)
R-Value Work: 0.187 (Depositor), 0.189 (DCC)
R-Value Observed: 0.188 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.52	α = 90
b = 73.79	β = 98.69
c = 73.66	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2011-08-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-08-10
Type: Initial release
Version 1.1: 2011-08-24
Changes: Database references
Version 1.2: 2018-01-24
Changes: Database references, Structure summary
Version 1.3: 2024-05-01
Changes: Data collection, Database references, Derived calculations, Other, Refinement description