4HIZ

Phage phi92 endosialidase

PDB DOI: https://doi.org/10.2210/pdb4HIZ/pdb

Classification: HYDROLASE,VIRAL PROTEIN
Organism(s): Escherichia phage phi92
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-10-12 Released: 2014-01-15
Deposition Author(s): Schwarzer, D., Browning, C., Leiman, P.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.147
R-Value Work: 0.107
R-Value Observed: 0.107

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Literature

Crystal Structure of Endosialidase from Phage phi92 that cleaves alpha2,8- and alpha2,9-linked polysialic acid

Schwarzer, D., Browning, C., Oberbeck, A., Stummeyer, K., Muhlenhoff, M., Gerardy-Schahn, R., Leiman, P.G.

To be published.

Macromolecule Content

Total Structure Weight: 234.2 kDa
Atom Count: 19,802
Modelled Residue Count: 1,965
Deposited Residue Count: 2,049
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endosialidase	A, B, C	683	Escherichia phage phi92	Mutation(s): 0 Gene Names: gene 143, PHI92_gene_143 EC: 3.2.1.129
UniProt
Find proteins for I7HXG2 (Escherichia phage phi92) Explore I7HXG2 Go to UniProtKB: I7HXG2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	I7HXG2
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-9)-N-acetyl-beta-neuraminic acid	D, E, F	2		N/A	Interactions Focus chain D Focus chain E Focus chain F Interactions & Density Focus chain D Focus chain E Focus chain F
Glycosylation Resources
GlyTouCan: G64530AY GlyCosmos: G64530AY GlyGen: G64530AY

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	G, H, I	2		N/A	Interactions Focus chain G Focus chain H Focus chain I Interactions & Density Focus chain G Focus chain H Focus chain I
Glycosylation Resources
GlyTouCan: G05551OP GlyCosmos: G05551OP

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain BB [auth C] SDF format, chain CB [auth C] SDF format, chain DB [auth C] SDF format, chain EB [auth C] SDF format, chain FB [auth C] SDF format, chain GB [auth C] SDF format, chain HB [auth C] SDF format, chain IB [auth C] SDF format, chain J [auth A] SDF format, chain JA [auth B] SDF format, chain JB [auth C] SDF format, chain K [auth A] SDF format, chain KA [auth B] SDF format, chain KB [auth C] SDF format, chain L [auth A] SDF format, chain LA [auth B] SDF format, chain LB [auth C] SDF format, chain M [auth A] SDF format, chain MA [auth B] SDF format, chain MB [auth C] SDF format, chain N [auth A] SDF format, chain NA [auth B] SDF format, chain NB [auth C] SDF format, chain O [auth A] SDF format, chain OA [auth B] SDF format, chain OB [auth C] SDF format, chain P [auth A] SDF format, chain PA [auth B] SDF format, chain Q [auth A] SDF format, chain QA [auth B] SDF format, chain R [auth A] SDF format, chain RA [auth B] SDF format, chain S [auth A] SDF format, chain SA [auth B] SDF format, chain T [auth A] SDF format, chain TA [auth B] SDF format, chain U [auth A] SDF format, chain UA [auth B] SDF format, chain V [auth A] SDF format, chain VA [auth B] SDF format, chain W [auth A] SDF format, chain X [auth A] SDF format, chain Y [auth A] MOL2 format, chain BB [auth C] MOL2 format, chain CB [auth C] MOL2 format, chain DB [auth C] MOL2 format, chain EB [auth C] MOL2 format, chain FB [auth C] MOL2 format, chain GB [auth C] MOL2 format, chain HB [auth C] MOL2 format, chain IB [auth C] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain JB [auth C] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain KB [auth C] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain LB [auth C] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth B] MOL2 format, chain MB [auth C] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth B] MOL2 format, chain NB [auth C] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth B] MOL2 format, chain OB [auth C] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth B] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth B] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth B] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth B] MOL2 format, chain V [auth A] MOL2 format, chain VA [auth B] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A]	BB [auth C] CB [auth C] DB [auth C] EB [auth C] FB [auth C] BB [auth C], CB [auth C], DB [auth C], EB [auth C], FB [auth C], GB [auth C], HB [auth C], IB [auth C], J [auth A], JA [auth B], JB [auth C], K [auth A], KA [auth B], KB [auth C], L [auth A], LA [auth B], LB [auth C], M [auth A], MA [auth B], MB [auth C], N [auth A], NA [auth B], NB [auth C], O [auth A], OA [auth B], OB [auth C], P [auth A], PA [auth B], Q [auth A], QA [auth B], R [auth A], RA [auth B], S [auth A], SA [auth B], T [auth A], TA [auth B], U [auth A], UA [auth B], V [auth A], VA [auth B], W [auth A], X [auth A], Y [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain BB [auth C] Focus chain CB [auth C] Focus chain DB [auth C] Focus chain EB [auth C] Focus chain FB [auth C] Focus chain GB [auth C] Focus chain HB [auth C] Focus chain IB [auth C] Focus chain J [auth A] Focus chain JA [auth B] Focus chain JB [auth C] Focus chain K [auth A] Focus chain KA [auth B] Focus chain KB [auth C] Focus chain L [auth A] Focus chain LA [auth B] Focus chain LB [auth C] Focus chain M [auth A] Focus chain MA [auth B] Focus chain MB [auth C] Focus chain N [auth A] Focus chain NA [auth B] Focus chain NB [auth C] Focus chain O [auth A] Focus chain OA [auth B] Focus chain OB [auth C] Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain T [auth A] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain VA [auth B] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Interactions & Density Focus chain BB [auth C] Focus chain CB [auth C] Focus chain DB [auth C] Focus chain EB [auth C] Focus chain FB [auth C] Focus chain GB [auth C] Focus chain HB [auth C] Focus chain IB [auth C] Focus chain J [auth A] Focus chain JA [auth B] Focus chain JB [auth C] Focus chain K [auth A] Focus chain KA [auth B] Focus chain KB [auth C] Focus chain L [auth A] Focus chain LA [auth B] Focus chain LB [auth C] Focus chain M [auth A] Focus chain MA [auth B] Focus chain MB [auth C] Focus chain N [auth A] Focus chain NA [auth B] Focus chain NB [auth C] Focus chain O [auth A] Focus chain OA [auth B] Focus chain OB [auth C] Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain T [auth A] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain VA [auth B] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain CA [auth A] SDF format, chain DA [auth A] SDF format, chain QB [auth C] SDF format, chain RB [auth C] SDF format, chain YA [auth B] SDF format, chain ZA [auth B] MOL2 format, chain CA [auth A] MOL2 format, chain DA [auth A] MOL2 format, chain QB [auth C] MOL2 format, chain RB [auth C] MOL2 format, chain YA [auth B] MOL2 format, chain ZA [auth B]	CA [auth A] DA [auth A] QB [auth C] RB [auth C] YA [auth B] CA [auth A], DA [auth A], QB [auth C], RB [auth C], YA [auth B], ZA [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain CA [auth A] Focus chain DA [auth A] Focus chain QB [auth C] Focus chain RB [auth C] Focus chain YA [auth B] Focus chain ZA [auth B] Interactions & Density Focus chain CA [auth A] Focus chain DA [auth A] Focus chain QB [auth C] Focus chain RB [auth C] Focus chain YA [auth B] Focus chain ZA [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain BA [auth A] SDF format, chain PB [auth C] SDF format, chain XA [auth B] MOL2 format, chain AA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain PB [auth C] MOL2 format, chain XA [auth B]	AA [auth A], BA [auth A], PB [auth C], XA [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain PB [auth C] Focus chain XA [auth B] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] Focus chain PB [auth C] Focus chain XA [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain WA [auth B] SDF format, chain Z [auth A] MOL2 format, chain WA [auth B] MOL2 format, chain Z [auth A]	WA [auth B], Z [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain WA [auth B] Focus chain Z [auth A] Interactions & Density Focus chain WA [auth B] Focus chain Z [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain AB [auth B] SDF format, chain EA [auth A] SDF format, chain FA [auth A] SDF format, chain GA [auth A] SDF format, chain HA [auth A] SDF format, chain IA [auth A] SDF format, chain SB [auth C] SDF format, chain TB [auth C] SDF format, chain UB [auth C] SDF format, chain VB [auth C] SDF format, chain WB [auth C] SDF format, chain XB [auth C] MOL2 format, chain AB [auth B] MOL2 format, chain EA [auth A] MOL2 format, chain FA [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain HA [auth A] MOL2 format, chain IA [auth A] MOL2 format, chain SB [auth C] MOL2 format, chain TB [auth C] MOL2 format, chain UB [auth C] MOL2 format, chain VB [auth C] MOL2 format, chain WB [auth C] MOL2 format, chain XB [auth C]	AB [auth B] EA [auth A] FA [auth A] GA [auth A] HA [auth A] AB [auth B], EA [auth A], FA [auth A], GA [auth A], HA [auth A], IA [auth A], SB [auth C], TB [auth C], UB [auth C], VB [auth C], WB [auth C], XB [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain AB [auth B] Focus chain EA [auth A] Focus chain FA [auth A] Focus chain GA [auth A] Focus chain HA [auth A] Focus chain IA [auth A] Focus chain SB [auth C] Focus chain TB [auth C] Focus chain UB [auth C] Focus chain VB [auth C] Focus chain WB [auth C] Focus chain XB [auth C] Interactions & Density Focus chain AB [auth B] Focus chain EA [auth A] Focus chain FA [auth A] Focus chain GA [auth A] Focus chain HA [auth A] Focus chain IA [auth A] Focus chain SB [auth C] Focus chain TB [auth C] Focus chain UB [auth C] Focus chain VB [auth C] Focus chain WB [auth C] Focus chain XB [auth C]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003 Query on PRD_900003	G, H, I	sucrose	Oligosaccharide / Nutrient		Interactions Focus chain G Focus chain H Focus chain I Interactions & Density Focus chain G Focus chain H Focus chain I

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.147
R-Value Work: 0.107
R-Value Observed: 0.107
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.858	α = 90
b = 137.584	β = 94.64
c = 140.778	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
RemDAq	data collection

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2014-01-15

Deposition Author(s):

Schwarzer, D.

Browning, C.

Leiman, P.G.

Revision History (Full details and data files)

Version 1.0: 2014-01-15
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2019-07-17
Changes: Data collection, Derived calculations, Refinement description
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2024-02-28
Changes: Data collection, Database references, Derived calculations, Structure summary