6E0V | pdb_00006e0v

Apo crystal structure of the colanidase tailspike protein gp150 of Phage Phi92

PDB DOI: https://doi.org/10.2210/pdb6E0V/pdb
Entry: 6E0V supersedes: 4RMX

Classification: HYDROLASE
Organism(s): Escherichia phage phi92
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-07-07 Released: 2019-07-17
Deposition Author(s): Leiman, P.G., Browning, C., Gerardy-Schahn, R., Shneider, M.M., Plattner, M., Schwarzer, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.163 (Depositor), 0.159 (DCC)
R-Value Work:
0.134 (Depositor), 0.131 (DCC)
R-Value Observed:
0.135 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of the colanidase tailspike protein gp150 of Phage Phi92 complexed with one repeating unit of colanic acid

Browning, C., Plattner, M., Shneider, M.M., Gerardy-Schahn, R., Leiman, P.G., Schwarzer, D.

To be published.

Macromolecule Content

Total Structure Weight: 205.8 kDa
Atom Count: 16,598
Modeled Residue Count: 1,806
Deposited Residue Count: 1,878
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bacteriophage Phi92 gp150	A, B, C	626	Escherichia phage phi92	Mutation(s): 0 Gene Names: PHI92_gene_150, PHI92_150
UniProt
Find proteins for I7I026 (Escherichia phage phi92) Explore I7I026 Go to UniProtKB: I7I026
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	I7I026
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain WA [auth C] SDF format, chain VA [auth C] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain GA [auth B] SDF format, chain FA [auth B] SDF format, chain EA [auth B] MOL2 format, chain WA [auth C] MOL2 format, chain VA [auth C] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain EA [auth B] mmCIF format, chain WA [auth C] mmCIF format, chain VA [auth C] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain GA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain EA [auth B]	EA [auth B] FA [auth B] GA [auth B] N [auth A] O [auth A] EA [auth B], FA [auth B], GA [auth B], N [auth A], O [auth A], P [auth A], VA [auth C], WA [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain VA [auth C] Focus chain WA [auth C] Interactions & Density Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain VA [auth C] Focus chain WA [auth C]
SR Query on SR Download:Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain Y [auth B] SDF format, chain X [auth B] SDF format, chain W [auth B] SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain RA [auth C] SDF format, chain QA [auth C] SDF format, chain PA [auth C] SDF format, chain OA [auth C] SDF format, chain NA [auth C] SDF format, chain MA [auth C] SDF format, chain LA [auth C] SDF format, chain KA [auth C] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain AA [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain W [auth B] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain RA [auth C] MOL2 format, chain QA [auth C] MOL2 format, chain PA [auth C] MOL2 format, chain OA [auth C] MOL2 format, chain NA [auth C] MOL2 format, chain MA [auth C] MOL2 format, chain LA [auth C] MOL2 format, chain KA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain AA [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain W [auth B] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain RA [auth C] mmCIF format, chain QA [auth C] mmCIF format, chain PA [auth C] mmCIF format, chain OA [auth C] mmCIF format, chain NA [auth C] mmCIF format, chain MA [auth C] mmCIF format, chain LA [auth C] mmCIF format, chain KA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain AA [auth B]	AA [auth B] D [auth A] E [auth A] F [auth A] G [auth A] AA [auth B], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], KA [auth C], LA [auth C], MA [auth C], NA [auth C], OA [auth C], PA [auth C], QA [auth C], RA [auth C], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	STRONTIUM ION Sr PWYYWQHXAPXYMF-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain ZA [auth C] SDF format, chain YA [auth C] SDF format, chain XA [auth C] SDF format, chain R [auth A] SDF format, chain Q [auth A] SDF format, chain JA [auth B] SDF format, chain IA [auth B] SDF format, chain HA [auth B] MOL2 format, chain ZA [auth C] MOL2 format, chain YA [auth C] MOL2 format, chain XA [auth C] MOL2 format, chain R [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain HA [auth B] mmCIF format, chain ZA [auth C] mmCIF format, chain YA [auth C] mmCIF format, chain XA [auth C] mmCIF format, chain R [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain JA [auth B] mmCIF format, chain IA [auth B] mmCIF format, chain HA [auth B]	HA [auth B] IA [auth B] JA [auth B] Q [auth A] R [auth A] HA [auth B], IA [auth B], JA [auth B], Q [auth A], R [auth A], XA [auth C], YA [auth C], ZA [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain HA [auth B] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain Q [auth A] Focus chain R [auth A] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain ZA [auth C] Interactions & Density Focus chain HA [auth B] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain Q [auth A] Focus chain R [auth A] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain ZA [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain UA [auth C] SDF format, chain TA [auth C] SDF format, chain SA [auth C] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain DA [auth B] SDF format, chain CA [auth B] SDF format, chain BA [auth B] MOL2 format, chain UA [auth C] MOL2 format, chain TA [auth C] MOL2 format, chain SA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain BA [auth B] mmCIF format, chain UA [auth C] mmCIF format, chain TA [auth C] mmCIF format, chain SA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain DA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain BA [auth B]	BA [auth B] CA [auth B] DA [auth B] K [auth A] L [auth A] BA [auth B], CA [auth B], DA [auth B], K [auth A], L [auth A], M [auth A], SA [auth C], TA [auth C], UA [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain UA [auth C] Interactions & Density Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain UA [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.163 (Depositor), 0.159 (DCC)
R-Value Work: 0.134 (Depositor), 0.131 (DCC)
R-Value Observed: 0.135 (Depositor)

Space Group: P 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.4	α = 90
b = 118.4	β = 90
c = 140.166	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2019-07-17

Deposition Author(s):

This entry supersedes: 4RMX

Revision History (Full details and data files)

Version 1.0: 2019-07-17
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, Derived calculations, Refinement description