7VU0 | pdb_00007vu0

Chitoporin from Escherichia coli

PDB DOI: https://doi.org/10.2210/pdb7VU0/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): No
Membrane Protein: Yes OPM PDBTM

Deposited: 2021-11-01 Released: 2022-11-09
Deposition Author(s): Suginta, W., Soysa, H.S.M., Amornloetwattana, R., van den Berg, B.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.253 (Depositor), 0.254 (DCC)
R-Value Work:
0.215 (Depositor), 0.218 (DCC)
R-Value Observed:
0.217 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Chitoporin from Escherichia coli

Suginta, W., Soysa, H.S.M., Amornloetwattana, R., van den Berg, B.

To be published.

Macromolecule Content

Total Structure Weight: 117.82 kDa
Atom Count: 8,223
Modeled Residue Count: 870
Deposited Residue Count: 884
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chitoporin	A, B	442	Escherichia coli K-12	Mutation(s): 0 Gene Names: chiP, ybfM, b0681, JW0667 Membrane Entity: Yes
UniProt
Find proteins for P75733 (Escherichia coli (strain K12)) Explore P75733 Go to UniProtKB: P75733
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P75733
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DMU Query on DMU Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain EA [auth B] SDF format, chain FA [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain EA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth A], EA [auth B], FA [auth B]	DECYL-BETA-D-MALTOPYRANOSIDE C₂₂ H₄₂ O₁₁ WOQQAWHSKSSAGF-WXFJLFHKSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain EA [auth B] Focus chain FA [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain EA [auth B] Focus chain FA [auth B]
C8E Query on C8E Download:Ideal Coordinates CCD File SDF format, chain AB [auth B] SDF format, chain CB [auth B] SDF format, chain DB [auth B] SDF format, chain EB [auth B] SDF format, chain FB [auth B] SDF format, chain GA [auth B] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain IA [auth B] SDF format, chain J [auth A] SDF format, chain JA [auth B] SDF format, chain K [auth A] SDF format, chain M [auth A] SDF format, chain MA [auth B] SDF format, chain N [auth A] SDF format, chain NA [auth B] SDF format, chain OA [auth B] 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 RA [auth B] SDF format, chain S [auth A] SDF format, chain T [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 WA [auth B] SDF format, chain X [auth A] SDF format, chain XA [auth B] SDF format, chain Y [auth A] SDF format, chain YA [auth B] SDF format, chain ZA [auth B] SDF format, chain Z [auth A] SDF format, chain U [auth A] SDF format, chain TA [auth B] SDF format, chain SA [auth B] SDF format, chain R [auth A] SDF format, chain O [auth A] SDF format, chain LA [auth B] SDF format, chain L [auth A] SDF format, chain KA [auth B] SDF format, chain HA [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain BB [auth B] SDF format, chain AA [auth A] MOL2 format, chain AB [auth B] MOL2 format, chain CB [auth B] MOL2 format, chain DB [auth B] MOL2 format, chain EB [auth B] MOL2 format, chain FB [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain K [auth A] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth B] MOL2 format, chain OA [auth B] 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 RA [auth B] MOL2 format, chain S [auth A] MOL2 format, chain T [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 WA [auth B] MOL2 format, chain X [auth A] MOL2 format, chain XA [auth B] MOL2 format, chain Y [auth A] MOL2 format, chain YA [auth B] MOL2 format, chain ZA [auth B] MOL2 format, chain Z [auth A] MOL2 format, chain U [auth A] MOL2 format, chain TA [auth B] MOL2 format, chain SA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain O [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain BB [auth B] MOL2 format, chain AA [auth A] mmCIF format, chain AB [auth B] mmCIF format, chain CB [auth B] mmCIF format, chain DB [auth B] mmCIF format, chain EB [auth B] mmCIF format, chain FB [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth B] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth B] mmCIF format, chain K [auth A] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth B] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth B] mmCIF format, chain OA [auth B] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth B] mmCIF format, chain RA [auth B] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain UA [auth B] mmCIF format, chain V [auth A] mmCIF format, chain VA [auth B] mmCIF format, chain W [auth A] mmCIF format, chain WA [auth B] mmCIF format, chain X [auth A] mmCIF format, chain XA [auth B] mmCIF format, chain Y [auth A] mmCIF format, chain YA [auth B] mmCIF format, chain ZA [auth B] mmCIF format, chain Z [auth A] mmCIF format, chain U [auth A] mmCIF format, chain TA [auth B] mmCIF format, chain SA [auth B] mmCIF format, chain R [auth A] mmCIF format, chain O [auth A] mmCIF format, chain LA [auth B] mmCIF format, chain L [auth A] mmCIF format, chain KA [auth B] mmCIF format, chain HA [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain BB [auth B] mmCIF format, chain AA [auth A]	AA [auth A] AB [auth B] BB [auth B] CB [auth B] DB [auth B] AA [auth A], AB [auth B], BB [auth B], CB [auth B], DB [auth B], E [auth A], EB [auth B], F [auth A], FB [auth B], G [auth A], GA [auth B], H [auth A], HA [auth B], I [auth A], IA [auth B], J [auth A], JA [auth B], K [auth A], KA [auth B], L [auth A], LA [auth B], M [auth A], MA [auth B], N [auth A], NA [auth B], O [auth A], OA [auth B], 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], WA [auth B], X [auth A], XA [auth B], Y [auth A], YA [auth B], Z [auth A], ZA [auth B]	(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE C₁₆ H₃₄ O₅ FEOZZFHAVXYAMB-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain AB [auth B] Focus chain BB [auth B] Focus chain CB [auth B] Focus chain DB [auth B] Focus chain E [auth A] Focus chain EB [auth B] Focus chain F [auth A] Focus chain FB [auth B] Focus chain G [auth A] Focus chain GA [auth B] Focus chain H [auth A] Focus chain HA [auth B] Focus chain I [auth A] Focus chain IA [auth B] Focus chain J [auth A] Focus chain JA [auth B] Focus chain K [auth A] Focus chain KA [auth B] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain NA [auth B] Focus chain O [auth A] Focus chain OA [auth B] 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 WA [auth B] Focus chain X [auth A] Focus chain XA [auth B] Focus chain Y [auth A] Focus chain YA [auth B] Focus chain Z [auth A] Focus chain ZA [auth B] Interactions & Density Focus chain AA [auth A] Focus chain AB [auth B] Focus chain BB [auth B] Focus chain CB [auth B] Focus chain DB [auth B] Focus chain E [auth A] Focus chain EB [auth B] Focus chain F [auth A] Focus chain FB [auth B] Focus chain G [auth A] Focus chain GA [auth B] Focus chain H [auth A] Focus chain HA [auth B] Focus chain I [auth A] Focus chain IA [auth B] Focus chain J [auth A] Focus chain JA [auth B] Focus chain K [auth A] Focus chain KA [auth B] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain NA [auth B] Focus chain O [auth A] Focus chain OA [auth B] 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 WA [auth B] Focus chain X [auth A] Focus chain XA [auth B] Focus chain Y [auth A] Focus chain YA [auth B] Focus chain Z [auth A] Focus chain ZA [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain BA [auth A] SDF format, chain GB [auth B] SDF format, chain HB [auth B] SDF format, chain IB [auth B] SDF format, chain JB [auth B] SDF format, chain KB [auth B] SDF format, chain DA [auth A] SDF format, chain CA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain GB [auth B] MOL2 format, chain HB [auth B] MOL2 format, chain IB [auth B] MOL2 format, chain JB [auth B] MOL2 format, chain KB [auth B] MOL2 format, chain DA [auth A] MOL2 format, chain CA [auth A] mmCIF format, chain BA [auth A] mmCIF format, chain GB [auth B] mmCIF format, chain HB [auth B] mmCIF format, chain IB [auth B] mmCIF format, chain JB [auth B] mmCIF format, chain KB [auth B] mmCIF format, chain DA [auth A] mmCIF format, chain CA [auth A]	BA [auth A] CA [auth A] DA [auth A] GB [auth B] HB [auth B] BA [auth A], CA [auth A], DA [auth A], GB [auth B], HB [auth B], IB [auth B], JB [auth B], KB [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth A] Focus chain CA [auth A] Focus chain DA [auth A] Focus chain GB [auth B] Focus chain HB [auth B] Focus chain IB [auth B] Focus chain JB [auth B] Focus chain KB [auth B] Interactions & Density Focus chain BA [auth A] Focus chain CA [auth A] Focus chain DA [auth A] Focus chain GB [auth B] Focus chain HB [auth B] Focus chain IB [auth B] Focus chain JB [auth B] Focus chain KB [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.253 (Depositor), 0.254 (DCC)
R-Value Work: 0.215 (Depositor), 0.218 (DCC)
R-Value Observed: 0.217 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.077	α = 90
b = 58.864	β = 110.826
c = 134.709	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-11-09

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2022-11-09
Type: Initial release
Version 1.1: 2023-07-12
Changes: Data collection, Database references, Structure summary
Version 1.2: 2023-11-29
Changes: Data collection, Refinement description