5I84 | pdb_00005i84

Structure of the Xanthomonas citri phosphate-binding protein PhoX

PDB DOI: https://doi.org/10.2210/pdb5I84/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Xanthomonas citri subsp. citri 306
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-02-18 Released: 2016-06-15
Deposition Author(s): Pegos, V.R., Medrano, F.J., Balan, A.
Funding Organization(s): Sao Paulo Research Foundation (FAPESP)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.98 Å
R-Value Free:
0.249 (Depositor), 0.269 (DCC)
R-Value Work:
0.174 (Depositor), 0.193 (DCC)
R-Value Observed:
0.178 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

A gene duplication in phosphate-binding proteins from pho regulon of Xanthomonas citri: functional and structural studies

Pegos, V.R., Santos, R.M.L., Medrano, F.J., Balan, A.

To be published.

Macromolecule Content

Total Structure Weight: 286.15 kDa
Atom Count: 18,875
Modeled Residue Count: 2,506
Deposited Residue Count: 2,680
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphate-binding protein PstS	A, B, C, D, E A, B, C, D, E, F, G, H	335	Xanthomonas citri subsp. citri 306	Mutation(s): 0 Gene Names: phoX, XAC1578

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain Y [auth D] SDF format, chain X [auth D] SDF format, chain W [auth D] SDF format, chain V [auth D] SDF format, chain U [auth C] SDF format, chain T [auth C] SDF format, chain S [auth C] SDF format, chain R [auth C] SDF format, chain Q [auth B] SDF format, chain PA [auth H] SDF format, chain P [auth B] SDF format, chain OA [auth H] SDF format, chain O [auth B] SDF format, chain NA [auth H] SDF format, chain N [auth B] SDF format, chain MA [auth G] SDF format, chain M [auth B] SDF format, chain LA [auth G] SDF format, chain L [auth A] SDF format, chain KA [auth F] SDF format, chain K [auth A] SDF format, chain JA [auth F] SDF format, chain J [auth A] SDF format, chain IA [auth F] SDF format, chain I [auth A] SDF format, chain HA [auth F] SDF format, chain GA [auth F] SDF format, chain FA [auth F] SDF format, chain EA [auth E] SDF format, chain DA [auth E] SDF format, chain CA [auth E] SDF format, chain BA [auth E] SDF format, chain AA [auth E] MOL2 format, chain Z [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain X [auth D] MOL2 format, chain W [auth D] MOL2 format, chain V [auth D] MOL2 format, chain U [auth C] MOL2 format, chain T [auth C] MOL2 format, chain S [auth C] MOL2 format, chain R [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain PA [auth H] MOL2 format, chain P [auth B] MOL2 format, chain OA [auth H] MOL2 format, chain O [auth B] MOL2 format, chain NA [auth H] MOL2 format, chain N [auth B] MOL2 format, chain MA [auth G] MOL2 format, chain M [auth B] MOL2 format, chain LA [auth G] MOL2 format, chain L [auth A] MOL2 format, chain KA [auth F] MOL2 format, chain K [auth A] MOL2 format, chain JA [auth F] MOL2 format, chain J [auth A] MOL2 format, chain IA [auth F] MOL2 format, chain I [auth A] MOL2 format, chain HA [auth F] MOL2 format, chain GA [auth F] MOL2 format, chain FA [auth F] MOL2 format, chain EA [auth E] MOL2 format, chain DA [auth E] MOL2 format, chain CA [auth E] MOL2 format, chain BA [auth E] MOL2 format, chain AA [auth E] mmCIF format, chain Z [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain X [auth D] mmCIF format, chain W [auth D] mmCIF format, chain V [auth D] mmCIF format, chain U [auth C] mmCIF format, chain T [auth C] mmCIF format, chain S [auth C] mmCIF format, chain R [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain PA [auth H] mmCIF format, chain P [auth B] mmCIF format, chain OA [auth H] mmCIF format, chain O [auth B] mmCIF format, chain NA [auth H] mmCIF format, chain N [auth B] mmCIF format, chain MA [auth G] mmCIF format, chain M [auth B] mmCIF format, chain LA [auth G] mmCIF format, chain L [auth A] mmCIF format, chain KA [auth F] mmCIF format, chain K [auth A] mmCIF format, chain JA [auth F] mmCIF format, chain J [auth A] mmCIF format, chain IA [auth F] mmCIF format, chain I [auth A] mmCIF format, chain HA [auth F] mmCIF format, chain GA [auth F] mmCIF format, chain FA [auth F] mmCIF format, chain EA [auth E] mmCIF format, chain DA [auth E] mmCIF format, chain CA [auth E] mmCIF format, chain BA [auth E] mmCIF format, chain AA [auth E]	AA [auth E] BA [auth E] CA [auth E] DA [auth E] EA [auth E] AA [auth E], BA [auth E], CA [auth E], DA [auth E], EA [auth E], FA [auth F], GA [auth F], HA [auth F], I [auth A], IA [auth F], J [auth A], JA [auth F], K [auth A], KA [auth F], L [auth A], LA [auth G], M [auth B], MA [auth G], N [auth B], NA [auth H], O [auth B], OA [auth H], P [auth B], PA [auth H], Q [auth B], R [auth C], S [auth C], T [auth C], U [auth C], V [auth D], W [auth D], X [auth D], Y [auth D], Z [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain AA [auth E] Focus chain BA [auth E] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain FA [auth F] Focus chain GA [auth F] Focus chain HA [auth F] Focus chain I [auth A] Focus chain IA [auth F] Focus chain J [auth A] Focus chain JA [auth F] Focus chain K [auth A] Focus chain KA [auth F] Focus chain L [auth A] Focus chain LA [auth G] Focus chain M [auth B] Focus chain MA [auth G] Focus chain N [auth B] Focus chain NA [auth H] Focus chain O [auth B] Focus chain OA [auth H] Focus chain P [auth B] Focus chain PA [auth H] Focus chain Q [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth E] Focus chain BA [auth E] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain FA [auth F] Focus chain GA [auth F] Focus chain HA [auth F] Focus chain I [auth A] Focus chain IA [auth F] Focus chain J [auth A] Focus chain JA [auth F] Focus chain K [auth A] Focus chain KA [auth F] Focus chain L [auth A] Focus chain LA [auth G] Focus chain M [auth B] Focus chain MA [auth G] Focus chain N [auth B] Focus chain NA [auth H] Focus chain O [auth B] Focus chain OA [auth H] Focus chain P [auth B] Focus chain PA [auth H] Focus chain Q [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.98 Å
R-Value Free: 0.249 (Depositor), 0.269 (DCC)
R-Value Work: 0.174 (Depositor), 0.193 (DCC)
R-Value Observed: 0.178 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.556	α = 90
b = 115.643	β = 90.33
c = 133.323	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2016-06-15

Deposition Author(s):

Pegos, V.R.

Medrano, F.J.

Balan, A.

Funding Organization	Location	Grant Number
Sao Paulo Research Foundation (FAPESP)	Brazil	2011-20468-1

Revision History (Full details and data files)

Version 1.0: 2016-06-15
Type: Initial release
Version 1.1: 2016-10-19
Changes: Data collection
Version 1.2: 2017-08-09
Changes: Database references, Derived calculations
Version 1.3: 2019-04-17
Changes: Author supporting evidence, Data collection
Version 1.4: 2020-01-01
Changes: Author supporting evidence
Version 1.5: 2023-09-27
Changes: Data collection, Database references, Refinement description