6DAY | pdb_00006day

Xanthomonas albilineans Dihydropteroate synthase with 4-aminobenzoic acid at 1.65 A

PDB DOI: https://doi.org/10.2210/pdb6DAY/pdb
Entry: 6DAY supersedes: 5UUR

Classification: TRANSFERASE
Organism(s): Xanthomonas albilineans GPE PC73
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-05-02 Released: 2018-06-06
Deposition Author(s): Oliveira, A.A., Guido, R.V.C., Lima, G.M.A., Bueno, R.V., Maluf, F.V.
Funding Organization(s): Sao Paulo Research Foundation (FAPESP)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.216 (Depositor), 0.215 (DCC)
R-Value Work:
0.177 (Depositor), 0.178 (DCC)
R-Value Observed:
0.179 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Xanthomonas albilineans Dihydropteroate synthase with 4-aminobenzoic acid

Oliveira, A.A., Guido, R.V.C., Lima, G.M.A., Maluf, F.V., Bueno, R.V.

To be published.

Macromolecule Content

Total Structure Weight: 129.48 kDa
Atom Count: 8,469
Modeled Residue Count: 1,065
Deposited Residue Count: 1,200
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydropteroate synthase	A, B, C, D	300	Xanthomonas albilineans GPE PC73	Mutation(s): 0 Gene Names: folP, XALc_1165 EC: 2.5.1.15
UniProt
Find proteins for D2UDM3 (Xanthomonas albilineans (strain GPE PC73 / CFBP 7063)) Explore D2UDM3 Go to UniProtKB: D2UDM3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D2UDM3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PAB Query on PAB Download Ideal Coordinates CCD File SDF format, chain T [auth D] SDF format, chain R [auth D] SDF format, chain N [auth C] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain T [auth D] MOL2 format, chain R [auth D] MOL2 format, chain N [auth C] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain T [auth D] mmCIF format, chain R [auth D] mmCIF format, chain N [auth C] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] I [auth B] J [auth B] K [auth B] E [auth A], F [auth A], I [auth B], J [auth B], K [auth B], N [auth C], R [auth D], T [auth D]	4-AMINOBENZOIC ACID C₇ H₇ N O₂ ALYNCZNDIQEVRV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth C] Focus chain R [auth D] Focus chain T [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth C] Focus chain R [auth D] Focus chain T [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain U [auth D] SDF format, chain Q [auth C] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain U [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain U [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] L [auth B] M [auth B] Q [auth C] G [auth A], H [auth A], L [auth B], M [auth B], Q [auth C], U [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain Q [auth C] Focus chain U [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain Q [auth C] Focus chain U [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain S [auth D] SDF format, chain P [auth C] SDF format, chain O [auth C] MOL2 format, chain S [auth D] MOL2 format, chain P [auth C] MOL2 format, chain O [auth C] mmCIF format, chain S [auth D] mmCIF format, chain P [auth C] mmCIF format, chain O [auth C]	O [auth C], P [auth C], S [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain O [auth C] Focus chain P [auth C] Focus chain S [auth D] Interactions & Density Focus chain O [auth C] Focus chain P [auth C] Focus chain S [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.216 (Depositor), 0.215 (DCC)
R-Value Work: 0.177 (Depositor), 0.178 (DCC)
R-Value Observed: 0.179 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.589	α = 90
b = 75.387	β = 101.102
c = 89.106	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2018-06-06

Deposition Author(s):

This entry supersedes: 5UUR

Funding Organization	Location	Grant Number
Sao Paulo Research Foundation (FAPESP)	Brazil	2015/07005-3

Revision History (Full details and data files)

Version 1.0: 2018-06-06
Type: Initial release
Version 1.1: 2020-01-01
Changes: Author supporting evidence
Version 1.2: 2023-10-04
Changes: Data collection, Database references, Refinement description
Version 1.3: 2024-12-25
Changes: Advisory, Derived calculations, Structure summary