3ED4 | pdb_00003ed4

Crystal structure of putative arylsulfatase from escherichia coli

PDB DOI: https://doi.org/10.2210/pdb3ED4/pdb

Classification: TRANSFERASE
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-09-02 Released: 2008-09-16
Deposition Author(s): Patskovsky, Y., Ozyurt, S., Gilmore, M., Chang, S., Bain, K., Wasserman, S., Koss, J., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.242 (Depositor), 0.240 (DCC)
R-Value Work:
0.196 (Depositor), 0.194 (DCC)
R-Value Observed:
0.198 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of Arylsulfatase from Escherichia Coli

Patskovsky, Y., Ozyurt, S., Gilmore, M., Chang, S., Bain, K., Wasserman, S., Koss, J., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 226.76 kDa
Atom Count: 16,828
Modeled Residue Count: 1,883
Deposited Residue Count: 2,008
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ARYLSULFATASE	A, B, C, D	502	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for A0A0H2V4H2 (Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)) Explore A0A0H2V4H2 Go to UniProtKB: A0A0H2V4H2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H2V4H2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain S [auth D] SDF format, chain P [auth C] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain S [auth D] MOL2 format, chain P [auth C] mmCIF format, chain H [auth A] mmCIF format, chain K [auth B] mmCIF format, chain S [auth D] mmCIF format, chain P [auth C]	H [auth A], K [auth B], P [auth C], S [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain S [auth D] Interactions & Density Focus chain H [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain S [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain M [auth B] SDF format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain M [auth B] MOL2 format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain M [auth B] mmCIF format, chain E [auth A]	E [auth A], J [auth B], M [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain M [auth B] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain M [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain O [auth C] SDF format, chain T [auth D] SDF format, chain Q [auth C] SDF format, chain L [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain O [auth C] MOL2 format, chain T [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain L [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain O [auth C] mmCIF format, chain T [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain L [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A] G [auth A] L [auth B] O [auth C] Q [auth C] F [auth A], G [auth A], L [auth B], O [auth C], Q [auth C], T [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain Q [auth C] Focus chain T [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain Q [auth C] Focus chain T [auth D]
UNL Query on UNL Download:Ideal Coordinates CCD File	I [auth A] N [auth B] R [auth C] U [auth D] V [auth D] I [auth A], N [auth B], R [auth C], U [auth D], V [auth D], W [auth D]	Unknown ligand FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain N [auth B] Focus chain R [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D] Interactions & Density Focus chain I [auth A] Focus chain N [auth B] Focus chain R [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.242 (Depositor), 0.240 (DCC)
R-Value Work: 0.196 (Depositor), 0.194 (DCC)
R-Value Observed: 0.198 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.932	α = 90
b = 178.858	β = 92.17
c = 76.284	γ = 90

Software Package:

Software Name	Purpose
SHELXD	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-09-16

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2008-09-16
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2012-10-24
Changes: Structure summary
Version 1.3: 2018-11-14
Changes: Data collection, Structure summary
Version 1.4: 2021-02-10
Changes: Database references, Derived calculations, Structure summary
Version 1.5: 2024-02-21
Changes: Data collection, Database references