3WUX | pdb_00003wux

Crystal structure of unsaturated glucuronyl hydrolase mutant D115N/K370S from Streptococcus agalactiae

PDB DOI: https://doi.org/10.2210/pdb3WUX/pdb

Classification: HYDROLASE
Organism(s): Streptococcus agalactiae NEM316
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2014-05-08 Released: 2014-05-28
Deposition Author(s): Nakamichi, Y., Oiki, S., Mikami, B., Murata, K., Hashimoto, W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free:
0.209 (Depositor), 0.209 (DCC)
R-Value Work:
0.182 (Depositor), 0.184 (DCC)
R-Value Observed:
0.184 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of unsaturated glucuronyl hydrolase mutant D115N/K370S from Streptococcus agalactiae

Nakamichi, Y., Oiki, S., Mikami, B., Murata, K., Hashimoto, W.

To be published.

Macromolecule Content

Total Structure Weight: 47.34 kDa
Atom Count: 3,355
Modeled Residue Count: 376
Deposited Residue Count: 398
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Unsaturated chondroitin disaccharide hydrolase	A	398	Streptococcus agalactiae NEM316	Mutation(s): 2 Gene Names: gbs1889 EC: 3.2.1.180
UniProt
Find proteins for Q8E372 (Streptococcus agalactiae serotype III (strain NEM316)) Explore Q8E372 Go to UniProtKB: Q8E372
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8E372
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain K [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain K [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain K [auth A] mmCIF format, chain B [auth A]	B [auth A] C [auth A] D [auth A] E [auth A] F [auth A] B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] 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 K [auth A] Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] 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 K [auth A] Focus chain L [auth A] Focus chain M [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free: 0.209 (Depositor), 0.209 (DCC)
R-Value Work: 0.182 (Depositor), 0.184 (DCC)
R-Value Observed: 0.184 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.628	α = 90
b = 53.458	β = 97.01
c = 70.185	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-05-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-05-28
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description