6XJ9 | pdb_00006xj9

Structure of PfGH50B

PDB DOI: https://doi.org/10.2210/pdb6XJ9/pdb

Classification: HYDROLASE
Organism(s): Pseudoalteromonas fuliginea
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-06-23 Released: 2020-09-16
Deposition Author(s): Pluvinage, B., Boraston, A.B.
Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.269 (Depositor), 0.270 (DCC)
R-Value Work:
0.224 (Depositor), 0.220 (DCC)
R-Value Observed:
0.227 (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

The structure of PfGH50B, an agarase from the marine bacterium Pseudoalteromonas fuliginea PS47

Pluvinage, B., Robb, C.S., Jeffries, R., Boraston, A.B.

(2020) Acta Crystallogr F Struct Biol Commun 76: 422-427

DOI: https://doi.org/10.1107/S2053230X20010328

Macromolecule Content

Total Structure Weight: 173.18 kDa
Atom Count: 11,402
Modeled Residue Count: 1,387
Deposited Residue Count: 1,530
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Agarase	A, B	765	Pseudoalteromonas fuliginea	Mutation(s): 0 Gene Names: EUZ79_06745
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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 D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.269 (Depositor), 0.270 (DCC)
R-Value Work: 0.224 (Depositor), 0.220 (DCC)
R-Value Observed: 0.227 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.24	α = 90
b = 76.26	β = 90
c = 269.86	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2020-09-16

Deposition Author(s):

Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	--

Revision History (Full details and data files)

Version 1.0: 2020-09-16
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Database references, Refinement description

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.