6B0J

Crystal structure of Ps i-CgsB in complex with k-i-k-neocarrahexaose

PDB DOI: https://doi.org/10.2210/pdb6B0J/pdb

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

Deposited: 2017-09-14 Released: 2018-03-14
Deposition Author(s): Hettle, A.G., Boraston, A.B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.234
R-Value Work: 0.214
R-Value Observed: 0.215

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 160.16 kDa
Atom Count: 11,252
Modelled Residue Count: 1,354
Deposited Residue Count: 1,356
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Iota-carrageenan sulfatase	A, B, C	452	Pseudoalteromonas	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
4-O-sulfo-beta-D-galactopyranose-(1-4)-3,6-anhydro-2-O-sulfo-alpha-D-galactopyranose-(1-3)-4-O-sulfo-beta-D-galactopyranose	D, F, G, H	3		N/A	Interactions Focus chain D Focus chain F Focus chain G Focus chain H Interactions & Density Focus chain D Focus chain F Focus chain G Focus chain H
Glycosylation Resources
GlyTouCan: G47184WN GlyCosmos: G47184WN

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
3,6-anhydro-2-O-sulfo-alpha-D-galactopyranose-(1-3)-4-O-sulfo-beta-D-galactopyranose	E	2		N/A	Interactions Focus chain E Interactions & Density Focus chain E
Glycosylation Resources
GlyTouCan: G58187OK GlyCosmos: G58187OK

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
G4S Query on G4S Download Ideal Coordinates CCD File SDF format, chain W [auth C] SDF format, chain J [auth A] SDF format, chain Q [auth B] MOL2 format, chain W [auth C] MOL2 format, chain J [auth A] MOL2 format, chain Q [auth B]	J [auth A], Q [auth B], W [auth C]	4-O-sulfo-beta-D-galactopyranose C₆ H₁₂ O₉ S LOTQRUGOUKUSEY-DGPNFKTASA-N		Interactions Focus chain J [auth A] Focus chain Q [auth B] Focus chain W [auth C] Interactions & Density Focus chain J [auth A] Focus chain Q [auth B] Focus chain W [auth C]
ARG Query on ARG Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain O [auth A] MOL2 format, chain AA [auth C] MOL2 format, chain O [auth A]	AA [auth C], O [auth A]	ARGININE C₆ H₁₅ N₄ O₂ ODKSFYDXXFIFQN-BYPYZUCNSA-O		Interactions Focus chain AA [auth C] Focus chain O [auth A] Interactions & Density Focus chain AA [auth C] Focus chain O [auth A]
9RN Query on 9RN Download Ideal Coordinates CCD File SDF format, chain X [auth C] SDF format, chain Y [auth C] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B]	K [auth A] L [auth A] R [auth B] S [auth B] T [auth B] K [auth A], L [auth A], R [auth B], S [auth B], T [auth B], X [auth C], Y [auth C]	3,6-anhydro-alpha-D-galactopyranose C₆ H₁₀ O₅ DCQFFOLNJVGHLW-RDQKPOQOSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain X [auth C] Focus chain Y [auth C] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain X [auth C] Focus chain Y [auth C]
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain U [auth B] SDF format, chain N [auth A] MOL2 format, chain U [auth B] MOL2 format, chain N [auth A]	N [auth A], U [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain N [auth A] Focus chain U [auth B] Interactions & Density Focus chain N [auth A] Focus chain U [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain M [auth A] MOL2 format, chain Z [auth C] MOL2 format, chain M [auth A]	M [auth A], Z [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain Z [auth C] Interactions & Density Focus chain M [auth A] Focus chain Z [auth C]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain P [auth B] SDF format, chain V [auth C] MOL2 format, chain I [auth A] MOL2 format, chain P [auth B] MOL2 format, chain V [auth C]	I [auth A], P [auth B], V [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain P [auth B] Focus chain V [auth C] Interactions & Density Focus chain I [auth A] Focus chain P [auth B] Focus chain V [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.234
R-Value Work: 0.214
R-Value Observed: 0.215
Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.39	α = 90
b = 123.39	β = 90
c = 240.11	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

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2018-03-14

Deposition Author(s):

Hettle, A.G.

Boraston, A.B.

Revision History (Full details and data files)

Version 1.0: 2018-03-14
Type: Initial release
Version 1.1: 2018-05-09
Changes: Data collection, Database references
Version 1.2: 2018-05-16
Changes: Data collection, Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary

Prepare Data

Validate Data

Deposit Data

Help and Resources

6B0J

Crystal structure of Ps i-CgsB in complex with k-i-k-neocarrahexaose

Entity ID: 1

Entity Groups

Sequence Annotations

Expand

Entity ID: 2

Glycosylation Resources