2Y6L

Xylopentaose binding X-2 engineered mutated CBM4-2 Carbohydrate Binding Module from a Thermostable Rhodothermus marinus Xylanase

PDB DOI: https://doi.org/10.2210/pdb2Y6L/pdb

Classification: HYDROLASE
Organism(s): Rhodothermus marinus
Expression System: Escherichia coli K-12
Mutation(s): Yes

Deposited: 2011-01-24 Released: 2012-03-07
Deposition Author(s): von Schantz, L., Hakansson, M., Logan, D.T., Walse, B., Osterlin, J., Nordberg-Karlsson, E., Ohlin, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.28 Å
R-Value Free: 0.183
R-Value Observed: 0.132

wwPDB Validation 3D Report Full Report

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

Macromolecule Content

Total Structure Weight: 18.66 kDa
Atom Count: 1,657
Modelled Residue Count: 167
Deposited Residue Count: 167
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
XYLANASE	A	167	Rhodothermus marinus	Mutation(s): 8 EC: 3.2.1.8
UniProt
Find proteins for Q7WTN6 (Rhodothermus marinus) Explore Q7WTN6 Go to UniProtKB: Q7WTN6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7WTN6
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose	B	5		N/A	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G47101GE GlyCosmos: G47101GE

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A]	C [auth A], D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-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: 1.28 Å
R-Value Free: 0.183
R-Value Observed: 0.132
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.9	α = 90
b = 49.48	β = 90
c = 62.49	γ = 90

Software Package:

Software Name	Purpose
SHELXL-97	refinement
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-03-07

Deposition Author(s):

Nordberg-Karlsson, E.

Ohlin, M.

Revision History (Full details and data files)

Version 1.0: 2012-03-07
Type: Initial release
Version 1.1: 2012-08-01
Changes: Database references
Version 1.2: 2018-01-17
Changes: Data collection, Database references, Structure summary
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
Version 2.1: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary

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Help and Resources

2Y6L

Xylopentaose binding X-2 engineered mutated CBM4-2 Carbohydrate Binding Module from a Thermostable Rhodothermus marinus Xylanase

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

Glycosylation Resources

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)