1X6N

Crystal structure of S. marcescens chitinase A mutant W167A in complex with allosamidin

PDB DOI: https://doi.org/10.2210/pdb1X6N/pdb

Classification: HYDROLASE
Organism(s): Serratia marcescens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2004-08-11 Released: 2005-07-26
Deposition Author(s): Aronson Jr., N.N., Halloran, B.A., Alexyev, M.F., Zhou, X.E., Wang, Y., Meehan, E.J., Chen, L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.238
R-Value Work: 0.214
R-Value Observed: 0.214

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

Muation of Trp167 at the -3 subsite of the chitin-binding cleft of S. marcescens chitinase A causes enhanced transglycosylation

Aronson Jr., N.N., Halloran, B.A., Alexyev, M.F., Zhou, X.E., Wang, Y., Meehan, E.J., Chen, L.

To be published.

Macromolecule Content

Total Structure Weight: 61.61 kDa
Atom Count: 4,347
Modelled Residue Count: 539
Deposited Residue Count: 563
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chitinase A	A	563	Serratia marcescens	Mutation(s): 1 Gene Names: chiA EC: 3.2.1.14
UniProt
Find proteins for P07254 (Serratia marcescens) Explore P07254 Go to UniProtKB: P07254
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P07254
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-allopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-allopyranose	B	2		N/A	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G77950XB GlyCosmos: G77950XB

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMI Query on AMI Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	ALLOSAMIZOLINE C₉ H₁₆ N₂ O₄ MKJAYSJDHSEFRI-PVFLNQBWSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000468 Query on PRD_000468	B	Allosamidin	Oligosaccharide / Inhibitor		Interactions Focus chain B Interactions & Density Focus chain B

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.238
R-Value Work: 0.214
R-Value Observed: 0.214
Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.67	α = 90
b = 133.07	β = 90
c = 192.22	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2005-07-26

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2005-07-26
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2016-11-09
Changes: Non-polymer description
Version 1.4: 2021-10-20
Changes: Advisory, Database references, Structure summary
Version 2.0: 2022-04-13
Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2023-08-23
Changes: Data collection, Refinement description
Version 2.2: 2024-11-20
Changes: Structure summary