4M4V | pdb_00004m4v

Structural evaluation R171L mutant of the aspergillus fumigatus kdnase (sialidase)

PDB DOI: https://doi.org/10.2210/pdb4M4V/pdb

Classification: HYDROLASE
Organism(s): Aspergillus fumigatus Af293
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2013-08-07 Released: 2014-09-17
Deposition Author(s): Telford, J.C., Taylor, G.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.84 Å
R-Value Free:
0.194 (Depositor), 0.194 (DCC)
R-Value Work:
0.154 (Depositor), 0.154 (DCC)
R-Value Observed:
0.156 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Active site mutants of a fungal KDNase

Yeung, J.Y., Telford, J.C., S Shidmoossavee, F., Bennet, A.J., Taylor, G.L., Moore, M.M.

To be published.

Macromolecule Content

Total Structure Weight: 93.3 kDa
Atom Count: 7,253
Modeled Residue Count: 769
Deposited Residue Count: 844
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Extracellular sialidase/neuraminidase, putative	A, B	422	Aspergillus fumigatus Af293	Mutation(s): 1 Gene Names: AFUA_4G13800 EC: 3.2.1.18
UniProt
Find proteins for Q4WQS0 (Aspergillus fumigatus (strain ATCC MYA-4609 / CBS 101355 / FGSC A1100 / Af293)) Explore Q4WQS0 Go to UniProtKB: Q4WQS0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q4WQS0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DAN Query on DAN 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]	2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID C₁₁ H₁₇ N O₈ JINJZWSZQKHCIP-UFGQHTETSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain H [auth A] SDF format, chain D [auth A] MOL2 format, chain I [auth B] MOL2 format, chain H [auth A] MOL2 format, chain D [auth A] mmCIF format, chain I [auth B] mmCIF format, chain H [auth A] mmCIF format, chain D [auth A]	D [auth A], H [auth A], I [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain H [auth A] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth A] Focus chain I [auth B]
NO3 Query on NO3 Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], J [auth B], K [auth B]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.84 Å
R-Value Free: 0.194 (Depositor), 0.194 (DCC)
R-Value Work: 0.154 (Depositor), 0.154 (DCC)
R-Value Observed: 0.156 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.88	α = 90
b = 57.97	β = 99.89
c = 94.64	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-09-17

Deposition Author(s):

Telford, J.C.

Taylor, G.L.

Revision History (Full details and data files)

Version 1.0: 2014-09-17
Type: Initial release
Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Refinement description, Structure summary

4M4V | pdb_00004m4v

Structural evaluation R171L mutant of the aspergillus fumigatus kdnase (sialidase)

Literature

Active site mutants of a fungal KDNase

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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