3JU4 | pdb_00003ju4

Crystal Structure Analysis of EndosialidaseNF at 0.98 A Resolution

PDB DOI: https://doi.org/10.2210/pdb3JU4/pdb

Classification: HYDROLASE
Organism(s): Escherichia phage K1F
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-09-14 Released: 2010-02-02
Deposition Author(s): Schulz, E.C., Neuman, P., Gerardy-Schahn, R., Sheldrick, G.M., Ficner, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 0.98 Å
R-Value Free:
0.133 (Depositor), 0.130 (DCC)
R-Value Work:
0.116 (Depositor), 0.120 (DCC)
R-Value Observed:
0.116 (Depositor)

Starting Model: experimental
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This is version 1.4 of the entry. See complete history.

Literature

Structure analysis of endosialidase NF at 0.98 A resolution.

Schulz, E.C., Neumann, P., Gerardy-Schahn, R., Sheldrick, G.M., Ficner, R.

(2010) Acta Crystallogr D Biol Crystallogr 66: 176-180

PubMed: 20124697 Search on PubMed
DOI: https://doi.org/10.1107/S0907444909048720
Primary Citation of Related Structures:
3JU4

PubMed Abstract:
Endosialidase NF (endoNF) is a bacteriophage-derived endosialidase that specifically degrades alpha-2,8-linked polysialic acid. The structure of a new crystal form of endoNF in complex with sialic acid has been refined at 0.98 A resolution. The 210 kDa homotrimeric multi-domain enzyme displays outstanding stability and resistance to SDS. Even at atomic resolution, only a minor fraction of side chains possess alternative conformations. However, multiple conformations of an active-site residue imply that it has an important catalytic function in the cleavage mechanism of polysialic acid.

Organizational Affiliation

Abteilung für Molekulare Strukturbiologie, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.

Macromolecule Content

Total Structure Weight: 75.05 kDa
Atom Count: 7,145
Modelled Residue Count: 670
Deposited Residue Count: 670
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endo-N-acetylneuraminidase	A	670	Escherichia phage K1F	Mutation(s): 0 EC: 3.2.1.129
UniProt
Find proteins for Q04830 (Escherichia phage K1F) Explore Q04830 Go to UniProtKB: Q04830
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q04830
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SLB Query on SLB Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	N-acetyl-beta-neuraminic acid C₁₁ H₁₉ N O₉ SQVRNKJHWKZAKO-PFQGKNLYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 0.98 Å
R-Value Free: 0.133 (Depositor), 0.130 (DCC)
R-Value Work: 0.116 (Depositor), 0.120 (DCC)
R-Value Observed: 0.116 (Depositor)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.04	α = 90
b = 119.04	β = 90
c = 175.69	γ = 120

Software Package:

Software Name	Purpose
DNA	data collection
MOLREP	phasing
SHELXL-97	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-02-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-02-02
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2012-04-18
Changes: Database references
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary
Version 1.4: 2023-11-01
Changes: Data collection, Database references, Refinement description, Structure summary