8U91

Crystal structure of N-acetylneuraminate lyase (NanA) from Klebsiella aerogenes (Apo, Orthorhombic P form)

PDB DOI: https://doi.org/10.2210/pdb8U91/pdb

Classification: LIPID TRANSPORT
Organism(s): Klebsiella aerogenes KCTC 2190
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2023-09-18 Released: 2023-09-27
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/Office of the Director

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.222
R-Value Work: 0.180
R-Value Observed: 0.182

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of N-acetylneuraminate lyase (NanA) from Klebsiella aerogenes (Apo, Orthorhombic P form)

Lovell, S., Liu, L., Seibold, S., Battaile, K.P.

To be published.

Macromolecule Content

Total Structure Weight: 204.18 kDa
Atom Count: 14,661
Modelled Residue Count: 1,783
Deposited Residue Count: 1,830
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-acetylneuraminate lyase	A, B, C, D, E A, B, C, D, E, F	305	Klebsiella aerogenes KCTC 2190	Mutation(s): 1 Gene Names: nanA
UniProt
Find proteins for A0A0H3FJT8 (Klebsiella aerogenes (strain ATCC 13048 / DSM 30053 / CCUG 1429 / JCM 1235 / KCTC 2190 / NBRC 13534 / NCIMB 10102 / NCTC 10006 / CDC 819-56)) Explore A0A0H3FJT8 Go to UniProtKB: A0A0H3FJT8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0H3FJT8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain G [auth A] SDF format, chain GA [auth F] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain V [auth D] SDF format, chain W [auth D] SDF format, chain EA [auth F] SDF format, chain FA [auth F] MOL2 format, chain AA [auth E] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth F] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain V [auth D] MOL2 format, chain W [auth D] MOL2 format, chain EA [auth F] MOL2 format, chain FA [auth F]	AA [auth E] EA [auth F] FA [auth F] G [auth A] GA [auth F] AA [auth E], EA [auth F], FA [auth F], G [auth A], GA [auth F], J [auth B], K [auth B], O [auth C], P [auth C], Q [auth C], V [auth D], W [auth D]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain AA [auth E] Focus chain EA [auth F] Focus chain FA [auth F] Focus chain G [auth A] Focus chain GA [auth F] Focus chain J [auth B] Focus chain K [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain V [auth D] Focus chain W [auth D] Interactions & Density Focus chain AA [auth E] Focus chain EA [auth F] Focus chain FA [auth F] Focus chain G [auth A] Focus chain GA [auth F] Focus chain J [auth B] Focus chain K [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain V [auth D] Focus chain W [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain CA [auth E] SDF format, chain DA [auth E] SDF format, chain HA [auth F] SDF format, chain I [auth A] SDF format, chain JA [auth F] SDF format, chain KA [auth F] SDF format, chain L [auth B] SDF format, chain LA [auth F] SDF format, chain M [auth B] SDF format, chain MA [auth F] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain U [auth C] SDF format, chain Y [auth D] SDF format, chain Z [auth D] SDF format, chain H [auth A] SDF format, chain IA [auth F] SDF format, chain N [auth B] SDF format, chain T [auth C] SDF format, chain X [auth D] MOL2 format, chain BA [auth E] MOL2 format, chain CA [auth E] MOL2 format, chain DA [auth E] MOL2 format, chain HA [auth F] MOL2 format, chain I [auth A] MOL2 format, chain JA [auth F] MOL2 format, chain KA [auth F] MOL2 format, chain L [auth B] MOL2 format, chain LA [auth F] MOL2 format, chain M [auth B] MOL2 format, chain MA [auth F] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain U [auth C] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D] MOL2 format, chain H [auth A] MOL2 format, chain IA [auth F] MOL2 format, chain N [auth B] MOL2 format, chain T [auth C] MOL2 format, chain X [auth D]	BA [auth E] CA [auth E] DA [auth E] H [auth A] HA [auth F] BA [auth E], CA [auth E], DA [auth E], H [auth A], HA [auth F], I [auth A], IA [auth F], JA [auth F], KA [auth F], L [auth B], LA [auth F], M [auth B], MA [auth F], N [auth B], R [auth C], S [auth C], T [auth C], U [auth C], X [auth D], Y [auth D], Z [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain BA [auth E] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain H [auth A] Focus chain HA [auth F] Focus chain I [auth A] Focus chain IA [auth F] Focus chain JA [auth F] Focus chain KA [auth F] Focus chain L [auth B] Focus chain LA [auth F] Focus chain M [auth B] Focus chain MA [auth F] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain BA [auth E] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain H [auth A] Focus chain HA [auth F] Focus chain I [auth A] Focus chain IA [auth F] Focus chain JA [auth F] Focus chain KA [auth F] Focus chain L [auth B] Focus chain LA [auth F] Focus chain M [auth B] Focus chain MA [auth F] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.222
R-Value Work: 0.180
R-Value Observed: 0.182
Space Group: P 2₁ 2₁ 2
Diffraction Data: https://doi.org/10.18430/M38U91

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.101	α = 90
b = 146.566	β = 90
c = 216.916	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-09-27

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	75N93022C00036
National Institutes of Health/Office of the Director	United States	S10OD030394