6WNG | pdb_00006wng

Crystal structure of an aspartate ammonia-lyase from Elizabethkingia anophelis NUHP1

PDB DOI: https://doi.org/10.2210/pdb6WNG/pdb

Classification: LYASE
Organism(s): Elizabethkingia anophelis NUH1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-04-22 Released: 2020-04-29
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.153 (Depositor), 0.156 (DCC)
R-Value Work:
0.134 (Depositor), 0.137 (DCC)
R-Value Observed:
0.134 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of an aspartate ammonia-lyase from Elizabethkingia anophelis NUHP1

Edwards, T.E., Mayclin, S.J., Abendroth, J., Horanyi, P.S., Lorimer, D.D., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

To be published.

Macromolecule Content

Total Structure Weight: 211.86 kDa
Atom Count: 16,954
Modeled Residue Count: 1,864
Deposited Residue Count: 1,900
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aspartate ammonia-lyase	A, B, C, D	475	Elizabethkingia anophelis NUH1	Mutation(s): 0 Gene Names: BD94_1127 EC: 4.3.1.1
UniProt
Find proteins for A0A077EBQ3 (Elizabethkingia anophelis NUHP1) Explore A0A077EBQ3 Go to UniProtKB: A0A077EBQ3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A077EBQ3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain W [auth D] SDF format, chain Q [auth C] SDF format, chain K [auth B] SDF format, chain E [auth A] MOL2 format, chain W [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain K [auth B] MOL2 format, chain E [auth A] mmCIF format, chain W [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain K [auth B] mmCIF format, chain E [auth A]	E [auth A], K [auth B], Q [auth C], W [auth D]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain E [auth A] Focus chain K [auth B] Focus chain Q [auth C] Focus chain W [auth D] Interactions & Density Focus chain E [auth A] Focus chain K [auth B] Focus chain Q [auth C] Focus chain W [auth D]
FUM (Subject of Investigation/LOI) Query on FUM Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain R [auth C] SDF format, chain X [auth D] SDF format, chain F [auth A] MOL2 format, chain L [auth B] MOL2 format, chain R [auth C] MOL2 format, chain X [auth D] MOL2 format, chain F [auth A] mmCIF format, chain L [auth B] mmCIF format, chain R [auth C] mmCIF format, chain X [auth D] mmCIF format, chain F [auth A]	F [auth A], L [auth B], R [auth C], X [auth D]	FUMARIC ACID C₄ H₄ O₄ VZCYOOQTPOCHFL-OWOJBTEDSA-N		Interactions Focus chain F [auth A] Focus chain L [auth B] Focus chain R [auth C] Focus chain X [auth D] Interactions & Density Focus chain F [auth A] Focus chain L [auth B] Focus chain R [auth C] Focus chain X [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain M [auth B] SDF format, chain Y [auth D] SDF format, chain S [auth C] MOL2 format, chain G [auth A] MOL2 format, chain M [auth B] MOL2 format, chain Y [auth D] MOL2 format, chain S [auth C] mmCIF format, chain G [auth A] mmCIF format, chain M [auth B] mmCIF format, chain Y [auth D] mmCIF format, chain S [auth C]	G [auth A], M [auth B], S [auth C], Y [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain M [auth B] Focus chain S [auth C] Focus chain Y [auth D] Interactions & Density Focus chain G [auth A] Focus chain M [auth B] Focus chain S [auth C] Focus chain Y [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain Z [auth D] SDF format, chain P [auth B] SDF format, chain N [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain BA [auth D] SDF format, chain AA [auth D] MOL2 format, chain O [auth B] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain Z [auth D] MOL2 format, chain P [auth B] MOL2 format, chain N [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain BA [auth D] MOL2 format, chain AA [auth D] mmCIF format, chain O [auth B] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain Z [auth D] mmCIF format, chain P [auth B] mmCIF format, chain N [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain BA [auth D] mmCIF format, chain AA [auth D]	AA [auth D] BA [auth D] H [auth A] I [auth A] J [auth A] AA [auth D], BA [auth D], H [auth A], I [auth A], J [auth A], N [auth B], O [auth B], P [auth B], T [auth C], U [auth C], V [auth C], Z [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain Z [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.153 (Depositor), 0.156 (DCC)
R-Value Work: 0.134 (Depositor), 0.137 (DCC)
R-Value Observed: 0.134 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.82	α = 90
b = 96.85	β = 90
c = 212.2	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
PHENIX	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: 2020-04-29

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2020-04-29
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Database references, Refinement description
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection
Version 2.1: 2025-10-22
Changes: Database references, Structure summary