3OUG | pdb_00003oug

Crystal structure of cleaved L-aspartate-alpha-decarboxylase from Francisella tularensis

PDB DOI: https://doi.org/10.2210/pdb3OUG/pdb

Classification: LYASE
Organism(s): Francisella tularensis subsp. tularensis SCHU S4
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-09-14 Released: 2010-10-20
Deposition Author(s): Nocek, B., Gu, M., Papazisi, L., Anderson, W., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.197 (Depositor), 0.210 (DCC)
R-Value Work:
0.172 (Depositor), 0.180 (DCC)
R-Value Observed:
0.172 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of cleaved L-aspartate-alpha-decarboxylase from Francisella tularensis

Nocek, B., Gu, M., Papazisi, L., Anderson, W., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 102.51 kDa
Atom Count: 7,776
Modeled Residue Count: 854
Deposited Residue Count: 912
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aspartate 1-decarboxylase	A B C D [auth E] E [auth F] A, B, C, D [auth E], E [auth F], F [auth G], G [auth H], H [auth I]	114	Francisella tularensis subsp. tularensis SCHU S4	Mutation(s): 0 EC: 4.1.1.11
UniProt
Find proteins for Q5NF56 (Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4)) Explore Q5NF56 Go to UniProtKB: Q5NF56
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5NF56
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain N [auth C] SDF format, chain P [auth F] SDF format, chain Q [auth G] SDF format, chain T [auth H] SDF format, chain U [auth H] MOL2 format, chain K [auth A] MOL2 format, chain N [auth C] MOL2 format, chain P [auth F] MOL2 format, chain Q [auth G] MOL2 format, chain T [auth H] MOL2 format, chain U [auth H] mmCIF format, chain K [auth A] mmCIF format, chain N [auth C] mmCIF format, chain P [auth F] mmCIF format, chain Q [auth G] mmCIF format, chain T [auth H] mmCIF format, chain U [auth H]	K [auth A] N [auth C] P [auth F] Q [auth G] T [auth H] K [auth A], N [auth C], P [auth F], Q [auth G], T [auth H], U [auth H]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain N [auth C] Focus chain P [auth F] Focus chain Q [auth G] Focus chain T [auth H] Focus chain U [auth H] Interactions & Density Focus chain K [auth A] Focus chain N [auth C] Focus chain P [auth F] Focus chain Q [auth G] Focus chain T [auth H] Focus chain U [auth H]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain L [auth B] SDF format, chain M [auth C] SDF format, chain O [auth F] SDF format, chain R [auth G] SDF format, chain S [auth H] SDF format, chain V [auth I] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth C] MOL2 format, chain O [auth F] MOL2 format, chain R [auth G] MOL2 format, chain S [auth H] MOL2 format, chain V [auth I] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth C] mmCIF format, chain O [auth F] mmCIF format, chain R [auth G] mmCIF format, chain S [auth H] mmCIF format, chain V [auth I]	I [auth A] J [auth A] L [auth B] M [auth C] O [auth F] I [auth A], J [auth A], L [auth B], M [auth C], O [auth F], R [auth G], S [auth H], V [auth I]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain M [auth C] Focus chain O [auth F] Focus chain R [auth G] Focus chain S [auth H] Focus chain V [auth I] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain M [auth C] Focus chain O [auth F] Focus chain R [auth G] Focus chain S [auth H] Focus chain V [auth I]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A B C D [auth E] E [auth F] A, B, C, D [auth E], E [auth F], F [auth G], G [auth H], H [auth I]	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.197 (Depositor), 0.210 (DCC)
R-Value Work: 0.172 (Depositor), 0.180 (DCC)
R-Value Observed: 0.172 (Depositor)

Diffraction Data: https://doi.org/10.18430/m33oug

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.934	α = 90
b = 80.525	β = 104.33
c = 85.025	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
Auto-Rickshaw	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2010-10-20

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2010-10-20
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2023-12-06
Changes: Data collection
Version 1.4: 2024-11-20
Changes: Structure summary