5HW2 | pdb_00005hw2

Crystal Structure of Adenylosuccinate Lyase from Francisella tularensis Complexed with fumaric acid

PDB DOI: https://doi.org/10.2210/pdb5HW2/pdb

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

Deposited: 2016-01-28 Released: 2016-02-10
Deposition Author(s): Chang, C., Maltseva, N., Kim, Y., Shatsman, S., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.245 (Depositor), 0.250 (DCC)
R-Value Work:
0.188 (Depositor), 0.190 (DCC)
R-Value Observed:
0.192 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Literature

Crystal Structure of Adenylosuccinate Lyase from Francisella tularensis Complexed with fumaric acid

Chang, C., Maltseva, N., Kim, Y., Shatsman, S., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 201.93 kDa
Atom Count: 14,356
Modeled Residue Count: 1,674
Deposited Residue Count: 1,752
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenylosuccinate lyase	A, B, C, D	438	Francisella tularensis subsp. tularensis SCHU S4	Mutation(s): 0 Gene Names: purB, FTT_0015, BZ14_879 EC: 4.3.2.2
UniProt
Find proteins for Q5NIQ1 (Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4)) Explore Q5NIQ1 Go to UniProtKB: Q5NIQ1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5NIQ1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FUM Query on FUM Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain N [auth C] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain N [auth C]	F [auth A], K [auth B], N [auth C]	FUMARIC ACID C₄ H₄ O₄ VZCYOOQTPOCHFL-OWOJBTEDSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Focus chain N [auth C] Interactions & Density Focus chain F [auth A] Focus chain K [auth B] Focus chain N [auth C]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain O [auth C] SDF format, chain S [auth D] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C] MOL2 format, chain S [auth D] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain O [auth C] mmCIF format, chain S [auth D]	G [auth A], L [auth B], O [auth C], S [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain G [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain S [auth D] Interactions & Density Focus chain G [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain S [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain T [auth D] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain T [auth D] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain T [auth D]	H [auth A], I [auth A], P [auth C], Q [auth C], T [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain P [auth C] Focus chain Q [auth C] Focus chain T [auth D] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain P [auth C] Focus chain Q [auth C] Focus chain T [auth D]
K Query on K Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] SDF format, chain M [auth C] SDF format, chain R [auth D] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] MOL2 format, chain R [auth D] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain M [auth C] mmCIF format, chain R [auth D]	E [auth A], J [auth B], M [auth C], R [auth D]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain R [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain R [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.245 (Depositor), 0.250 (DCC)
R-Value Work: 0.188 (Depositor), 0.190 (DCC)
R-Value Observed: 0.192 (Depositor)

Diffraction Data: https://doi.org/10.18430/m35hw2

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.68	α = 90
b = 88.68	β = 90
c = 255.665	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
MOLREP	phasing
SBC-Collect	data collection
Coot	model building

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2016-02-10

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2016-02-10
Type: Initial release
Version 1.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection