6PFN | pdb_00006pfn

Succinyl-CoA synthase from Francisella tularensis

PDB DOI: https://doi.org/10.2210/pdb6PFN/pdb

Classification: LIGASE
Organism(s): Francisella tularensis subsp. tularensis SCHU S4
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2019-06-21 Released: 2019-07-03
Deposition Author(s): Osipiuk, J., Maltseva, N., Jedrzejczak, R., Satchell, K.J.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free:
0.218 (Depositor), 0.220 (DCC)
R-Value Work:
0.186 (Depositor), 0.190 (DCC)
R-Value Observed:
0.187 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Succinyl-CoA synthase from Francisella tularensis

Osipiuk, J., Maltseva, N., Jedrzejczak, R., Satchell, K.J.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 146.8 kDa
Atom Count: 10,365
Modeled Residue Count: 1,250
Deposited Residue Count: 1,366
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinate--CoA ligase [ADP-forming] subunit alpha	A, C	296	Francisella tularensis subsp. tularensis SCHU S4	Mutation(s): 1 Gene Names: sucD, BZ14_337 EC: 6.2.1.5
UniProt
Find proteins for Q5NHF4 (Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4)) Explore Q5NHF4 Go to UniProtKB: Q5NHF4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5NHF4
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinate--CoA ligase [ADP-forming] subunit beta	B, D	387	Francisella tularensis subsp. tularensis SCHU S4	Mutation(s): 1 Gene Names: sucC, FTT_0504c EC: 6.2.1.5
UniProt
Find proteins for Q5NHF3 (Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4)) Explore Q5NHF3 Go to UniProtKB: Q5NHF3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5NHF3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
COA Query on COA Download Ideal Coordinates CCD File SDF format, chain F [auth C] SDF format, chain E [auth A] MOL2 format, chain F [auth C] MOL2 format, chain E [auth A] mmCIF format, chain F [auth C] mmCIF format, chain E [auth A]	E [auth A], F [auth C]	COENZYME A C₂₁ H₃₆ N₇ O₁₆ P₃ S RGJOEKWQDUBAIZ-IBOSZNHHSA-N		Interactions Focus chain E [auth A] Focus chain F [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain H [auth D] MOL2 format, chain H [auth D] mmCIF format, chain H [auth D]	H [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth D] Interactions & Density Focus chain H [auth D]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain G [auth D] MOL2 format, chain G [auth D] mmCIF format, chain G [auth D]	G [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain G [auth D] Interactions & Density Focus chain G [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free: 0.218 (Depositor), 0.220 (DCC)
R-Value Work: 0.186 (Depositor), 0.190 (DCC)
R-Value Observed: 0.187 (Depositor)

Diffraction Data: https://doi.org/10.18430/m36pfn

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.073	α = 90
b = 158.735	β = 113.11
c = 73.017	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2019-07-03

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201200026C
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700060C

Revision History (Full details and data files)

Version 1.0: 2019-07-03
Type: Initial release
Version 1.1: 2019-12-18
Changes: Author supporting evidence
Version 1.2: 2023-10-11
Changes: Data collection, Database references, Refinement description