5TGD | pdb_00005tgd

Crystal structure of FolM Alternative dihydrofolate reductase 1 from Brucella suis in complex with NADP

PDB DOI: https://doi.org/10.2210/pdb5TGD/pdb

Classification: OXIDOREDUCTASE
Organism(s): Brucella suis 92/29
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-09-27 Released: 2016-10-12
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.198 (Depositor), 0.198 (DCC)
R-Value Work:
0.163 (Depositor), 0.164 (DCC)
R-Value Observed:
0.163 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Crystal structures of FolM alternative dihydrofolate reductase 1 from Brucella suis and Brucella canis.

Porter, I., Neal, T., Walker, Z., Hayes, D., Fowler, K., Billups, N., Rhoades, A., Smith, C., Smith, K., Staker, B.L., Dranow, D.M., Mayclin, S.J., Subramanian, S., Edwards, T.E., Myler, P.J., Asojo, O.A.

(2022) Acta Crystallogr F Struct Biol Commun 78: 31-38

PubMed: 34981773 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S2053230X21013078
Primary Citation Related Structures:
5BT9, 5TGD

PubMed Abstract:
Members of the bacterial genus Brucella cause brucellosis, a zoonotic disease that affects both livestock and wildlife. Brucella are category B infectious agents that can be aerosolized for biological warfare. As part of the structural genomics studies at the Seattle Structural Genomics Center for Infectious Disease (SSGCID), FolM alternative dihydrofolate reductases 1 from Brucella suis and Brucella canis were produced and their structures are reported. The enzymes share ∼95% sequence identity but have less than 33% sequence identity to other homologues with known structure. The structures are prototypical NADPH-dependent short-chain reductases that share their highest tertiary-structural similarity with protozoan pteridine reductases, which are being investigated for rational therapeutic development.

Organizational Affiliation

Department of Chemistry and Biochemistry, Hampton University, 100 William R. Harvey Way, Hampton, VA 23668, USA.

Macromolecule Content

Total Structure Weight: 122.09 kDa
Atom Count: 8,598
Modeled Residue Count: 983
Deposited Residue Count: 1,068
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FolM Alternative dihydrofolate reductase	A, B, C, D	267	Brucella suis 92/29	Mutation(s): 0 Gene Names: C062_00524

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download:Ideal Coordinates CCD File SDF format, chain I [auth C] SDF format, chain K [auth D] SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A], H [auth B], I [auth C], K [auth D]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain K [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth C] SDF format, chain L [auth D] SDF format, chain M [auth D] MOL2 format, chain F [auth A] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] MOL2 format, chain M [auth D] mmCIF format, chain F [auth A] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D] mmCIF format, chain M [auth D]	F [auth A], J [auth C], L [auth D], M [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth C] Focus chain L [auth D] Focus chain M [auth D] Interactions & Density Focus chain F [auth A] Focus chain J [auth C] Focus chain L [auth D] Focus chain M [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.198 (Depositor), 0.198 (DCC)
R-Value Work: 0.163 (Depositor), 0.164 (DCC)
R-Value Observed: 0.163 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.35	α = 90
b = 76.52	β = 109.47
c = 98.26	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-10-12

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2016-10-12
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations
Version 1.2: 2023-10-04
Changes: Refinement description