5JV4 | pdb_00005jv4

Structure of F420 binding protein, MSMEG_6526, from Mycobacterium smegmatis with F420 bound

PDB DOI: https://doi.org/10.2210/pdb5JV4/pdb

Classification: OXIDOREDUCTASE
Organism(s): Mycolicibacterium smegmatis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-05-10 Released: 2017-08-09
Deposition Author(s): Lee, B.M., Carr, P.D., Jackson, C.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.231 (Depositor), 0.241 (DCC)
R-Value Work:
0.189 (Depositor), 0.198 (DCC)
R-Value Observed:
0.191 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure of F420 binding protein, MSMEG_6526, from Mycobacterium smegmatis with F420 bound

Lee, B.M., Carr, P.D., Jackson, C.J.

To be published.

Macromolecule Content

Total Structure Weight: 109.74 kDa
Atom Count: 7,362
Modeled Residue Count: 833
Deposited Residue Count: 924
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyridoxamine 5'-phosphate oxidase-like FMN-binding protein	A, B, C, D, E A, B, C, D, E, F	154	Mycolicibacterium smegmatis	Mutation(s): 0 Gene Names: ERS451418_06325
UniProt
Find proteins for A0R6F1 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0R6F1 Go to UniProtKB: A0R6F1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0R6F1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
F42 Query on F42 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain N [auth C] SDF format, chain R [auth D] SDF format, chain T [auth F] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain N [auth C] MOL2 format, chain R [auth D] MOL2 format, chain T [auth F] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain N [auth C] mmCIF format, chain R [auth D] mmCIF format, chain T [auth F]	G [auth A] I [auth B] J [auth B] N [auth C] R [auth D] G [auth A], I [auth B], J [auth B], N [auth C], R [auth D], T [auth F]	COENZYME F420 C₂₉ H₃₆ N₅ O₁₈ P GEHSZWRGPHDXJO-NALJQGANSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain N [auth C] Focus chain R [auth D] Focus chain T [auth F] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain N [auth C] Focus chain R [auth D] Focus chain T [auth F]
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain V [auth F] SDF format, chain U [auth F] SDF format, chain S [auth E] SDF format, chain O [auth C] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain H [auth A] MOL2 format, chain V [auth F] MOL2 format, chain U [auth F] MOL2 format, chain S [auth E] MOL2 format, chain O [auth C] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain H [auth A] mmCIF format, chain V [auth F] mmCIF format, chain U [auth F] mmCIF format, chain S [auth E] mmCIF format, chain O [auth C] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain H [auth A]	H [auth A] K [auth B] L [auth B] O [auth C] S [auth E] H [auth A], K [auth B], L [auth B], O [auth C], S [auth E], U [auth F], V [auth F]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain O [auth C] Focus chain S [auth E] Focus chain U [auth F] Focus chain V [auth F] Interactions & Density Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain O [auth C] Focus chain S [auth E] Focus chain U [auth F] Focus chain V [auth F]
MRD Query on MRD Download:Ideal Coordinates CCD File SDF format, chain P [auth C] SDF format, chain M [auth B] MOL2 format, chain P [auth C] MOL2 format, chain M [auth B] mmCIF format, chain P [auth C] mmCIF format, chain M [auth B]	M [auth B], P [auth C]	(4R)-2-METHYLPENTANE-2,4-DIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-RXMQYKEDSA-N		Interactions Focus chain M [auth B] Focus chain P [auth C] Interactions & Density Focus chain M [auth B] Focus chain P [auth C]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain Q [auth D] MOL2 format, chain Q [auth D] mmCIF format, chain Q [auth D]	Q [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain Q [auth D] Interactions & Density Focus chain Q [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.231 (Depositor), 0.241 (DCC)
R-Value Work: 0.189 (Depositor), 0.198 (DCC)
R-Value Observed: 0.191 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.951	α = 90
b = 84.241	β = 90.85
c = 75.98	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2017-08-09

Deposition Author(s):

Lee, B.M.

Carr, P.D.

Jackson, C.J.

Revision History (Full details and data files)

Version 1.0: 2017-08-09
Type: Initial release
Version 1.1: 2023-09-27
Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-10-16
Changes: Structure summary