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- PDB-6wta: Structure of F420-H2 Dependent Oxidoreductase (FDOR-A) MSMEG_2027... -

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Basic information

Entry
Database: PDB / ID: 6wta
TitleStructure of F420-H2 Dependent Oxidoreductase (FDOR-A) MSMEG_2027 in complex with F420
ComponentsUncharacterized protein
KeywordsOXIDOREDUCTASE / F420 / Complex / Cofactor
Function / homologyF420H(2)-dependent quinone reductase / F420H(2)-dependent quinone reductase / FMN-binding split barrel / oxidoreductase activity / COENZYME F420-4 / Nitroreductase
Function and homology information
Biological speciesMycolicibacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsJackson, C.J. / Antoney, J.P.
CitationJournal: Biorxiv / Year: 2022
Title: A F420-dependent single domain chemogenetic tool for protein de-dimerization
Authors: Antoney, J. / Kainrath, S. / Ahmed, F.H. / Kang, S.W. / Mackie, E.R. / Soares da Costa, T.P. / Jackson, C.J. / Janovjak, H.
History
DepositionMay 1, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein
Z: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0883
Polymers32,0562
Non-polymers1,0321
Water1,56787
1
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0602
Polymers16,0281
Non-polymers1,0321
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
Z: Uncharacterized protein


  • defined by author&software
  • 16 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)16,0281
Polymers16,0281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.364, 63.022, 65.366
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Uncharacterized protein


Mass: 16028.034 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_2027 / Plasmid: pETMCSIII / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0QU01
#2: Chemical ChemComp-UBM / COENZYME F420-4 / (2~{S})-2-[[(4~{S})-5-oxidanyl-5-oxidanylidene-4-[[(4~{S})-5-oxidanyl-5-oxidanylidene-4-[[(4~{S})-5-oxidanyl-5-oxidanyl idene-4-[[(2~{S})-2-[oxidanyl-[(2~{R},3~{S},4~{S})-2,3,4-tris(oxidanyl)-5-[8-oxidanyl-2,4-bis(oxidanylidene)-1~{H}-pyrim ido[4,5-b]quinolin-10-yl]pentoxy]phosphoryl]oxypropanoyl]amino]pentanoyl]amino]pentanoyl]amino]pentanoyl]amino]pentanedi oic acid


Mass: 1031.821 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C39H50N7O24P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.5 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 3.4
Details: 0.07 M citrate, 0.03 M bis-tris propane, 16% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953729987144 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953729987144 Å / Relative weight: 1
ReflectionResolution: 1.67→32.68 Å / Num. obs: 17596 / % possible obs: 99.8 % / Redundancy: 10.6 % / Biso Wilson estimate: 19.79 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.173 / Rpim(I) all: 0.078 / Rrim(I) all: 0.183 / Χ2: 0.93 / Net I/σ(I): 11.8
Reflection shellResolution: 1.67→1.7 Å / Redundancy: 10.1 % / Rmerge(I) obs: 1.556 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 886 / CC1/2: 0.91 / Rpim(I) all: 0.511 / Χ2: 1.02 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660)refinement
XDS20200131data reduction
Aimless1.11.21data scaling
PHASER2.8.3phasing
Coot0.8.6.1model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Y9I

4y9i


Resolution: 1.67→32.68 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2409 907 5.2 %
Rwork0.2002 --
obs0.2022 17438 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.67→32.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1152 0 71 87 1310
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041283
X-RAY DIFFRACTIONf_angle_d0.6831751
X-RAY DIFFRACTIONf_dihedral_angle_d20.681470
X-RAY DIFFRACTIONf_chiral_restr0.046186
X-RAY DIFFRACTIONf_plane_restr0.004225
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.67-1.770.40851490.37852722X-RAY DIFFRACTION100
1.77-1.910.30541560.27362686X-RAY DIFFRACTION99
1.91-2.10.28561520.2332670X-RAY DIFFRACTION98
2.1-2.410.23741570.2042738X-RAY DIFFRACTION99
2.41-3.030.26311380.18692791X-RAY DIFFRACTION100
3.03-32.680.18191550.16572924X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.16270.35660.1240.7830.24180.9944-0.0748-0.07830.1012-0.14460.2369-0.22160.38740.3042-0.00080.62440.07140.07510.3121-0.19840.8615-24.0656111.402666.7058
25.5780.2773-0.83423.6018-2.07052.16050.03970.2726-0.33820.0422-0.0102-0.12520.11010.4939-0.10820.26620.01180.0030.359-0.04510.2507-21.4152118.668769.8868
35.1969-0.1391.32072.5693-0.73887.66990.0815-0.10360.0060.10230.12020.0575-0.06-0.1178-0.19210.17820.02080.00780.1810.02480.1875-29.8737124.4677.3376
45.00421.22330.02442.03660.56243.4080.09090.11180.16320.09250.01340.3099-0.2438-0.5766-0.05640.23560.07880.03190.40050.04240.2399-36.6807126.755276.0896
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'Z' and (resid 1 through 6 )
2X-RAY DIFFRACTION2chain 'A' and (resid 4 through 34 )
3X-RAY DIFFRACTION3chain 'A' and (resid 35 through 75 )
4X-RAY DIFFRACTION4chain 'A' and (resid 76 through 140 )

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