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- PDB-7mgt: Ftp from Treponema pallidum bound to an ADP-like inhibitor -

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Basic information

Entry
Database: PDB / ID: 7mgt
TitleFtp from Treponema pallidum bound to an ADP-like inhibitor
ComponentsFAD:protein FMN transferase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


protein flavinylation / FAD:protein FMN transferase / membrane => GO:0016020 / transferase activity / metal ion binding / plasma membrane
Similarity search - Function
Flavin transferase ApbE / ApbE family / ApbE-like superfamily
Similarity search - Domain/homology
2-chloroadenosine 5'-(trihydrogen diphosphate) / FAD:protein FMN transferase
Similarity search - Component
Biological speciesTreponema pallidum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsBrautigam, C.A. / Deka, R. / Norgard, M.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Protein Sci. / Year: 2022
Title: Inhibition of bacterial FMN transferase: A potential avenue for countering antimicrobial resistance.
Authors: Deka, R.K. / Deka, A. / Liu, W.Z. / Norgard, M.V. / Brautigam, C.A.
History
DepositionApr 13, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.identifier_ORCID
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: FAD:protein FMN transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9645
Polymers40,3921
Non-polymers5724
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)116.483, 47.106, 57.472
Angle α, β, γ (deg.)90.000, 102.298, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-561-

HOH

21A-625-

HOH

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Components

#1: Protein FAD:protein FMN transferase / Flavin transferase


Mass: 40391.848 Da / Num. of mol.: 1 / Mutation: A96T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Treponema pallidum (bacteria) / Gene: FA890_04115 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A5J6YQV1, FAD:protein FMN transferase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ZD4 / 2-chloroadenosine 5'-(trihydrogen diphosphate)


Mass: 461.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14ClN5O10P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 1.91 Å3/Da / Density % sol: 35.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M magnesium formate dihydrate 15% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.54→35.844 Å / Num. obs: 43888 / % possible obs: 97 % / Redundancy: 6.8 % / Biso Wilson estimate: 12.42 Å2 / CC1/2: 0.994 / Net I/σ(I): 40.8
Reflection shellResolution: 1.54→1.57 Å / Num. unique obs: 2200 / CC1/2: 0.931

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IFU

4ifu


Resolution: 1.54→35.84 Å / SU ML: 0.165 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.1392
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1977 2000 4.62 %
Rwork0.1503 41277 -
obs0.1525 43277 95.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.89 Å2
Refinement stepCycle: LAST / Resolution: 1.54→35.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2442 0 34 125 2601
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00642526
X-RAY DIFFRACTIONf_angle_d0.96083432
X-RAY DIFFRACTIONf_chiral_restr0.0566396
X-RAY DIFFRACTIONf_plane_restr0.0054443
X-RAY DIFFRACTIONf_dihedral_angle_d14.4963900
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.580.25151250.16882585X-RAY DIFFRACTION83.64
1.58-1.620.25761380.15122836X-RAY DIFFRACTION93.35
1.62-1.670.24471430.1292940X-RAY DIFFRACTION96.19
1.67-1.720.21571420.12752966X-RAY DIFFRACTION96.58
1.72-1.780.22511410.13012898X-RAY DIFFRACTION94.61
1.78-1.860.19371460.13623020X-RAY DIFFRACTION97.99
1.86-1.940.20091450.13462995X-RAY DIFFRACTION97.94
1.94-2.040.19831450.12993000X-RAY DIFFRACTION97.37
2.04-2.170.20551440.13852949X-RAY DIFFRACTION95.37
2.17-2.340.18131470.13793025X-RAY DIFFRACTION98.51
2.34-2.570.17251450.14633007X-RAY DIFFRACTION97.8
2.57-2.940.19461440.16372967X-RAY DIFFRACTION95.52
2.95-3.710.2171470.16483036X-RAY DIFFRACTION97.43
3.71-35.840.17141480.16683053X-RAY DIFFRACTION95.84

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