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- PDB-4fdo: Mycobacterium tuberculosis DprE1 in complex with CT319 -

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Basic information

Entry
Database: PDB / ID: 4fdo
TitleMycobacterium tuberculosis DprE1 in complex with CT319
Componentsoxidoreductase DprE1
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / ALPHA+BETA / OXIDOREDUCTASE / decaprenylphosphoryl-beta-D-ribose / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


arabinan biosynthetic process / cell wall polysaccharide biosynthetic process / decaprenylphospho-beta-D-ribofuranose 2-dehydrogenase / D-arabinono-1,4-lactone oxidase activity / capsule polysaccharide biosynthetic process / FAD binding / cell wall organization / periplasmic space / oxidoreductase activity / response to antibiotic / plasma membrane
Similarity search - Function
D-arabinono-1,4-lactone oxidase, C-terminal domain / D-arabinono-1,4-lactone oxidase / FAD linked oxidase, N-terminal / FAD binding domain / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily
Similarity search - Domain/homology
Chem-0T5 / FLAVIN-ADENINE DINUCLEOTIDE / Decaprenylphosphoryl-beta-D-ribose oxidase / Decaprenylphosphoryl-beta-D-ribose oxidase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.403 Å
AuthorsBatt, S.M. / Besra, G.S. / Futterer, K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural basis of inhibition of Mycobacterium tuberculosis DprE1 by benzothiazinone inhibitors.
Authors: Batt, S.M. / Jabeen, T. / Bhowruth, V. / Quill, L. / Lund, P.A. / Eggeling, L. / Alderwick, L.J. / Futterer, K. / Besra, G.S.
History
DepositionMay 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: oxidoreductase DprE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5153
Polymers52,3911
Non-polymers1,1242
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)127.884, 127.884, 64.177
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

#1: Protein oxidoreductase DprE1


Mass: 52391.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: dprE1, MT3898, Rv3790 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P72056, UniProt: P9WJF1*PLUS, Oxidoreductases
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-0T5 / 3-nitro-N-[(1R)-1-phenylethyl]-5-(trifluoromethyl)benzamide


Mass: 338.281 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H13F3N2O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O

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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: 2.89 Å3/Da / Density % sol: 57.46 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M sodium cacodylate, 36% ethylene glycol, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: May 21, 2012 / Details: Varimax
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→45.25 Å / Num. all: 23613 / Num. obs: 23613 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 16
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 7 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 4.8 / Rsym value: 0.338 / % possible all: 98.1

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: DprE1 - monoclinic crystal form

Resolution: 2.403→41.86 Å / SU ML: 0.29 / σ(F): 1.41 / Phase error: 17.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2048 1206 5.13 %
Rwork0.1673 --
obs0.1692 23489 99.91 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 26.347 Å2 / ksol: 0.345 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.4055 Å20 Å20 Å2
2---0.4055 Å2-0 Å2
3---0.8111 Å2
Refinement stepCycle: LAST / Resolution: 2.403→41.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3222 0 77 194 3493
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083380
X-RAY DIFFRACTIONf_angle_d1.1384609
X-RAY DIFFRACTIONf_dihedral_angle_d14.0671193
X-RAY DIFFRACTIONf_chiral_restr0.077512
X-RAY DIFFRACTIONf_plane_restr0.005590
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.403-2.49910.24771290.19372436X-RAY DIFFRACTION99
2.4991-2.61280.23491490.19212446X-RAY DIFFRACTION100
2.6128-2.75050.22021360.16972472X-RAY DIFFRACTION100
2.7505-2.92280.24851590.17472444X-RAY DIFFRACTION100
2.9228-3.14840.20591290.16462439X-RAY DIFFRACTION100
3.1484-3.46510.2061220.17172492X-RAY DIFFRACTION100
3.4651-3.96620.19821130.17272508X-RAY DIFFRACTION100
3.9662-4.99570.16321350.13532494X-RAY DIFFRACTION100
4.9957-41.86620.19611340.17432552X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 39.4006 Å / Origin y: 8.9742 Å / Origin z: 4.3822 Å
111213212223313233
T0.0684 Å20.0013 Å2-0.0006 Å2-0.0552 Å2-0.0153 Å2--0.0539 Å2
L0.788 °2-0.2259 °2-0.0025 °2-0.6757 °2-0.0339 °2--0.6115 °2
S0.0054 Å °-0.0555 Å °0.0767 Å °0.0114 Å °-0.002 Å °-0.0365 Å °-0.0774 Å °-0.0289 Å °-0.0001 Å °
Refinement TLS groupSelection details: all

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