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- PDB-4fdn: Mycobacterium tuberculosis DprE1 in complex with CT325 - hexagona... -

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Basic information

Entry
Database: PDB / ID: 4fdn
TitleMycobacterium tuberculosis DprE1 in complex with CT325 - hexagonal crystal form
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-0T4 / 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: 2.4 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 1.2Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)53,5013
Polymers52,3911
Non-polymers1,1102
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)127.700, 127.700, 64.400
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


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-0T4 / 3-(hydroxyamino)-N-[(1R)-1-phenylethyl]-5-(trifluoromethyl)benzamide


Mass: 324.298 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H15F3N2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 57.49 %
Crystal growTemperature: 288 K / pH: 6
Details: 0.1 M sodium cacodylate 44% ethylene glycol, pH 6.0, 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
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: May 9, 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→45.36 Å / Num. obs: 23678 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 10.6 % / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 20.8
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 7 % / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 3.3 / Rsym value: 0.565 / % possible all: 99.3

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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: 2.4→28.75 Å / SU ML: 0.32 / σ(F): 1.4 / Phase error: 20.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.226 1218 5.16 %
Rwork0.182 --
obs0.184 23593 100 %
all-22379 -
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.56 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.2166 Å20 Å20 Å2
2---2.2166 Å2-0 Å2
3---4.4332 Å2
Refinement stepCycle: LAST / Resolution: 2.4→28.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3141 0 76 147 3364
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083296
X-RAY DIFFRACTIONf_angle_d1.1584490
X-RAY DIFFRACTIONf_dihedral_angle_d13.6821165
X-RAY DIFFRACTIONf_chiral_restr0.074504
X-RAY DIFFRACTIONf_plane_restr0.005574
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.49610.29961390.21922473X-RAY DIFFRACTION100
2.4961-2.60970.23341240.20772467X-RAY DIFFRACTION100
2.6097-2.74720.25511330.18172486X-RAY DIFFRACTION100
2.7472-2.91910.22521570.18422453X-RAY DIFFRACTION100
2.9191-3.14430.22741270.17932451X-RAY DIFFRACTION100
3.1443-3.46020.23151300.18442501X-RAY DIFFRACTION100
3.4602-3.95980.23841300.18922488X-RAY DIFFRACTION100
3.9598-4.98470.22131480.16042490X-RAY DIFFRACTION100
4.9847-28.75290.1861300.18082566X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 39.3609 Å / Origin y: 8.9376 Å / Origin z: 3.947 Å
111213212223313233
T0.2048 Å20.0055 Å2-0.0005 Å2-0.1451 Å2-0.0153 Å2--0.1443 Å2
L2.308 °2-0.5672 °2-0.0572 °2-1.4787 °2-0.0814 °2--1.2351 °2
S-0.02 Å °-0.1958 Å °0.25 Å °0.0883 Å °0.0241 Å °0.0276 Å °-0.1939 Å °-0.0819 Å °-0.0078 Å °
Refinement TLS groupSelection details: all

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