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- PDB-4aut: Crystal structure of the tuberculosis drug target Decaprenyl- Pho... -

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Basic information

Entry
Database: PDB / ID: 4aut
TitleCrystal structure of the tuberculosis drug target Decaprenyl- Phosphoryl-beta-D-Ribofuranose-2-oxidoreductase (DprE1) from Mycobacterium smegmatis
ComponentsDECAPRENYL-PHOSPHORYL-BETA-D-RIBOFURANOSE-2-OXIDOREDUCTASE
KeywordsOXIDOREDUCTASE / TUBERCULOSIS / BENZOTHIAZINONE / MYCOBACTERIA
Function / homology
Function and homology information


decaprenylphospho-beta-D-ribofuranose 2-dehydrogenase / D-arabinono-1,4-lactone oxidase activity / capsule polysaccharide biosynthetic process / FAD binding / cell wall organization / periplasmic space / response to antibiotic / membrane
Similarity search - Function
D-arabinono-1,4-lactone oxidase, C-terminal domain / D-arabinono-1,4-lactone oxidase / Vanillyl-alcohol oxidase, C-terminal subdomain 2 / FAD linked oxidase, N-terminal / FAD binding domain / FAD-binding, type PCMH, subdomain 1 / 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
FLAVIN-ADENINE DINUCLEOTIDE / Decaprenylphosphoryl-beta-D-ribose oxidase
Similarity search - Component
Biological speciesMYCOBACTERIUM SMEGMATIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsNeres, J. / Pojer, F. / Molteni, E. / Chiarelli, L.R. / Dhar, N. / Boy-Rottger, S. / Buroni, S. / Fullam, E. / Degiacomi, G. / Lucarelli, A. ...Neres, J. / Pojer, F. / Molteni, E. / Chiarelli, L.R. / Dhar, N. / Boy-Rottger, S. / Buroni, S. / Fullam, E. / Degiacomi, G. / Lucarelli, A. / Read, R.J. / Zanoni, G. / Edmondson, D.E. / De Rossi, E. / Pasca, M. / Riccardi, G. / Mattevi, A. / Dyson, P.J. / Cole, S.T. / Binda, C.
CitationJournal: Sci. Transl. Med. / Year: 2012
Title: Structural Basis for Benzothiazinone-Mediated Killing of Mycobacterium Tuberculosis.
Authors: Neres, J. / Pojer, F. / Molteni, E. / Chiarelli, L.R. / Dhar, N. / Boy-Rottger, S. / Buroni, S. / Fullam, E. / Degiacomi, G. / Lucarelli, A.P. / Read, R.J. / Zanoni, G. / Edmondson, D.E. / ...Authors: Neres, J. / Pojer, F. / Molteni, E. / Chiarelli, L.R. / Dhar, N. / Boy-Rottger, S. / Buroni, S. / Fullam, E. / Degiacomi, G. / Lucarelli, A.P. / Read, R.J. / Zanoni, G. / Edmondson, D.E. / De Rossi, E. / Pasca, M.R. / Mckinney, J.D. / Dyson, P.J. / Riccardi, G. / Mattevi, A. / Cole, S.T. / Binda, C.
History
DepositionMay 21, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2012Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: DECAPRENYL-PHOSPHORYL-BETA-D-RIBOFURANOSE-2-OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9762
Polymers51,1911
Non-polymers7861
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.139, 64.139, 191.204
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein DECAPRENYL-PHOSPHORYL-BETA-D-RIBOFURANOSE-2-OXIDOREDUCTASE / OXIDOREDUCTASE / FAD-BINDING


Mass: 51190.887 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM SMEGMATIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0R607
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsWITH RESPECT TO THE REPORTED SEQUENCE, THE CRYSTALLIZED PROTEIN CORRESPONDS TO A CONSTRUCT DELETED ...WITH RESPECT TO THE REPORTED SEQUENCE, THE CRYSTALLIZED PROTEIN CORRESPONDS TO A CONSTRUCT DELETED OF THE FIRST 5 AMINO ACIDS. IN ADDITION, THE COORDINATES FILE DOES NOT INCLUDE RESIDUES 6-13, 275-303, 330-336 BECAUSE THEY WERE NOT VISIBLE IN THE ELECTRON DENSITY MAP.

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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: 2.23 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growpH: 6.5
Details: 30% PEG 4000, 100 MM SODIUM CITRATE PH 5.6, 200 MM SODIUM ACETATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 22, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.1→60 Å / Num. obs: 27565 / % possible obs: 99.9 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.7

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
Rosettaphasing
REFMAC5.6.0117refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1W1O

1w1o


Resolution: 2.1→63.73 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.919 / SU B: 5.762 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.224 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27104 1413 5.1 %RANDOM
Rwork0.20238 ---
obs0.20589 26106 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.136 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å2-0.13 Å20 Å2
2---0.27 Å20 Å2
3---0.4 Å2
Refinement stepCycle: LAST / Resolution: 2.1→63.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3229 0 53 95 3377
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0193363
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9391.9724573
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3325416
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.04822.789147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.94915524
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8271528
X-RAY DIFFRACTIONr_chiral_restr0.1440.2501
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212569
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 101 -
Rwork0.279 1702 -
obs--99.89 %

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