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- PDB-6de5: Mycobacterium tuberculosis Rv2671 complexed with beta-NADPH and 6... -

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Basic information

Entry
Database: PDB / ID: 6de5
TitleMycobacterium tuberculosis Rv2671 complexed with beta-NADPH and 6-ethyl-5-{(3S)-3-[2-methoxy-5-(pyridin-4-yl)phenyl]but-1-yn-1-yl}pyrimidine-2,4-diamine
Componentsriboflavin biosynthesis protein RibD
Keywordsoxidoreductase/oxidoreductase inhibitor / DHFR / Antifolates / oxidoreductase-oxidoreductase inhibitor complex
Function / homology
Function and homology information


5-amino-6-(5-phosphoribosylamino)uracil reductase activity / riboflavin biosynthetic process / nucleotide binding / cytosol
Similarity search - Function
: / Bacterial bifunctional deaminase-reductase, C-terminal / RibD C-terminal domain / Dihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / Dihydrofolate reductase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-G8J / Chem-NDP / Bacterial bifunctional deaminase-reductase C-terminal domain-containing protein
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHajian, B. / Wright, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI104841 United States
CitationJournal: Cell Chem Biol / Year: 2019
Title: Drugging the Folate Pathway in Mycobacterium tuberculosis: The Role of Multi-targeting Agents.
Authors: Hajian, B. / Scocchera, E. / Shoen, C. / Krucinska, J. / Viswanathan, K. / G-Dayanandan, N. / Erlandsen, H. / Estrada, A. / Mikusova, K. / Kordulakova, J. / Cynamon, M. / Wright, D.
History
DepositionMay 11, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: riboflavin biosynthesis protein RibD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8403
Polymers27,7211
Non-polymers1,1192
Water63135
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)70.440, 94.631, 75.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-434-

HOH

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Components

#1: Protein riboflavin biosynthesis protein RibD


Mass: 27721.494 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: ribD, Rv2671 / Production host: Escherichia coli (E. coli) / References: UniProt: P71968
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-G8J / 6-ethyl-5-{(3S)-3-[2-methoxy-5-(pyridin-4-yl)phenyl]but-1-yn-1-yl}pyrimidine-2,4-diamine


Mass: 373.451 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H23N5O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.27 Å3/Da / Density % sol: 45.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 0.1-0.3 M NaCli, 0.1M Bis-Tris pH 5.5-7.5, 20-30% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X17B1 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.3→56.505 Å / Num. obs: 11313 / % possible obs: 98 % / Redundancy: 1.9 % / Rpim(I) all: 0.091 / Rsym value: 0.091 / Net I/σ(I): 5.5
Reflection shellResolution: 2.3→2.38 Å / Rpim(I) all: 0.236 / Rsym value: 0.236

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XT7

4xt7


Resolution: 2.3→56.505 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.54
RfactorNum. reflection% reflection
Rfree0.2477 1132 10.01 %
Rwork0.187 --
obs0.193 11313 98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→56.505 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1858 0 76 35 1969
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011967
X-RAY DIFFRACTIONf_angle_d1.2362685
X-RAY DIFFRACTIONf_dihedral_angle_d14.615713
X-RAY DIFFRACTIONf_chiral_restr0.043316
X-RAY DIFFRACTIONf_plane_restr0.005343
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3002-2.40490.30681390.2181252X-RAY DIFFRACTION98
2.4049-2.53170.33881400.22421250X-RAY DIFFRACTION97
2.5317-2.69030.27991400.22041269X-RAY DIFFRACTION99
2.6903-2.8980.28281370.22611227X-RAY DIFFRACTION97
2.898-3.18960.29461410.2091275X-RAY DIFFRACTION98
3.1896-3.65110.28711430.18741281X-RAY DIFFRACTION99
3.6511-4.59960.19771430.14761289X-RAY DIFFRACTION98
4.5996-56.52160.17341490.16421338X-RAY DIFFRACTION97

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