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- PDB-9b2e: DHNA associated with an inhibitor -

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Basic information

Entry
Database: PDB / ID: 9b2e
TitleDHNA associated with an inhibitor
Components7,8-dihydroneopterin aldolase
KeywordsLYASE / protein complex
Function / homology
Function and homology information


dihydroneopterin aldolase / dihydroneopterin aldolase activity / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / cytoplasm
Similarity search - Function
Dihydroneopterin aldolase / Dihydroneopterin aldolase/epimerase domain / Dihydroneopterin aldolase / Dihydroneopterin aldolase / GTP cyclohydrolase I, C-terminal/NADPH-dependent 7-cyano-7-deazaguanine reductase
Similarity search - Domain/homology
2-amino-8-sulfanyl-1,9-dihydro-6H-purin-6-one / 7,8-dihydroneopterin aldolase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsCzeczot, A.M. / Silva, E.E.D. / Timmers, L.F.S.M. / Machado, P. / Basso, L.A. / Bizarro, C.V.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Brazilian National Council for Scientific and Technological Development (CNPq)42170320172 Brazil
CitationJournal: J Enzyme Inhib Med Chem / Year: 2024
Title: Crystal structure of dihydroneopterin aldolase from Mycobacterium tuberculosis associated with 8-mercaptoguanine, and development of novel S8-functionalized analogues as inhibitors: Synthesis, ...Title: Crystal structure of dihydroneopterin aldolase from Mycobacterium tuberculosis associated with 8-mercaptoguanine, and development of novel S8-functionalized analogues as inhibitors: Synthesis, enzyme inhibition, in vitro toxicity and antitubercular activity.
Authors: Czeczot, A.M. / Muniz, M.N. / Perello, M.A. / Silva, E.E.D. / Timmers, L.F.S.M. / Berger, A. / Gonzalez, L.C. / Arrache Goncalves, G. / Moura, S. / Machado, P. / Bizarro, C.V. / Basso, L.A.
History
DepositionMar 15, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 7,8-dihydroneopterin aldolase
B: 7,8-dihydroneopterin aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2994
Polymers26,9322
Non-polymers3662
Water5,080282
1
A: 7,8-dihydroneopterin aldolase
B: 7,8-dihydroneopterin aldolase
hetero molecules

A: 7,8-dihydroneopterin aldolase
B: 7,8-dihydroneopterin aldolase
hetero molecules

A: 7,8-dihydroneopterin aldolase
B: 7,8-dihydroneopterin aldolase
hetero molecules

A: 7,8-dihydroneopterin aldolase
B: 7,8-dihydroneopterin aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,19516
Polymers107,7298
Non-polymers1,4668
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
Buried area21370 Å2
ΔGint-89 kcal/mol
Surface area34180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.386, 81.386, 74.862
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-425-

HOH

21B-345-

HOH

31B-447-

HOH

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Components

#1: Protein 7,8-dihydroneopterin aldolase


Mass: 13466.166 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: folB, A4S10_03776, DSI28_17580, DSI46_08595, ERS007661_01319, ERS007679_04035, ERS007681_03220, ERS027646_01565, ERS027659_03938, ERS027661_02230, ERS053720_02853, GJE03_18950, SAMEA2683035_00705
Production host: Escherichia coli (E. coli) / References: UniProt: A0A045KE67, dihydroneopterin aldolase
#2: Chemical ChemComp-B55 / 2-amino-8-sulfanyl-1,9-dihydro-6H-purin-6-one / 2-amino-8-mercapto-1H-purin-6(9H)-one


Mass: 183.191 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H5N5OS / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.3 Å3/Da / Density % sol: 46.55 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / Details: 8% PEG4000, 100 mM lithium sulfate

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Data collection

DiffractionMean temperature: 125 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER X8 PROTEUM / Wavelength: 0.56 Å
DetectorType: Bruker PHOTON III / Detector: PIXEL / Date: Nov 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.56 Å / Relative weight: 1
ReflectionResolution: 1.95→19.33 Å / Num. obs: 34614 / % possible obs: 97.95 % / Redundancy: 1.8 % / CC1/2: 0.997 / Net I/σ(I): 11.45
Reflection shellResolution: 1.95→2.02 Å / Num. unique obs: 1847 / CC1/2: 0.939

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
SCALAdata scaling
MOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→19.33 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2131 3393 10.06 %
Rwork0.2048 --
obs0.2056 33742 96.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→19.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1845 0 24 282 2151
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091937
X-RAY DIFFRACTIONf_angle_d1.0892648
X-RAY DIFFRACTIONf_dihedral_angle_d14.847704
X-RAY DIFFRACTIONf_chiral_restr0.071301
X-RAY DIFFRACTIONf_plane_restr0.009350
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.980.21311230.20481169X-RAY DIFFRACTION88
1.98-2.010.29961270.25611214X-RAY DIFFRACTION93
2.01-2.040.28951500.22521251X-RAY DIFFRACTION96
2.04-2.070.24661520.22611289X-RAY DIFFRACTION98
2.07-2.110.19051320.22711275X-RAY DIFFRACTION99
2.11-2.150.24331490.21561327X-RAY DIFFRACTION99
2.15-2.190.18221460.21061300X-RAY DIFFRACTION100
2.19-2.230.26611360.21981294X-RAY DIFFRACTION100
2.23-2.280.24421560.21751304X-RAY DIFFRACTION98
2.28-2.330.20851450.24451317X-RAY DIFFRACTION99
2.33-2.390.24711460.22751265X-RAY DIFFRACTION98
2.39-2.460.26581520.26021259X-RAY DIFFRACTION96
2.46-2.530.29451310.2981187X-RAY DIFFRACTION91
2.53-2.610.31911220.27191162X-RAY DIFFRACTION89
2.61-2.70.2551440.24961261X-RAY DIFFRACTION94
2.7-2.810.3131350.23411218X-RAY DIFFRACTION93
2.81-2.940.19911380.2171255X-RAY DIFFRACTION97
2.94-3.090.21871490.19121285X-RAY DIFFRACTION99
3.09-3.280.18971440.1811321X-RAY DIFFRACTION99
3.29-3.540.16861490.17531293X-RAY DIFFRACTION99
3.54-3.890.15841420.15041307X-RAY DIFFRACTION100
3.89-4.440.15221480.16591286X-RAY DIFFRACTION97
4.45-5.580.18191390.17711209X-RAY DIFFRACTION93
5.58-19.330.22841380.20791301X-RAY DIFFRACTION97

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