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- PDB-3h2c: Structural Studies of Pterin-Based Inhibitors of Dihydropteroate ... -

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Basic information

Entry
Database: PDB / ID: 3h2c
TitleStructural Studies of Pterin-Based Inhibitors of Dihydropteroate Synthase
ComponentsDihydropteroate synthase
KeywordsTransferase/Transferase Inhibitor / ANTHRACIS / FOLATE BIOSYNTHESIS / DIHYDROPTEROATE / PTERINE / Transferase / Transferase-Transferase Inhibitor COMPLEX
Function / homology
Function and homology information


dihydropteroate synthase / dihydropteroate synthase activity / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / metal ion binding
Similarity search - Function
Dihydropteroate synthase signature 1. / Dihydropteroate synthase / Dihydropteroate synthase domain / Dihydropteroate synthase signature 2. / Dihydropteroate synthase-like / Pterin-binding domain / Pterin binding enzyme / Pterin-binding domain profile. / Dihydropteroate synthase-like / TIM Barrel ...Dihydropteroate synthase signature 1. / Dihydropteroate synthase / Dihydropteroate synthase domain / Dihydropteroate synthase signature 2. / Dihydropteroate synthase-like / Pterin-binding domain / Pterin binding enzyme / Pterin-binding domain profile. / Dihydropteroate synthase-like / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
1H-imidazo[4,5-d]pyridazine-4,7-diamine / : / Dihydropteroate synthase
Similarity search - Component
Biological speciesBacillus anthracis str. A2012 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsYun, M.-K. / White, S.W.
CitationJournal: J.Med.Chem. / Year: 2010
Title: Structural studies of pterin-based inhibitors of dihydropteroate synthase.
Authors: Hevener, K.E. / Yun, M.K. / Qi, J. / Kerr, I.D. / Babaoglu, K. / Hurdle, J.G. / Balakrishna, K. / White, S.W. / Lee, R.E.
History
DepositionApr 14, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 2023Group: 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dihydropteroate synthase
B: Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,12415
Polymers65,7672
Non-polymers1,35713
Water59433
1
A: Dihydropteroate synthase
hetero molecules

A: Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,02814
Polymers65,7672
Non-polymers1,26112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_475-x-1,-y+2,z1
Buried area4160 Å2
ΔGint-132 kcal/mol
Surface area21550 Å2
MethodPISA
2
B: Dihydropteroate synthase
hetero molecules

B: Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,22116
Polymers65,7672
Non-polymers1,45314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_465-x-1,-y+1,z1
Buried area4280 Å2
ΔGint-146 kcal/mol
Surface area21950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.667, 97.667, 263.574
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein Dihydropteroate synthase


Mass: 32883.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis str. A2012 (bacteria)
Gene: folP, BAO_0074 / Plasmid: PET-28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: B1UXN2, UniProt: Q81VW8*PLUS, dihydropteroate synthase
#2: Chemical ChemComp-B58 / 1H-imidazo[4,5-d]pyridazine-4,7-diamine


Mass: 150.141 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6N6
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9
Details: LITHIUM SULFATE, propane, Bis-Tris, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 23, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→48.02 Å / Num. obs: 26492 / % possible obs: 88.5 % / Redundancy: 7.6 % / Rsym value: 0.101 / Net I/σ(I): 19
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 1.6 / Num. unique all: 1706 / Rsym value: 0.309 / % possible all: 58.2

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Processing

Software
NameVersionClassification
SERGUIControldata collection
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1TX0

1tx0


Resolution: 2.6→48.02 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.927 / SU B: 35.471 / SU ML: 0.343 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.608 / ESU R Free: 0.352 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29823 1126 5 %RANDOM
Rwork0.24643 ---
obs0.24897 22577 94.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.96 Å2
Baniso -1Baniso -2Baniso -3
1-5.45 Å22.72 Å20 Å2
2--5.45 Å20 Å2
3----8.17 Å2
Refinement stepCycle: LAST / Resolution: 2.6→48.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4010 0 77 33 4120
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0224147
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1481.995603
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4195516
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.08525.193181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.47715752
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3921523
X-RAY DIFFRACTIONr_chiral_restr0.1350.2629
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023035
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2580.22051
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3310.22848
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2157
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2990.291
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.141.52624
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.70624136
X-RAY DIFFRACTIONr_scbond_it2.72831688
X-RAY DIFFRACTIONr_scangle_it4.1964.51465
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 60 -
Rwork0.37 1248 -
obs-1308 76.94 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.9231-0.4772-0.87552.9309-0.15374.7648-0.0144-0.13820.02670.1441-0.12680.00350.15831.20340.14120.03670.31520.0077-0.26690.1036-0.3287-78.861479.893991.2975
21.6127-0.32760.99562.59710.3044.9709-0.08980.14040.1205-0.3848-0.1527-0.1061-1.25860.45660.2425-0.02250.2657-0.04780.00720.0681-0.3805-67.989360.8046139.6182
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 274
2X-RAY DIFFRACTION2B-7 - 274

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