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- PDB-3h2o: Structural Studies of Pterin-Based Inhibitors of Dihydropteroate ... -

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Basic information

Entry
Database: PDB / ID: 3h2o
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
Chem-B63 / : / Dihydropteroate synthase
Similarity search - Component
Biological speciesBacillus anthracis str. A2012 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)66,8088
Polymers65,7672
Non-polymers1,0416
Water905
1
A: Dihydropteroate synthase
hetero molecules

A: Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,8088
Polymers65,7672
Non-polymers1,0416
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_475-x-1,-y+2,z1
Buried area3050 Å2
ΔGint-63 kcal/mol
Surface area21560 Å2
MethodPISA
2
B: Dihydropteroate synthase
hetero molecules

B: Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,8088
Polymers65,7672
Non-polymers1,0416
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_465-x-1,-y+1,z1
Buried area3030 Å2
ΔGint-65 kcal/mol
Surface area21890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.292, 99.292, 263.051
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TYRTYRLEULEUAA5 - 2625 - 46
21TYRTYRLEULEUBB5 - 2625 - 46
12VALVALASPASPAA42 - 6162 - 81
22VALVALASPASPBB42 - 6162 - 81
13GLUGLULYSLYSAA79 - 27499 - 294
23GLUGLULYSLYSBB79 - 27499 - 294

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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-B63 / 4-{[2-(2-amino-4-oxo-3,4,7,8-tetrahydropteridin-6-yl)ethyl]amino}benzoic acid


Mass: 328.326 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H16N6O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.85 Å3/Da / Density % sol: 56.78 %
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: 2.61→48.78 Å / Num. obs: 22826 / % possible obs: 93.9 % / Redundancy: 11.9 % / Rsym value: 0.066 / Net I/σ(I): 38.2
Reflection shellResolution: 2.61→2.69 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 7.1 / Num. unique all: 1451 / Rsym value: 0.16 / % possible all: 62

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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: 2.7→48.78 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.91 / SU B: 51.803 / SU ML: 0.448 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.757 / ESU R Free: 0.386 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.31097 1084 5.1 %RANDOM
Rwork0.27128 ---
obs0.27323 21380 97.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.878 Å2
Baniso -1Baniso -2Baniso -3
1-6.56 Å23.28 Å20 Å2
2--6.56 Å20 Å2
3----9.84 Å2
Refinement stepCycle: LAST / Resolution: 2.7→48.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3996 0 68 5 4069
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0224121
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1271.9855573
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9715521
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.75525.145173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.09515723
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5981522
X-RAY DIFFRACTIONr_chiral_restr0.1360.2631
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023056
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.280.22116
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3330.22846
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.2204
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2380.282
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2510.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7541.52665
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.30324163
X-RAY DIFFRACTIONr_scbond_it2.10331670
X-RAY DIFFRACTIONr_scangle_it3.2594.51410
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1764 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.350.5
medium thermal1.242
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.463 63 -
Rwork0.403 1201 -
obs-1264 79.55 %
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)
11.369-0.51070.04161.96190.27452.47820.1424-0.3364-0.02620.1332-0.1248-0.04180.0151.0573-0.01760.20150.2340.0255-0.22250.1137-0.225-80.237981.59191.4784
21.5582-0.1618-0.05831.44510.10762.5270.0540.17820.0251-0.1014-0.09360.0159-0.91120.47550.0396-0.08590.23-0.05070.2240.0933-0.2575-69.155561.7201139.1712
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 274
2X-RAY DIFFRACTION2B1 - 274

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