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- PDB-3h2e: Structural Studies of Pterin-Based Inhibitors of Dihydropteroate ... -

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Basic information

Entry
Database: PDB / ID: 3h2e
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-B59 / : / Dihydropteroate synthase
Similarity search - Component
Biological speciesBacillus anthracis str. A2012 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)67,00812
Polymers65,7672
Non-polymers1,24110
Water4,612256
1
A: Dihydropteroate synthase
hetero molecules

A: Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,53610
Polymers65,7672
Non-polymers7698
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_475-x-1,-y+2,z1
Buried area3750 Å2
ΔGint-108 kcal/mol
Surface area22030 Å2
MethodPISA
2
B: Dihydropteroate synthase
hetero molecules

B: Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,48114
Polymers65,7672
Non-polymers1,71312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_465-x-1,-y+1,z1
Buried area3670 Å2
ΔGint-95 kcal/mol
Surface area21970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.063, 98.063, 263.945
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-B59 / 1,3-dimethyl-2,4,7-trioxo-1,2,3,4,7,8-hexahydropteridine-6-carbaldehyde


Mass: 236.184 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H8N4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.79 Å3/Da / Density % sol: 55.84 %
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→48.21 Å / Num. obs: 48615 / % possible obs: 94.2 % / Redundancy: 11.5 % / Rsym value: 0.102 / Net I/σ(I): 32.3
Reflection shellResolution: 2→2.07 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 3.1 / Rsym value: 0.346 / % possible all: 60.8

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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→48.21 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.945 / SU B: 7.966 / SU ML: 0.111 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23735 2447 5 %RANDOM
Rwork0.20176 ---
obs0.20361 48547 94.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.345 Å2
Baniso -1Baniso -2Baniso -3
1-1.43 Å20.72 Å20 Å2
2--1.43 Å20 Å2
3----2.15 Å2
Refinement stepCycle: LAST / Resolution: 2→48.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4131 0 73 256 4460
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224267
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3171.995765
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.245533
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.2225.08187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.78515785
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8071525
X-RAY DIFFRACTIONr_chiral_restr0.0960.2643
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023141
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2020.21780
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.22915
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2228
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.272
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.350.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0071.52743
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.48224255
X-RAY DIFFRACTIONr_scbond_it2.3431810
X-RAY DIFFRACTIONr_scangle_it3.7864.51508
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.054 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 101 -
Rwork0.224 2050 -
obs--58.14 %
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)
11.38-0.07020.53030.89620.08712.0022-0.02880.0071-0.00250.06450.03220.02770.02360.1465-0.0035-0.07820.11370.0103-0.03350.0289-0.2085-78.43980.83491.339
20.79230.0247-0.24461.1985-0.25251.5735-0.00890.0538-0.0109-0.1512-0.0733-0.0245-0.23670.09080.08220.0559-0.0151-0.0453-0.10460.0352-0.1959-68.26761.351138.426
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 274
2X-RAY DIFFRACTION2B2 - 274

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