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- PDB-4nil: Crystal structure of B. anthracis DHPS with compound 5: 4-[(trifl... -

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Basic information

Entry
Database: PDB / ID: 4nil
TitleCrystal structure of B. anthracis DHPS with compound 5: 4-[(trifluoromethyl)sulfanyl]benzamide
ComponentsDihydropteroate Synthase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / TIM Barrel / transferase / Pterin and pABA binding / 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 / cytosol
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
4-[(trifluoromethyl)sulfanyl]benzamide / Dihydropteroate synthase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsHammoudeh, D.I. / White, S.W.
CitationJournal: Acs Chem.Biol. / Year: 2014
Title: Identification and characterization of an allosteric inhibitory site on dihydropteroate synthase.
Authors: Hammoudeh, D.I. / Date, M. / Yun, M.K. / Zhang, W. / Boyd, V.A. / Viacava Follis, A. / Griffith, E. / Lee, R.E. / Bashford, D. / White, S.W.
History
DepositionNov 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Sep 20, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / 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)67,26715
Polymers65,7672
Non-polymers1,49913
Water57632
1
A: Dihydropteroate Synthase
hetero molecules

A: Dihydropteroate Synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,17014
Polymers65,7672
Non-polymers1,40312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_475-x-1,-y+2,z1
Buried area2480 Å2
ΔGint-26 kcal/mol
Surface area21660 Å2
MethodPISA
2
B: Dihydropteroate Synthase
hetero molecules

B: Dihydropteroate Synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,36316
Polymers65,7672
Non-polymers1,59514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_465-x-1,-y+1,z1
Buried area2480 Å2
ΔGint-23 kcal/mol
Surface area21560 Å2
MethodPISA
3
A: Dihydropteroate Synthase
hetero molecules

A: Dihydropteroate Synthase
hetero molecules

B: Dihydropteroate Synthase
hetero molecules

B: Dihydropteroate Synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,53330
Polymers131,5354
Non-polymers2,99826
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_475-x-1,-y+2,z1
crystal symmetry operation2_574-y,x-y+2,z-1/31
crystal symmetry operation5_454y-1,-x+y,z-1/31
Buried area7310 Å2
ΔGint-58 kcal/mol
Surface area40870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.739, 99.739, 263.296
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-306-

2O8

21B-307-

2O8

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Components

#1: Protein Dihydropteroate Synthase


Mass: 32883.734 Da / Num. of mol.: 2 / Fragment: UNP residues 5-280
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: A2012 / Gene: folP, BAS0071, BA_0071, GBAA_0071 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q81VW8, dihydropteroate synthase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-2O8 / 4-[(trifluoromethyl)sulfanyl]benzamide


Mass: 221.200 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H6F3NOS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.87 Å3/Da / Density % sol: 57.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9
Details: Lithium sulfate, Bis-Tris propane, pH 9.0, 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: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 1, 2012 / Details: Rosenbaum-Rock double-crystal monochromator
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.18→50 Å / Num. obs: 35835 / % possible obs: 86.3 % / Observed criterion σ(I): -3 / Redundancy: 11 % / Biso Wilson estimate: 31.86 Å2 / Rmerge(I) obs: 0.074 / Χ2: 2.045 / Net I/σ(I): 11.7
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allRsym valueΧ2Diffraction-ID% possible all
2.18-2.266.326510.4141.192165.6
2.26-2.357.631750.4581.027178.2
2.35-2.468.231570.2271.292177.8
2.46-2.589.728620.1861.422169.9
2.58-2.7510.538460.1851.511194.1
2.75-2.9613.341020.1541.614199.9
2.96-3.2614.241310.1081.8661100
3.26-3.7312.733740.0812.312180.8
3.73-4.712.440940.0583.147196.5
4.7-5011.744430.0483.203197.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TWS

1tws


Resolution: 2.18→36.11 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.627 / SU ML: 0.36 / σ(F): 1.33 / Phase error: 40.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2804 1772 5.02 %
Rwork0.2264 --
obs0.2291 35313 85.16 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.959 Å2 / ksol: 0.343 e/Å3
Displacement parametersBiso max: 170.23 Å2 / Biso mean: 64.8752 Å2 / Biso min: 28.48 Å2
Baniso -1Baniso -2Baniso -3
1-14.3206 Å2-0 Å2-0 Å2
2--14.3206 Å20 Å2
3----28.6412 Å2
Refinement stepCycle: LAST / Resolution: 2.18→36.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4157 0 83 32 4272
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074309
X-RAY DIFFRACTIONf_angle_d1.0655824
X-RAY DIFFRACTIONf_chiral_restr0.074648
X-RAY DIFFRACTIONf_plane_restr0.005747
X-RAY DIFFRACTIONf_dihedral_angle_d14.4271634
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.18-2.23730.65341160.5491877199384
2.2373-2.30310.5827790.54211649172857
2.3031-2.37740.33031440.32362880302496
2.3774-2.46240.37891260.2741972209868
2.4624-2.5610.30321010.24572058215969
2.561-2.67750.32631320.27742621275388
2.6775-2.81860.39661490.27642951310098
2.8186-2.99510.33921600.25632991315199
2.9951-3.22620.31051560.248930003156100
3.2262-3.55060.27621650.22362995316099
3.5506-4.06380.25981030.18822198230171
4.0638-5.11770.19161800.15463079325999
5.1177-36.11460.23421610.20113270343198
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)
11.71590.35020.51222.9237-0.34852.792-0.10540.250.1552-0.31380.0001-0.0755-0.30550.09880.09510.36010.0482-0.00470.24740.04890.2677-69.274962.0954138.8656
23.1301-1.02820.57371.3896-0.11412.9374-0.0331-0.22770.01010.19160.0126-0.10010.14760.22670.00010.3925-0.0456-0.03420.26050.03280.3364-80.154582.411591.7865
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B'B2 - 274
2X-RAY DIFFRACTION2chain 'A'A1 - 274

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