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- PDB-4nl1: Crystal structure of B. anthracis DHPS with compound 11: (E)-N-[4... -

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Basic information

Entry
Database: PDB / ID: 4nl1
TitleCrystal structure of B. anthracis DHPS with compound 11: (E)-N-[4-(trifluoromethyl)benzyl]-1-[4-(trifluoromethyl)phenyl]methanimine
ComponentsDihydropteroate Synthase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / TIM Barrel / TIM barel / Transferase / Pterin / pABA / 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-Z13 / Dihydropteroate synthase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 13, 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_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)67,19812
Polymers65,7672
Non-polymers1,43110
Water52229
1
A: Dihydropteroate Synthase
hetero molecules

A: Dihydropteroate Synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,19812
Polymers65,7672
Non-polymers1,43110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z1
Buried area2510 Å2
ΔGint-26 kcal/mol
Surface area21260 Å2
MethodPISA
2
B: Dihydropteroate Synthase
hetero molecules

B: Dihydropteroate Synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,19812
Polymers65,7672
Non-polymers1,43110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455-x-1,-y,z1
Buried area2490 Å2
ΔGint-27 kcal/mol
Surface area21160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.798, 98.798, 263.278
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-301-

Z13

21A-301-

Z13

31A-301-

Z13

41A-301-

Z13

51B-301-

Z13

61B-301-

Z13

71B-301-

Z13

81B-301-

Z13

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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-Z13 / (E)-N-[4-(trifluoromethyl)benzyl]-1-[4-(trifluoromethyl)phenyl]methanimine


Mass: 331.256 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H11F6N
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.82 Å3/Da / Density % sol: 56.38 %
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 monochrometer
RadiationMonochromator: Rosenbaum-Rock double crystal monochrometer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 31293 / % possible obs: 90.5 % / Observed criterion σ(I): -3 / Redundancy: 11.1 % / Rmerge(I) obs: 0.174 / Χ2: 0.995 / Net I/σ(I): 6.9
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allRsym valueΧ2Diffraction-ID% possible all
2.3-2.387.418150.4851.253154
2.38-2.487.124570.4211.335172.9
2.48-2.598.731780.4531.319193.4
2.59-2.7312.133710.4211.377199.8
2.73-2.913.534150.321.612199.8
2.9-3.1213.533980.2510.829199.9
3.12-3.431334270.2040.773199.3
3.43-3.9311.933660.1870.732196.8
3.93-4.9511.133240.1610.589193.8
4.95-309.835420.1330.445193.5

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Processing

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

1tws


Resolution: 2.3→29.94 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.3059 / WRfactor Rwork: 0.2383 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.7686 / SU B: 15.52 / SU ML: 0.167 / SU R Cruickshank DPI: 0.294 / SU Rfree: 0.2333 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.294 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2525 1565 5.1 %RANDOM
Rwork0.2068 ---
obs0.209 30972 89.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 132.76 Å2 / Biso mean: 64.7842 Å2 / Biso min: 43.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å20.58 Å20 Å2
2--0.58 Å20 Å2
3----1.89 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4128 0 66 29 4223
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194274
X-RAY DIFFRACTIONr_bond_other_d0.0020.024143
X-RAY DIFFRACTIONr_angle_refined_deg1.4481.9865779
X-RAY DIFFRACTIONr_angle_other_deg0.80939545
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6345539
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.49925186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.79815777
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6491525
X-RAY DIFFRACTIONr_chiral_restr0.0790.2655
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214768
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02881
LS refinement shellResolution: 2.302→2.361 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 60 -
Rwork0.29 1157 -
all-1217 -
obs--48.45 %
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)
10.2482-0.32340.30510.782-0.10161.2839-0.0277-0.03750.0260.0450.00560.02470.2278-0.00290.0220.3663-0.04280.02920.24590.01730.0379-19.13624.2493.028
21.09210.40160.0330.49550.0020.963-0.03130.0929-0.0412-0.0643-0.06250.0365-0.05810.19280.09380.3174-0.01880.01060.28020.04380.0301-30.614.91751.516
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 274
2X-RAY DIFFRACTION2B2 - 274

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