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- PDB-4d9p: Crystal structure of B. anthracis DHPS with compound 17 -

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Basic information

Entry
Database: PDB / ID: 4d9p
TitleCrystal structure of B. anthracis DHPS with compound 17
ComponentsDihydropteroate Synthase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / TIM Barrel / transferase / DHPS inhibitors / pABA / pterin / DHPP / 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
Chem-Z17 / : / Dihydropteroate synthase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsHammoudeh, D. / Lee, R.E. / White, S.W.
CitationJournal: Chemmedchem / Year: 2012
Title: Structure-Based Design of Novel Pyrimido[4,5-c]pyridazine Derivatives as Dihydropteroate Synthase Inhibitors with Increased Affinity.
Authors: Zhao, Y. / Hammoudeh, D. / Yun, M.K. / Qi, J. / White, S.W. / Lee, R.E.
History
DepositionJan 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 1.1May 9, 2012Group: Database references
Revision 1.2Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Sep 13, 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)67,28714
Polymers65,7672
Non-polymers1,51912
Water90150
1
A: Dihydropteroate Synthase
hetero molecules

A: Dihydropteroate Synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,28714
Polymers65,7672
Non-polymers1,51912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z1
Buried area3670 Å2
ΔGint-97 kcal/mol
Surface area21650 Å2
MethodPISA
2
B: Dihydropteroate Synthase
hetero molecules

B: Dihydropteroate Synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,28714
Polymers65,7672
Non-polymers1,51912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455-x-1,-y,z1
Buried area3960 Å2
ΔGint-117 kcal/mol
Surface area21590 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)134,57328
Polymers131,5354
Non-polymers3,03824
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z1
crystal symmetry operation2_564-y,x-y+1,z-1/31
crystal symmetry operation5_554y,-x+y,z-1/31
Buried area10350 Å2
ΔGint-236 kcal/mol
Surface area40520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.667, 99.667, 261.081
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-426-

HOH

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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 (anthrax bacterium) / Strain: A2012 / Gene: folP / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: C3P9L8, UniProt: Q81VW8*PLUS, dihydropteroate synthase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-Z17 / (3R)-3-(7-amino-1-methyl-4,5-dioxo-1,4,5,6-tetrahydropyrimido[4,5-c]pyridazin-3-yl)butanoic acid


Mass: 279.252 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H13N5O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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, 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: Oct 22, 2011
Details: Si 111. Rosenbaum-Rock double-crystal monochromator: liquid nitrogen cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror
RadiationMonochromator: double crystal - liquid nitrogen cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.26→30 Å / Num. all: 31293 / 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

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.26-2.387.40.485318151.25354
2.38-2.487.10.4213.14824571.33972.9
2.48-2.598.70.4534.38131781.31993.4
2.59-2.7312.10.4217.81333711.37899.8
2.73-2.913.50.3213.43834151.61299.8
2.9-3.1213.50.2518.76233980.82999.9
3.12-3.43130.2049.35334270.77499.3
3.43-3.9311.90.1878.69433660.73296.8
3.93-4.9511.10.1618.77733240.58993.8
4.95-309.80.1337.54335420.44593.5

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Processing

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

1tws


Resolution: 2.26→30 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.3173 / WRfactor Rwork: 0.2746 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.743 / SU B: 19.155 / SU ML: 0.206 / SU R Cruickshank DPI: 0.3325 / SU Rfree: 0.2487 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.333 / ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2685 1525 5 %RANDOM
Rwork0.234 ---
obs0.2357 30739 83.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 157.4 Å2 / Biso mean: 56.2133 Å2 / Biso min: 32.61 Å2
Baniso -1Baniso -2Baniso -3
1-3.43 Å21.71 Å2-0 Å2
2--3.43 Å2-0 Å2
3----5.14 Å2
Refinement stepCycle: LAST / Resolution: 2.26→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4063 0 90 50 4203
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224200
X-RAY DIFFRACTIONr_angle_refined_deg1.1981.9945673
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1175520
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.6225.163184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.50315767
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9161524
X-RAY DIFFRACTIONr_chiral_restr0.0830.2633
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213083
X-RAY DIFFRACTIONr_mcbond_it1.0891.52597
X-RAY DIFFRACTIONr_mcangle_it1.62724171
X-RAY DIFFRACTIONr_scbond_it1.70731603
X-RAY DIFFRACTIONr_scangle_it2.8534.51502
LS refinement shellResolution: 2.26→2.317 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.472 45 -
Rwork0.404 1150 -
all-1195 -
obs--44.66 %
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)
10.2776-0.17760.09711.5663-0.20871.0726-0.0349-0.1709-0.01960.00770.0824-0.0620.1123-0.064-0.04740.0918-0.0383-0.00320.25780.06250.0298-18.966124.43673.6695
21.37980.5157-0.07050.6913-0.11440.9298-0.00420.1397-0.04260.0067-0.0176-0.0643-0.03750.0460.02180.1419-0.03070.0120.14990.02490.0469-30.84564.829650.6438
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 274
2X-RAY DIFFRACTION2B2 - 274

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