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- PDB-4daf: Crystal structure of B. anthracis DHPS with compound 19 -

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Basic information

Entry
Database: PDB / ID: 4daf
TitleCrystal structure of B. anthracis DHPS with compound 19
ComponentsDihydropteroate Synthase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / TIM Barrel / DHPS inhibitor / Transferase / pABA / 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
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-0J4 / : / Dihydropteroate synthase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.501 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 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release
Revision 1.1May 9, 2012Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Sep 13, 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_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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)67,03812
Polymers65,7672
Non-polymers1,27110
Water48627
1
A: Dihydropteroate Synthase
hetero molecules

A: Dihydropteroate Synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,03812
Polymers65,7672
Non-polymers1,27110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z1
Buried area3770 Å2
ΔGint-103 kcal/mol
Surface area20740 Å2
MethodPISA
2
B: Dihydropteroate Synthase
hetero molecules

B: Dihydropteroate Synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,03812
Polymers65,7672
Non-polymers1,27110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455-x-1,-y,z1
Buried area3730 Å2
ΔGint-106 kcal/mol
Surface area20700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.371, 98.371, 263.131
Angle α, β, γ (deg.)90.000, 90.000, 120.000
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 (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-0J4 / (2R)-2-(7-amino-4,5-dioxo-1,4,5,6-tetrahydropyrimido[4,5-c]pyridazin-3-yl)propanoic acid


Mass: 251.199 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H9N5O4
#3: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.79 Å3/Da / Density % sol: 55.98 %
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 23, 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: 2.5→50 Å / Num. obs: 24748 / % possible obs: 92 % / Observed criterion σ(I): -3 / Redundancy: 11.7 % / Rmerge(I) obs: 0.07 / Χ2: 1.414 / Net I/σ(I): 11.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.5-2.548.20.2336.4657681.14559.3
2.54-2.598.20.2326.168711.18866.3
2.59-2.648.80.2127.4769461.13372.4
2.64-2.698.90.2176.87510761.13682.7
2.69-2.759.70.2198.44811661.05489.3
2.75-2.8210.50.21410.12412840.99997.1
2.82-2.8911.70.21611.69313220.94699.2
2.89-2.9612.80.18215.75312940.97499.1
2.96-3.0513.10.1619.61613151.05399.5
3.05-3.1513.20.13922.85913041.10199.2
3.15-3.2613.20.11530.57913381.24599.6
3.26-3.3913.20.10633.70913191.31599.4
3.39-3.5513.10.09139.69413241.54999.1
3.55-3.73130.07942.37613081.63798.5
3.73-3.97130.07447.66513331.87598.8
3.97-4.2712.70.06551.67113311.9397.7
4.27-4.712.80.05856.18513531.92299.3
4.7-5.3812.60.0554.21613731.83898.9
5.38-6.7812.30.04356.95513931.66798.4
6.78-508.90.04138.78813301.84385

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.6.1_357refinement
PDB_EXTRACT3.1data extraction
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TWS

1tws


Resolution: 2.501→48.348 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.6417 / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 0.04 / Phase error: 38.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2698 1104 5.04 %Random
Rwork0.2356 ---
obs0.237 21918 81.25 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.534 Å2 / ksol: 0.348 e/Å3
Displacement parametersBiso max: 181.87 Å2 / Biso mean: 81.0258 Å2 / Biso min: 43.8 Å2
Baniso -1Baniso -2Baniso -3
1-24.2888 Å2-0 Å2-0 Å2
2--24.2888 Å20 Å2
3----48.5775 Å2
Refinement stepCycle: LAST / Resolution: 2.501→48.348 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3932 0 76 27 4035
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084058
X-RAY DIFFRACTIONf_angle_d1.1425477
X-RAY DIFFRACTIONf_chiral_restr0.074614
X-RAY DIFFRACTIONf_plane_restr0.005699
X-RAY DIFFRACTIONf_dihedral_angle_d15.911539
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.501-2.61480.3554760.31641466154247
2.6148-2.75270.36661090.31582016212564
2.7527-2.92510.31611190.29622554267381
2.9251-3.15090.28741140.29772747286186
3.1509-3.46790.30351760.26042815299190
3.4679-3.96960.25631840.22152903308792
3.9696-5.00040.19531840.18443086327095
5.0004-48.35710.32931420.22913227336992
Refinement TLS params.

S33: 0 Å ° / 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 °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.92740.1965-0.07480.9919-0.36021.6131-0.065-0.06740.00910.02150.0229-0.02090.37980.1150.5605-0.13930.01350.44130.03740.5044-19.262224.15883.0634
20.81330.4173-0.05630.9406-0.23321.4681-0.05680.0932-0.0609-0.05-0.04090.0239-0.09160.4660.6781-0.04540.01760.55340.04820.584-30.58044.749951.5733
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A'A2 - 274
2X-RAY DIFFRACTION2chain 'B'B2 - 274

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