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- PDB-4dai: Crystal structure of B. anthracis DHPS with compound 23 -

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Basic information

Entry
Database: PDB / ID: 4dai
TitleCrystal structure of B. anthracis DHPS with compound 23
ComponentsDihydropteroate Synthase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / pABA / DHPP / Pterin / DHPS inhibitors / TIM barrel / 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-0J5 / : / Dihydropteroate synthase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 1.0Mar 28, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)67,10613
Polymers65,7672
Non-polymers1,33911
Water45025
1
A: Dihydropteroate Synthase
hetero molecules

A: Dihydropteroate Synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,01012
Polymers65,7672
Non-polymers1,24310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z1
Buried area3790 Å2
ΔGint-103 kcal/mol
Surface area21140 Å2
MethodPISA
2
B: Dihydropteroate Synthase
hetero molecules

B: Dihydropteroate Synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,20214
Polymers65,7672
Non-polymers1,43512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455-x-1,-y,z1
Buried area3980 Å2
ΔGint-120 kcal/mol
Surface area20830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.291, 98.291, 263.584
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-0J5 / (7-amino-4,5-dioxo-1,4,5,6-tetrahydropyrimido[4,5-c]pyridazin-3-yl)acetic acid


Mass: 237.172 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H7N5O4
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / 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
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: 23163 / % possible obs: 86.2 % / Observed criterion σ(I): -3 / Redundancy: 9.1 % / Rmerge(I) obs: 0.071 / Χ2: 1.28 / Net I/σ(I): 11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.5-2.546.40.27.8485690.93743.8
2.54-2.596.40.1997.5366290.99147.8
2.59-2.646.40.197.4357190.94755.4
2.64-2.696.70.1997.3037870.99660.2
2.69-2.756.80.1947.8829160.9570
2.75-2.826.70.1847.98610851.01182.7
2.82-2.897.40.1948.5512160.89892.1
2.89-2.968.60.18510.65612630.86796.6
2.96-3.059.40.16613.79713090.87598.9
3.05-3.1510.30.15216.56513240.91199.8
3.15-3.2610.70.11923.81913341.00199.8
3.26-3.3910.80.10925.84513161.02899.7
3.39-3.5510.70.08731.92813281.15799.7
3.55-3.7310.20.07535.45613141.30298.4
3.73-3.9710.60.0741.08613401.52899.6
3.97-4.279.50.0644011071.75681.5
4.27-4.710.30.05748.15613631.67899.8
4.7-5.38100.05648.26413781.77799.6
5.38-6.789.80.05547.94414081.81299.5
6.78-507.40.05239.03714582.00293.2

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Processing

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

1tws


Resolution: 2.5→30 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.6635 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2818 1249 4.6 %Random
Rwork0.2529 ---
obs-24881 92.2 %-
Solvent computationBsol: 71.1378 Å2
Displacement parametersBiso max: 157.33 Å2 / Biso mean: 73.695 Å2 / Biso min: 34.51 Å2
Baniso -1Baniso -2Baniso -3
1-6.273 Å20 Å20 Å2
2--6.273 Å20 Å2
3----12.545 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4026 0 79 25 4130
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.19
X-RAY DIFFRACTIONc_mcbond_it1.4821.5
X-RAY DIFFRACTIONc_scbond_it2.1612
X-RAY DIFFRACTIONc_mcangle_it2.5782
X-RAY DIFFRACTIONc_scangle_it3.3032.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top
X-RAY DIFFRACTION5inh1578_steve.parinh1578_steve.top

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