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- PDB-4d8a: Crystal structure of B. anthracis DHPS with compound 21 -

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Basic information

Entry
Database: PDB / ID: 4d8a
TitleCrystal structure of B. anthracis DHPS with compound 21
ComponentsDihydropteroate synthase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / TIM Barrel / TIM narrel / Synthase / 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-0HY / LYSINE / : / Dihydropteroate synthase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.183 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 10, 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: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
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)67,24213
Polymers65,7672
Non-polymers1,47411
Water39622
1
A: Dihydropteroate synthase
hetero molecules

A: Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,19712
Polymers65,7672
Non-polymers1,42910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z1
Buried area3340 Å2
ΔGint-73 kcal/mol
Surface area21200 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 area4000 Å2
ΔGint-118 kcal/mol
Surface area20660 Å2
MethodPISA
3
B: Dihydropteroate synthase
hetero molecules

B: Dihydropteroate synthase
hetero molecules

A: Dihydropteroate synthase
hetero molecules

A: Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,48326
Polymers131,5354
Non-polymers2,94822
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455-x-1,-y,z1
crystal symmetry operation3_455-x+y-1,-x,z+1/31
crystal symmetry operation6_555x-y,x,z+1/31
Buried area9800 Å2
ΔGint-201 kcal/mol
Surface area39400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.177, 98.177, 262.867
Angle α, β, γ (deg.)90.00, 90.00, 120.00
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-LYS / LYSINE / Lysine


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N2O2
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-0HY / methyl (3R)-3-(7-amino-4,5-dioxo-1,4,5,6-tetrahydropyrimido[4,5-c]pyridazin-3-yl)butanoate


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


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.78 Å3/Da / Density % sol: 55.76 %
Crystal growTemperature: 291 K / Method: hanging drop / pH: 9
Details: Lithium sulfate, Bis-Tris propane, pH 9.0, hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 23, 2011
RadiationMonochromator: Silicon / 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: 37033 / % possible obs: 92.7 % / Redundancy: 12.5 % / Rsym value: 0.087 / Net I/σ(I): 7.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.18-2.269.90.242160.1
2.26-2.3510.10.241176.1
2.35-2.4610.40.203193
2.46-2.5812.70.204199.8
2.58-2.7514.20.1681100
2.75-2.9614.20.128199.9
2.96-3.2614.10.1199.9
3.26-3.7313.50.09199.2
3.73-4.712.60.09198.8
4.7-5011.90.054198.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.6.1_357refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TWS

1tws


Resolution: 2.183→35.88 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.33 / σ(F): 0.13 / Phase error: 37.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2597 1714 5.03 %
Rwork0.2194 --
obs0.2215 34049 85.3 %
all-36993 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.331 Å2 / ksol: 0.332 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-10.5349 Å2-0 Å2-0 Å2
2--10.5349 Å20 Å2
3----21.0698 Å2
Refinement stepCycle: LAST / Resolution: 2.183→35.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4001 0 89 22 4112
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074144
X-RAY DIFFRACTIONf_angle_d1.0315594
X-RAY DIFFRACTIONf_dihedral_angle_d14.0211565
X-RAY DIFFRACTIONf_chiral_restr0.071627
X-RAY DIFFRACTIONf_plane_restr0.007714
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.183-2.26060.3433940.26131773X-RAY DIFFRACTION48
2.2606-2.35110.31521080.28242296X-RAY DIFFRACTION62
2.3511-2.45810.38261560.27332919X-RAY DIFFRACTION78
2.4581-2.58760.35351840.28223291X-RAY DIFFRACTION88
2.5876-2.74970.33431690.27793443X-RAY DIFFRACTION92
2.7497-2.96190.29511810.27943515X-RAY DIFFRACTION94
2.9619-3.25980.33992130.26093616X-RAY DIFFRACTION96
3.2598-3.73110.25481760.21143706X-RAY DIFFRACTION97
3.7311-4.69910.20012290.16413741X-RAY DIFFRACTION97
4.6991-35.88440.21512040.1914035X-RAY DIFFRACTION98
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)
10.366-0.11170.37040.2608-0.5321.26330.0545-0.1512-0.08410.1938-0.08580.00110.35470.0590.03740.5957-0.17890.01830.34370.04670.3379-18.81223.80233.6174
20.65380.34160.12260.872-0.03051.2375-0.13310.20280.0472-0.1995-0.0251-0.0332-0.15430.50060.15030.4851-0.0680.0210.42230.06620.283-30.49964.781551.3348
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2Chain B

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