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- PDB-4nir: Crystal structure of B. anthracis DHPS with compound 6: 3-[6-(tri... -

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Basic information

Entry
Database: PDB / ID: 4nir
TitleCrystal structure of B. anthracis DHPS with compound 6: 3-[6-(trifluoromethyl)-1H-benzimidazol-2-yl]propan-1-ol
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-6DH / Dihydropteroate synthase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.772 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 6, 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: Refinement description / Category: 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 20, 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 / pdbx_struct_special_symmetry / 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)67,55716
Polymers65,7672
Non-polymers1,78914
Water5,639313
1
A: Dihydropteroate Synthase
hetero molecules

A: Dihydropteroate Synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,89718
Polymers65,7672
Non-polymers2,13016
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z1
Buried area2450 Å2
ΔGint-27 kcal/mol
Surface area21620 Å2
MethodPISA
2
B: Dihydropteroate Synthase
hetero molecules

B: Dihydropteroate Synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,21714
Polymers65,7672
Non-polymers1,44912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455-x-1,-y,z1
Buried area2480 Å2
ΔGint-26 kcal/mol
Surface area21400 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)135,11432
Polymers131,5354
Non-polymers3,57928
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 area7240 Å2
ΔGint-61 kcal/mol
Surface area40710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.338, 98.338, 263.415
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-308-

6DH

21A-308-

6DH

31A-308-

6DH

41B-306-

6DH

51B-306-

6DH

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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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-6DH / 3-[6-(trifluoromethyl)-1H-benzimidazol-2-yl]propan-1-ol


Mass: 244.213 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H11F3N2O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / 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: 2.8 Å3/Da / Density % sol: 56 %
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 monochromator
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. obs: 70993 / % possible obs: 94.8 % / Observed criterion σ(I): -3 / Redundancy: 11.2 % / Biso Wilson estimate: 23.73 Å2 / Rmerge(I) obs: 0.089 / Χ2: 1.405 / Net I/σ(I): 10.7
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allRsym valueΧ2Diffraction-ID% possible all
1.77-1.836.252450.5970.989171.6
1.83-1.919.671400.5271.007197.4
1.91-1.9911.371940.3861.17197.8
1.99-2.11272270.281.39197.9
2.1-2.2312.172430.2111.545198.1
2.23-2.411.873080.1631.561198.3
2.4-2.6412.473450.1321.605198.7
2.64-3.0312.574090.0961.579198.6
3.03-3.8111.773720.0711.536196.8
3.81-5011.275100.0481.255193.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
SERGUIdata collection
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TWS

1tws


Resolution: 1.772→32.189 Å / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.8464 / SU ML: 0.22 / σ(F): 1.33 / Phase error: 21.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2202 3575 5.04 %
Rwork0.1923 --
obs0.1937 70904 95.98 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.565 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 119.71 Å2 / Biso mean: 28.1906 Å2 / Biso min: 10.48 Å2
Baniso -1Baniso -2Baniso -3
1-2.9875 Å2-0 Å20 Å2
2--2.9875 Å2-0 Å2
3----5.9749 Å2
Refinement stepCycle: LAST / Resolution: 1.772→32.189 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4159 0 106 313 4578
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064363
X-RAY DIFFRACTIONf_angle_d1.0625904
X-RAY DIFFRACTIONf_chiral_restr0.076651
X-RAY DIFFRACTIONf_plane_restr0.004754
X-RAY DIFFRACTIONf_dihedral_angle_d13.6871662
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7725-1.79580.3441060.35361808191469
1.7958-1.82040.34941160.30562354247089
1.8204-1.84640.26331260.25882588271497
1.8464-1.87390.26551220.23292550267297
1.8739-1.90320.28011500.22172584273497
1.9032-1.93440.23711240.19742612273698
1.9344-1.96780.25041510.18932580273198
1.9678-2.00350.2261370.18612606274398
2.0035-2.04210.21221360.18092582271898
2.0421-2.08370.2251370.18222610274798
2.0837-2.1290.21481560.17972605276198
2.129-2.17860.21341550.18372607276298
2.1786-2.2330.21411610.17672596275798
2.233-2.29340.22451260.17912615274198
2.2934-2.36090.20991500.18032638278899
2.3609-2.4370.2221340.18062639277399
2.437-2.52410.231400.19792667280799
2.5241-2.62510.24281480.20782641278999
2.6251-2.74450.2451320.21252687281999
2.7445-2.88910.2321250.21322704282999
2.8891-3.070.23071330.21082678281199
3.07-3.30680.21861610.20232658281998
3.3068-3.63920.20421410.1842642278396
3.6392-4.16490.18791410.15842653279496
4.1649-5.24360.18481530.1552698285196
5.2436-32.1940.22761140.21612727284189
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)
10.7768-0.02730.08821.4036-0.36881.307-0.0307-0.0777-0.00890.10940.0467-0.0024-0.0513-0.0245-0.01360.16860.01470.0160.06690.00670.1314-18.435323.72863.7644
21.5440.39750.01971.1419-0.32251.2221-0.02630.17960.0259-0.0737-0.0333-0.051-0.02610.11960.05170.07790.00020.00920.13120.02330.0761-30.4154.869351.0651
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A'A1 - 274
2X-RAY DIFFRACTION2chain 'B'B1 - 209

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