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- PDB-4nhv: Crystal structure of B. anthracis DHPS with interfacial compound ... -

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Basic information

Entry
Database: PDB / ID: 4nhv
TitleCrystal structure of B. anthracis DHPS with interfacial compound 4: 5-(trifluoromethyl)-1,2-benzoxazol-3-amine
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
5-(trifluoromethyl)-1,2-benzoxazol-3-amine / Dihydropteroate synthase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.992 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 5, 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: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Sep 20, 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_struct_special_symmetry / 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)67,61319
Polymers65,7672
Non-polymers1,84517
Water1,51384
1
A: Dihydropteroate synthase
hetero molecules

A: Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,51718
Polymers65,7672
Non-polymers1,74916
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z1
Buried area2490 Å2
ΔGint-25 kcal/mol
Surface area21200 Å2
MethodPISA
2
B: Dihydropteroate synthase
hetero molecules

B: Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,70920
Polymers65,7672
Non-polymers1,94118
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455-x-1,-y,z1
Buried area2480 Å2
ΔGint-26 kcal/mol
Surface area21410 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)135,22538
Polymers131,5354
Non-polymers3,69034
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 area7300 Å2
ΔGint-60 kcal/mol
Surface area40280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.457, 98.457, 262.172
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-

2O6

21A-308-

2O6

31A-308-

2O6

41B-309-

2O6

51B-309-

2O6

61B-309-

2O6

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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: BAS0071, BA_0071, folP, 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.: 15 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-2O6 / 5-(trifluoromethyl)-1,2-benzoxazol-3-amine


Mass: 202.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H5F3N2O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 55.89 %
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: 1.99→50 Å / Num. obs: 47488 / % possible obs: 90.5 % / Observed criterion σ(I): -3 / Redundancy: 11.5 % / Biso Wilson estimate: 36.37 Å2 / Rmerge(I) obs: 0.078 / Χ2: 1.455 / Net I/σ(I): 12.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique allRsym valueΧ2% possible all
2-2.076.73.97424730.351.13448.1
2.07-2.157.43.68637060.3441.22772.2
2.15-2.2584.72149930.3541.48296.9
2.25-2.3710.67.40350940.3171.16299.3
2.37-2.5213.114.73651620.2321.28999.9
2.52-2.7114.119.42151940.1841.34399.9
2.71-2.991426.26952080.1291.46199.7
2.99-3.4213.733.61152110.0881.64698.9
3.42-4.311234.550930.0681.93195.2
4.31-5011.934.11453540.051.48494.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TWS

1tws


Resolution: 1.992→32.679 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.6926 / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2504 2397 5.09 %RANDOM
Rwork0.2191 ---
obs0.2207 47064 89.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.445 Å2 / ksol: 0.353 e/Å3
Displacement parametersBiso max: 144.68 Å2 / Biso mean: 54.9652 Å2 / Biso min: 24.63 Å2
Baniso -1Baniso -2Baniso -3
1-10.6778 Å2-0 Å20 Å2
2--10.6778 Å2-0 Å2
3----21.3555 Å2
Refinement stepCycle: LAST / Resolution: 1.992→32.679 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4153 0 103 84 4340
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074340
X-RAY DIFFRACTIONf_angle_d1.055878
X-RAY DIFFRACTIONf_chiral_restr0.074650
X-RAY DIFFRACTIONf_plane_restr0.004751
X-RAY DIFFRACTIONf_dihedral_angle_d13.9581634
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.992-2.03270.4127700.31561291136145
2.0327-2.07680.371730.26851510158352
2.0768-2.12510.29191010.29151928202968
2.1251-2.17830.35751360.30432720285695
2.1783-2.23720.3841300.31192795292596
2.2372-2.3030.36251480.29452793294197
2.303-2.37730.30561560.24162845300199
2.3773-2.46220.2741700.24572858302899
2.4622-2.56080.33441550.26842830298599
2.5608-2.67730.31531560.26952877303399
2.6773-2.81840.30291540.26322888304299
2.8184-2.99480.32971460.25242895304199
2.9948-3.22590.25981560.25342885304199
3.2259-3.55010.24751510.22512865301697
3.5501-4.0630.22451640.18262805296994
4.063-5.11580.17091540.15212837299194
5.1158-32.68350.21491770.19893045322294
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)
11.66410.4467-0.33421.816-0.64672.3748-0.08480.1548-0.0184-0.23-0.0528-0.2416-0.07130.33110.1410.281-0.01180.03180.34060.02420.2464-30.36844.643550.7285
21.1579-0.11750.10771.6472-0.69832.4255-0.011-0.1181-0.15340.1432-0.0095-0.06670.19930.08260.02780.4116-0.01270.02910.17190.01110.2769-18.502823.75043.8617
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B'B2 - 275
2X-RAY DIFFRACTION2chain 'A'A1 - 274

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