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- PDB-3tyb: Dihydropteroate Synthase in complex with pHBA and DHP+ -

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Basic information

Entry
Database: PDB / ID: 3tyb
TitleDihydropteroate Synthase in complex with pHBA and DHP+
ComponentsDihydropteroate synthase
KeywordsTRANSFERASE / anthracis / folate biosynthesis / dihydropteroate / pterine / tim barrel
Function / homology
Function and homology information


dihydropteroate synthase / dihydropteroate synthase activity / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / metal ion binding / cytosol
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
P-HYDROXYBENZOIC ACID / Chem-XHP / Dihydropteroate synthase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsYun, M.-K. / White, S.W.
CitationJournal: Science / Year: 2012
Title: Catalysis and sulfa drug resistance in dihydropteroate synthase.
Authors: Yun, M.K. / Wu, Y. / Li, Z. / Zhao, Y. / Waddell, M.B. / Ferreira, A.M. / Lee, R.E. / Bashford, D. / White, S.W.
History
DepositionSep 24, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 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)67,16714
Polymers65,7672
Non-polymers1,39912
Water36020
1
A: Dihydropteroate synthase
hetero molecules

A: Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,97412
Polymers65,7672
Non-polymers1,20710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_475-x-1,-y+2,z1
Buried area4150 Å2
ΔGint-81 kcal/mol
Surface area21590 Å2
MethodPISA
2
B: Dihydropteroate synthase
hetero molecules

B: Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,35916
Polymers65,7672
Non-polymers1,59114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_465-x-1,-y+1,z1
Buried area4610 Å2
ΔGint-123 kcal/mol
Surface area21370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.676, 98.676, 264.297
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, BAS0071, BA_0071, GBAA_0071 / Plasmid: PET-28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q81VW8, dihydropteroate synthase
#2: Chemical ChemComp-XHP / 2-amino-6-methylidene-6,7-dihydropteridin-4(3H)-one


Mass: 177.163 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H7N5O
#3: Chemical ChemComp-PHB / P-HYDROXYBENZOIC ACID


Mass: 138.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.82 Å3/Da / Density % sol: 56.44 %
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 291.0K

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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: Dec 3, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 22912 / % possible obs: 93.9 % / Observed criterion σ(I): -3 / Redundancy: 8.1 % / Rsym value: 0.106 / Net I/σ(I): 20.7
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 3.1 / Num. unique all: 1636 / Rsym value: 0.295 / % possible all: 69.6

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TWS

1tws


Resolution: 2.6→49.34 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.927 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 42.482 / SU ML: 0.372 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.618 / ESU R Free: 0.353 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2965 1166 5.1 %RANDOM
Rwork0.2457 ---
obs0.2482 22768 93.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 183.88 Å2 / Biso mean: 91.1345 Å2 / Biso min: 25.56 Å2
Baniso -1Baniso -2Baniso -3
1-5.8 Å22.9 Å20 Å2
2--5.8 Å20 Å2
3----8.7 Å2
Refinement stepCycle: LAST / Resolution: 2.6→49.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4064 0 86 20 4170
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224221
X-RAY DIFFRACTIONr_angle_refined_deg1.4011.9945700
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7355524
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.18525.163184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.96715772
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5511524
X-RAY DIFFRACTIONr_chiral_restr0.0940.2636
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213110
X-RAY DIFFRACTIONr_mcbond_it0.5121.52608
X-RAY DIFFRACTIONr_mcangle_it1.01224192
X-RAY DIFFRACTIONr_scbond_it1.53831613
X-RAY DIFFRACTIONr_scangle_it2.5184.51506
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.549 64 -
Rwork0.448 1097 -
all-1161 -
obs-1164 66.38 %
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)
12.2044-0.17540.16552.40670.03894.8826-0.0879-0.3063-0.06530.2019-0.066-0.22260.34531.04310.15390.71160.28380.00380.36640.09880.1036-79.557280.905891.8886
21.6905-0.1420.28362.9397-0.27814.4108-0.04980.20520.1645-0.3741-0.1705-0.0676-1.05710.52530.22030.56680.2408-0.04280.61420.09020.069-68.5361.5305139.657
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 274
2X-RAY DIFFRACTION2B2 - 274

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