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- PDB-3tyd: Dihydropteroate Synthase in complex with PPi and DHP+ -

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Basic information

Entry
Database: PDB / ID: 3tyd
TitleDihydropteroate Synthase in complex with PPi 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
PYROPHOSPHATE 2- / Chem-XHP / Dihydropteroate synthase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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)67,62618
Polymers65,7672
Non-polymers1,85916
Water52229
1
A: Dihydropteroate synthase
hetero molecules

A: Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,62618
Polymers65,7672
Non-polymers1,85916
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_475-x-1,-y+2,z1
Buried area4750 Å2
ΔGint-124 kcal/mol
Surface area22540 Å2
MethodPISA
2
B: Dihydropteroate synthase
hetero molecules

B: Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,62618
Polymers65,7672
Non-polymers1,85916
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_465-x-1,-y+1,z1
Buried area4870 Å2
ΔGint-127 kcal/mol
Surface area21720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.440, 99.440, 262.130
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 / Fragment: DIHYDROPTEROATE SYNTHASE
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-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2O7P2
#3: 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
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.84 Å3/Da / Density % sol: 56.76 %
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: Apr 8, 2011
RadiationProtocol: 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: 25528 / % possible obs: 92.4 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Rsym value: 0.085 / Net I/σ(I): 23.6
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 2 / Num. unique all: 1858 / Rsym value: 0.214 / % possible all: 70.1

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0102refinement
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: 2.5→49.72 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.938 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 29.971 / SU ML: 0.276 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.456 / ESU R Free: 0.305 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2777 1283 5 %RANDOM
Rwork0.2243 ---
obs0.2268 25433 92.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 160.44 Å2 / Biso mean: 81.9003 Å2 / Biso min: 22.64 Å2
Baniso -1Baniso -2Baniso -3
1-4.78 Å22.39 Å20 Å2
2--4.78 Å20 Å2
3----7.18 Å2
Refinement stepCycle: LAST / Resolution: 2.5→49.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4135 0 104 29 4268
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224298
X-RAY DIFFRACTIONr_angle_refined_deg1.4621.9975810
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7925530
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.24125.053188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.33315785
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5111525
X-RAY DIFFRACTIONr_chiral_restr0.10.2643
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213139
X-RAY DIFFRACTIONr_mcbond_it0.5751.52646
X-RAY DIFFRACTIONr_mcangle_it1.15324264
X-RAY DIFFRACTIONr_scbond_it1.88931652
X-RAY DIFFRACTIONr_scangle_it3.084.51545
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.42 60 -
Rwork0.41 1319 -
all-1379 -
obs-1379 69.82 %
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)
14.1107-0.39990.01951.4660.05594.6668-0.0301-0.4413-0.040.3324-0.0303-0.21870.27691.05270.06040.89110.1785-0.05770.37270.11750.1644-77.653577.2821100.1019
22.7093-0.349-0.15611.8063-0.06373.6916-0.0143-0.07260.02690.1033-0.0381-0.17270.08190.95630.05240.6870.0654-0.03010.25480.02570.0567-81.368684.348388.0737
32.23930.4032-1.32585.0378-2.25578.10150.05790.29220.3134-0.6764-0.0837-0.0057-0.9220.40150.02590.69650.251-0.08050.45180.08690.1208-73.531766.4053130.8136
41.24560.07110.4413.4267-0.05613.6577-0.04680.17050.1468-0.3006-0.0166-0.279-0.61560.52280.06340.38680.20560.02810.43350.05030.0746-67.293859.6912142.0781
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 90
2X-RAY DIFFRACTION2A91 - 274
3X-RAY DIFFRACTION3B2 - 90
4X-RAY DIFFRACTION4B91 - 274

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