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- PDB-3v5o: Structural and Mechanistic Studies of Catalysis and Sulfa Drug Re... -

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Basic information

Entry
Database: PDB / ID: 3v5o
TitleStructural and Mechanistic Studies of Catalysis and Sulfa Drug Resistance in Dihydropteroate Synthase
ComponentsDihydropteroate synthase
KeywordsTRANSFERASE / Tim Barrel / DHPP and pABA
Function / homologyDihydropteroate synthase-like / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / :
Function and homology information
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.5 Å
AuthorsYun, M. / Wu, Y. / Li, Z. / Zhao, Y. / Waddell, M.B. / Ferreira, A.M. / Lee, R.E. / Bashford, D. / 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
DepositionDec 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2Sep 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

Downloads & links

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Assembly

Deposited unit
A: Dihydropteroate synthase
B: Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,82213
Polymers65,7652
Non-polymers1,05711
Water34219
1
A: Dihydropteroate synthase
hetero molecules

A: Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,72612
Polymers65,7652
Non-polymers96110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_475-x-1,-y+2,z1
Buried area4100 Å2
ΔGint-124 kcal/mol
Surface area21540 Å2
MethodPISA
2
B: Dihydropteroate synthase
hetero molecules

B: Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,91814
Polymers65,7652
Non-polymers1,15312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_465-x-1,-y+1,z1
Buried area4360 Å2
ΔGint-140 kcal/mol
Surface area21220 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)133,64426
Polymers131,5314
Non-polymers2,11322
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_465-x-1,-y+1,z1
crystal symmetry operation3_355-x+y-2,-x,z+1/31
crystal symmetry operation6_665x-y+1,x+1,z+1/31
Buried area10840 Å2
ΔGint-273 kcal/mol
Surface area40380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.023, 98.023, 264.145
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: 32882.746 Da / Num. of mol.: 2 / Mutation: D184N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: A0248 / Gene: folP, BAA_0084 / Plasmid: PET-28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C3P9L8, dihydropteroate synthase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 55.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9
Details: Bis-Tris propane, Lithium Sulfate, pH 9, 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: Feb 5, 2011 / Details: Si 111
RadiationMonochromator: double crystal - liquid nitrogen cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 23961 / Num. obs: 23961 / % possible obs: 88.8 % / Observed criterion σ(I): -3 / Redundancy: 12.3 % / Rsym value: 0.079 / Net I/σ(I): 33.6
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 9.2 % / Mean I/σ(I) obs: 7.2 / Num. unique all: 1307 / Rsym value: 0.195 / % possible all: 49.8

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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: FOURIER SYNTHESIS
Starting model: 1TWS

1tws


Resolution: 2.5→48.19 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.943 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 27.965 / SU ML: 0.261 / Cross valid method: THROUGHOUT / ESU R: 0.506 / ESU R Free: 0.309 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2736 1208 5.1 %RANDOM
Rwork0.2338 ---
obs0.2357 23860 88.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 179.09 Å2 / Biso mean: 75.2803 Å2 / Biso min: 19.7 Å2
Baniso -1Baniso -2Baniso -3
1-4.4 Å22.2 Å20 Å2
2--4.4 Å20 Å2
3----6.59 Å2
Refinement stepCycle: LAST / Resolution: 2.5→48.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4038 0 55 19 4112
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224151
X-RAY DIFFRACTIONr_angle_refined_deg1.1071.9835606
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8785517
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.97525.135185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.65615766
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4591524
X-RAY DIFFRACTIONr_chiral_restr0.0760.2629
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213041
X-RAY DIFFRACTIONr_mcbond_it2.0851.52578
X-RAY DIFFRACTIONr_mcangle_it3.86324148
X-RAY DIFFRACTIONr_scbond_it4.22931573
X-RAY DIFFRACTIONr_scangle_it5.7874.51457
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 46 -
Rwork0.347 886 -
all-932 -
obs--48.29 %
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)
10.8343-0.21460.24730.45560.10242.26630.0198-0.07260.03770.027-0.09640.07890.15420.53060.07660.50020.1533-0.00270.41180.08310.1668-78.984480.246291.8826
20.0780.05370.1261.17130.01232.4964-0.0570.0154-0.0895-0.113-0.13360.0168-0.69450.23910.19060.55540.1072-0.05530.49940.06140.1726-68.242661.0906139.5236
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 274
2X-RAY DIFFRACTION2B2 - 274

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