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- PDB-1tws: Dihydropteroate Synthetase From Bacillus anthracis -

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Basic information

Entry
Database: PDB / ID: 1tws
TitleDihydropteroate Synthetase From Bacillus anthracis
ComponentsDHPS, Dihydropteroate synthase
KeywordsTRANSFERASE / anthracis / folate biosynthesis / dihydropteroate / pterine
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
Dihydropteroate synthase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBabaoglu, K. / Qi, J. / Lee, R.E. / White, S.W.
CitationJournal: STRUCTURE / Year: 2004
Title: Crystal Structure of 7,8-Dihydropteroate Synthase from Bacillus anthracis; Mechanism and Novel Inhibitor Design.
Authors: Babaoglu, K. / Qi, J. / Lee, R.E. / White, S.W.
History
DepositionJul 1, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Refinement description / Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.classification / _software.name
Revision 1.4Aug 23, 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_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: DHPS, Dihydropteroate synthase
B: DHPS, Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,92014
Polymers65,7672
Non-polymers1,15312
Water5,855325
1
A: DHPS, Dihydropteroate synthase
hetero molecules

A: DHPS, Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,92014
Polymers65,7672
Non-polymers1,15312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_475-x-1,-y+2,z1
Buried area4470 Å2
ΔGint-157 kcal/mol
Surface area21790 Å2
MethodPISA, PQS
2
B: DHPS, Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4607
Polymers32,8841
Non-polymers5766
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: DHPS, Dihydropteroate synthase
hetero molecules

B: DHPS, Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,92014
Polymers65,7672
Non-polymers1,15312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_465-x-1,-y+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)97.441, 97.441, 263.615
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
DetailsThe biological dimer is generated by the two fold axis: X,Y,Z

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Components

#1: Protein DHPS, 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: str. A2012 / Gene: folp / Plasmid: pET-28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL 21 DE3 / References: UniProt: Q81VW8, dihydropteroate synthase
#2: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 325 / 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: 3 Å3/Da / Density % sol: 58.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9
Details: Lithium Sulfate, Tris, 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 225 mm CCD / Detector: CCD / Date: Jun 7, 2003 / Details: mirrors
RadiationMonochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 47517 / Num. obs: 47517 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Rsym value: 0.079 / Net I/σ(I): 26.1
Reflection shellResolution: 2→2.07 Å / Redundancy: 4 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 47517 / Rsym value: 0.324 / % possible all: 68.2

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MAR345data collection
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1AD1

1ad1


Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.878 / SU ML: 0.122 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): -3 / σ(I): 0 / ESU R: 0.181 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. TLS REFINEMENT WAS USED THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25459 2422 5.1 %RANDOM
Rwork0.21202 ---
all0.2141 47517 --
obs0.2141 45053 92.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.936 Å2
Baniso -1Baniso -2Baniso -3
1-3.32 Å21.66 Å20 Å2
2--3.32 Å20 Å2
3----4.99 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4186 0 60 325 4571
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0224242
X-RAY DIFFRACTIONr_bond_other_d0.0020.023917
X-RAY DIFFRACTIONr_angle_refined_deg1.6851.9795724
X-RAY DIFFRACTIONr_angle_other_deg0.89139095
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6385535
X-RAY DIFFRACTIONr_chiral_restr0.1040.2642
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024662
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02776
X-RAY DIFFRACTIONr_nbd_refined0.2160.2958
X-RAY DIFFRACTIONr_nbd_other0.2460.24709
X-RAY DIFFRACTIONr_nbtor_other0.090.22605
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2040.2237
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4350.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2340.2102
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3510.215
X-RAY DIFFRACTIONr_mcbond_it0.8981.52670
X-RAY DIFFRACTIONr_mcangle_it1.66824279
X-RAY DIFFRACTIONr_scbond_it2.81131572
X-RAY DIFFRACTIONr_scangle_it4.6124.51445
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.329 121
Rwork0.36 2299
obs-2299
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)
10.73620.16580.43610.50120.13481.7909-0.0493-0.0598-0.0313-0.0306-0.0279-0.01350.14220.35270.07720.14480.16890.02910.21750.06650.1529-78.14280.149191.969
20.44680.02160.09011.0104-0.08251.3368-0.03120.10640.0283-0.1004-0.1117-0.0596-0.28390.12430.14290.1550.0485-0.02380.24270.06190.1505-67.360160.9408138.9179
30.1234-2.04461.24322.7329-3.36623.0716-0.0444-0.07040.1189-0.1227-0.0618-0.2264-0.0613-0.01740.10620.17080.0279-0.03270.18750.00020.1808-77.17467.8467115.1693
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 274
2X-RAY DIFFRACTION2B2 - 274
3X-RAY DIFFRACTION3A343 - 506
4X-RAY DIFFRACTION3B342 - 502

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