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- PDB-2vef: Dihydropteroate synthase from Streptococcus pneumoniae -

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Basic information

Entry
Database: PDB / ID: 2vef
TitleDihydropteroate synthase from Streptococcus pneumoniae
ComponentsDIHYDROPTEROATE SYNTHASE
KeywordsTRANSFERASE / ANTIBIOTIC RESISTANCE / FOLATE BIOSYNTHESIS
Function / homology
Function and homology information


dihydropteroate synthase / dihydropteroate synthase activity / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / response to antibiotic / 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
PHOSPHATE ION / Dihydropteroate synthase
Similarity search - Component
Biological speciesSTREPTOCOCCUS PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsDerrick, J.P. / Levy, C.
CitationJournal: Biochem.J. / Year: 2008
Title: Dihydropteroate Synthase from Streptococcus Pneumoniae: Structure, Ligand Recognition and Mechanism of Sulfonamide Resistance.
Authors: Levy, C. / Minnis, D. / Derrick, J.P.
History
DepositionOct 24, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Refinement description / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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)69,0093
Polymers68,9142
Non-polymers951
Water9,332518
1
A: DIHYDROPTEROATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5522
Polymers34,4571
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DIHYDROPTEROATE SYNTHASE


Theoretical massNumber of molelcules
Total (without water)34,4571
Polymers34,4571
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.613, 90.382, 138.656
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.97, -0.194, 0.148), (-0.204, 0.312, -0.928), (0.134, -0.93, -0.342)
Vector: 85.55718, 63.41175, 70.95837)

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Components

#1: Protein DIHYDROPTEROATE SYNTHASE / DHPS / DIHYDROPTEROATE PYROPHOSPHORYLASE


Mass: 34457.195 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P59655, dihydropteroate synthase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 518 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsDIPEPTIDE 'IE' REMOVED FROM THE SEQUENCE AT POSITION 65, AS THIS CORRESPONDS TO THE SULPHONAMIDE ...DIPEPTIDE 'IE' REMOVED FROM THE SEQUENCE AT POSITION 65, AS THIS CORRESPONDS TO THE SULPHONAMIDE RESISTANT PHENOTYPE AND THIS STRUCTURE IS FOR THE SENSITIVE FORM OF THE ENZYME (SEE LOPEZ,P., ESPINOSA,M., GREENBERG,B., LACKS, S.A., SULFONAMIDE RESISTANCE IN STREPTOCOCCUS PNEUMONIAE DNA SEQUENCE OF THE GENE ENCODING DIHYDROPTEROATE SYNTHASE AND CHARACTERIZATION OF THE ENZYME.(1987) J. BACTERIOL. 169 4320-4326)

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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: 2.2 Å3/Da / Density % sol: 44.1 % / Description: NONE
Crystal growDetails: 0.2 M AMMONIUM IODIDE, 20% (W/V) POLYETHYLENE GLYCOL 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 1.8→55 Å / Num. obs: 65291 / % possible obs: 99 % / Observed criterion σ(I): 4 / Redundancy: 3.43 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.7
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 2.89 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 4.5 / % possible all: 93.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalCleardata reduction
CrystalCleardata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.8→45.18 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.928 / SU B: 5.816 / SU ML: 0.098 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24 2767 5.2 %RANDOM
Rwork0.194 ---
obs0.197 50714 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å20 Å2
2---0.22 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.8→45.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4271 0 5 518 4794
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0224339
X-RAY DIFFRACTIONr_bond_other_d0.0020.022926
X-RAY DIFFRACTIONr_angle_refined_deg1.6221.9675865
X-RAY DIFFRACTIONr_angle_other_deg1.08237148
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.545545
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.75724.315197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.54515758
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1961532
X-RAY DIFFRACTIONr_chiral_restr0.1040.2687
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024796
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02838
X-RAY DIFFRACTIONr_nbd_refined0.2220.2875
X-RAY DIFFRACTIONr_nbd_other0.2020.23110
X-RAY DIFFRACTIONr_nbtor_refined0.170.22021
X-RAY DIFFRACTIONr_nbtor_other0.0880.22178
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2368
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2360.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2270.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2071.52909
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.60524417
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.65331645
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.8694.51448
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.35 170
Rwork0.277 3338
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)
10.705-0.071-0.18012.46790.69221.6677-0.01760.1312-0.23780.0141-0.05060.16380.3047-0.18150.0682-0.1859-0.0233-0.0121-0.1491-0.0339-0.107334.33345.71641.8431
20.82350.10610.03871.62570.97133.010.0751-0.21890.08540.5292-0.0236-0.17360.06150.155-0.05150.0044-0.0558-0.0623-0.1182-0.0035-0.142143.840468.581932.519
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 303
2X-RAY DIFFRACTION2B5 - 303

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